Dynamo - User contributions [en]

User:Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)

2025-12-11T14:59:28Z

Miguel Sanchez: /* Alignment projects */

[[Category:WalkthroughsSpecific]]

This tutorial shows how to manually pick particles in a tomogram, extract them, align and classify them. This tutorial is a shortened version of the original [[Starters_guide | starters guide]] that was adapted for the use in ''Dynamo'' workshops.

=Manual particle picking and ''Dynamo'' catalogues=
The ''Dynamo'' catalogues are databases that manage tomograms and link the tomographic data to the extracted particles. Start the catalogue manager by typing the command:

<tt>dcm</tt>
After the catalogue manager opens, we create 3 synthetic tomograms that include our particles (thermosomes) in the following way:

[[File:StartersGuideFigure1.png|thumb|center|600px| Figure 1: creating a set of synthetic tomograms with ''Dynamo'' Catalogue Manager]]

You can see the list of your tomograms and their metadata in a table in the bottom of your catalogue manager. When workin on your own projects, you can add tomograms to the catalogue by ''Catalogue -> Browse for new volume''. The tomograms are situated in the directory <tt>testCatalogue</tt>. They contain a small amount of noise and a missing wedge associated to rotation around Y-axis. We added the information about location of the particles in the tomograms in an additional catalogue called <tt>testCatalogue_withmodels</tt>. If needed, it can be opened from the current folder with ''Catalogue -> look for local catalogues'' in the catalogue manager window.

==Viewing tomograms==
Select the first tomogram in the list and go to ''View volume>Full tomogram file in tomoslice''.

[[ File:StartersSelectTomoSliceInCatalogue.png |thumb| center |600px| Figure 2: Selecting a volume in the catalogue manager to be inspected in <tt>dpreview</tt>]]

The volume browser tomoslicer loads the entire tomograms into memory and allows making annotations to the regions of interest. The tomograms in this tutorial are small, and you can load them directly into memory. For real life tomograms, bear in mind that you will need to [[Prebinned tomograms| prebin]] the files before loading them into memory. Tomoslice has a simple set of controls and is suitable for visualization tasks that require oblique sections through the tomogram. It uses the same tool as other ''Dynamo'' browsers to keep track of your annotations: a pool of models. You might need to adjust the contrast (blue arrow). To move through the tomogram slices, you can either use the mouse wheel, click and drag the tomogram slice up and down (orange arrows), or move the position control left and right (orange box).

[[ File:StartersTomoSlice.png |thumb| center |600px|]]

==Picking and extracting particles in tomograms==
Coordinates of picked particles are represented by data types called models. In the tomoslicer window go to ''Model Pool -> Create new model in pool (choose type) -> General''. This is the simplest type of [[model]] where each clicked/model point corresponds to a single isolated particle. Now you can navigate up and down the tomogram, place the mouse on the center of a particle and press the [c] key on your keyboard to add a new model point. (Note the ''Help -> all hot keys'' options that lists the different the actions of the different keystrokes). Backspace button deletes the last clicked point (you can also use the right-click to delete single points).

[[File:StartersGuideFigure4.png|thumb|center|600px| Generating a new model]]

After you are done clicking about 10 particles click on ''Active model > Update Crop points'' in the tomoslice window.

[[File:StartersGuideUpdate.png|thumb|center|600px|]]

Save the model into the catalogue by ''Active model -> Save active model into catalogue (disk)'' and close the slicer window.

[[File:StartersGuideFigure6.png|thumb|center|600px| ]]

Pick particles for tomograms 2 and 3. In total, there are around 30-40 particles in the generated dataset. When you open a new tomogram, make sure that you delete the pool of models from memory when asked. This will have no effect onto the models stored in disk, and it is necessary in order to ensure that you are not mixing models from different tomograms.

==An alternate visualization: orthogonal projections==

Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen where the x-y projection of the tomogram is shown. Use the secondary click on it to launch the orthogonal views of x-z and y-z planes that traverse that point. These views can also be used to click particles, in case the standard view is not sufficient.

{|style="margin: 0 auto;"
| [[File:orthoPickMain.png|thumb|upright|250px| click on the main projection determines two orthogonal slices]]
| [[File:orthoPickX.png|thumb|upright|250px| Slice xz ]]
| [[File:orthoPickY.png|thumb|upright|250px| Slice xy]]
|}

=Extracting particles from tomograms=
In the catalogue manager window select the rows for tomograms from which you want to extract particles from. You can either select them one by one with a mouse click and holding the [ctrl] key or by clicking the ''Select all'' button. Then, go to ''Crop Particles -> Open Volume List Manager''.

[[File:StartersGuideopenVolumeList.png|thumb|center|600px|]]

A new window opens with all the models in the catalogue listed in the bottom. Pick (by checking boxes) the models of type ''general'' that you have just clicked. Click ''Create list'' and then ''Crop particle''.

[[File:StartersGuideSelectModels.png|thumb|center|600px|]]

In the new window, change the data name to something meaningful, such as ''thermosomeParticles'', change the sidelength from 32 to 48 and click start cropping.

[[File:StartersGuideCrop.png|thumb|center|600px|]]

After cropping is done, explore your cropped particles by clicking ''ddbrowse'' (in the window above). A new window opens where you can simply click on ''show''.

[[File:StartersGuideShow.png|thumb|center|500px|]]

You see a 2D representation (projections) of all cropped 3D subtomograms. Make sure your particles are well centered and fit the box.

[[File:StartersGuideParticles.png|thumb|center|500px|]]

We also introduce the concept of the ''dynamo'' table: The information about each particle is stored in tables. Each particle has an entry in the table that contains shifts and rotations to describe its orientation (by default these values are initialized as zeroes). It also contains the particle ID (tag), the orientation of the missing wedge and others. For full info type the command <tt>dthelp</tt>. The ''Dynamo'' catalogue generates an initial table during particle extraction. Its location is in <tt>particles/crop.tbl </tt>.

=Subtomogram alignment and averaging=

==Initial reference generation==
We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually aligning a few particles and averaging them. We use the command <tt>dpkdata.montage</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all open ''Dynamo'' windows and type into the ''Dynamo'' command line:

<tt> gui = dpkdata.montage('thermosomeParticles.Data', 't', 'thermosomeParticles.Data/crop.tbl'); </tt>

''Attention''': only if you find an error in the Matlab version running the command above, please try instead this version of the command:
<nowiki>slt = dpktbl.star.FullTable();
tbl = dread('thermosomeParticles.Data/crop.tbl');
slt.fillFromClassicalTable(tbl);
gui = dpkdata.montage('thermosomeParticles.Data', 't', slt);
</nowiki>

The gui opens. Click the bottons below to show more or fewer images.

[[File:DpkdataMontage.png|thumb|center|600px|]]

To manually align the particles, do the following for about 10 particles:
# Place the mouse over the particle center and press the key [c] (this centers the particle).
# Place the mouse over its top (or bottom) part and press the key [n] (this aligns the particle).
This is just done to create an initial reference, so orientations don't need to be very exact.

[[File:DpkdataMontage Aligned.png|thumb|center|500px|]]

Save the corresponding table by clicking ''Table'' and ''save edited table'' button in the top and save. It saves an editedTable.tbl that will be used later. To generate the average you need to apply the table on the particles. For this, type

<tt> oa = daverage('thermosomeParticles.Data', 't', 'editedTable.tbl'); </tt>

and save the result with

<tt> dwrite(oa.average, 'my_average.em') </tt>

You can see the result by typing

<tt> dview('my_average.em');</tt>

==Alignment projects==
Iterative alignment of subtomograms to their average is performed by ''dynamo'' projects that you can run in various high-performance computational environments. To run an alignment project you need the particles, an initial reference and a table. All of these files we generated before. Start the alignment project GUI by typing

<tt> dcp</tt>

In thw new window, do the following:
# Add the project name ''drun1'', press the ''enter'' key and select ''create a new project'' in the pop-up window.
# Click on ''particles'' and provide the particle folder name ''thermosomeParticles.Data''. Click ok.
# Click on ''table'' and provide the table name ''thermosomeParticles.Data/crop.tbl''. Click ok.
# Click on ''template'' and provide the initial reference name ''my_average.em''. Click ok.
# Click on ''masks'' and simply click on ''use default masks''. Click ok. You could also specify the semi-axis of the ellipsoid masks or go to “Mask editor” to make more sophisticated masks. Note that ''Dynamo'' by default uses Rossman correlation which eliminates the artefacts associated with hard (non-soft) mask.

[[File:StartersGuideAli1.png|thumb|center|500px|]]

Click on ''numerical parameters'' to set all parameters and details about the different iterations of the alignment project. You can select any parameter in the table with a mouse and click the ''?'' button on the top right of the parameter window to see a description of the parameters. The most important parameters to consider are:

* ''Number of iterations'': Make 3 rounds with 2 iterations each. The first round will be a global search with a coarse angular step and the following rounds will be used for refinement.
* ''Angular search ranges'': Cone aperture is the scan range for the first two Euler angles around the initial orientation defined in the table. 360 degrees is the full scan range. Azimuth rotation range defines the rotation range around the new vertical axis of the particle.
* ''High- and lowpass values'': Fourier voxels to limit the used frequency range.
*''Particle dimensions'': Defined as sidelength of your subvolume. If you put a lower value, the particles will be downsampled for the particular round. This will speed up the process.
* ''Refine'': After each angular scan, the search step is reduced by the ''refine factor''. This is repeated ''refine'' times. I.e., if your cone sampling is 10 degrees, ''refine'' is 3 and ''refine factor'' is 2, then 10, 5, 2.5 and 1.25 degrees will be sampled. This is the optimization of angular search space.
*''Shift limits'': Limits the translation of particles from the center of the box (if shifts limiting way is 1) or from the previously estimated center (if shifts limiting way is 2). The previous estimates for the shifts and rotations are taken from input tables and are updated at the end of each iteration.
*''Symmetry'': If you know the symmetry of your protein it will speed up the convergence and result in higher resolution.

Set the parameters as follows and click ''ok'':

[[File:StartersGuideFigure10.png|thumb|center|600px|]]

Click on ''Computing environment'' and select your computing environment (choose ''standalone'' if you are working on the standalone version or GPU standalone if you are working in the AWS Machine). Set ''CPU cores'' and ''parallelize averaging step'' to the maximum available (e.g., 4). Leave the rest as it is and click ''ok''. In the alignment GUI click ''check'' and ''unfold''. To run the project

* in a Matlab session, you can just click on “run”.
* in a standalone project it is more convenient to write in the terminal <tt>"dynamo_execute_project drun1"</tt> or to open a new terminal, load ''Dynamo'' (but do not run it) and run the project by typing <tt>./drun1.exe</tt>.

While the project is running, open another Matlab window (or in standalone open another terminal with ''Dynamo'' running) and you can monitor the progress of the alignment project by typing:

<tt>dvstatus drun1</tt>

While the project is running, you can look at projections of the intermediate results by typing:

<tt>ddb drun1:a:ite=* -j c10</tt>

or at the latest average by typing:

<tt>ddb drun1:a -v </tt>

The final result should look similar to:

[[File:StartersGuideResultsAlignment.png|thumb|center|400px| Results of alignment.]]

=Subtomogram classification=
To demonstrate a classification example we provide particles with 2 slightly different sizes. We can then classify them with a simple Multi-reference Analysis (MRA). To do that, we first generate a dataset which has 2 populations of particles. For this, type:

<tt>dynamo_tutorial('data_classification','M',8,'N',8);</tt>

It generates two sets of particles, 8 particles in each including their table. The idea behind [[Multireference Analysis|MRA]] is the following: The particles are aligned to several references (here only 2). After each iteration, each particle is assigned to only one single reference where it fits the best. This procedure is repeated iteratively. Similar particles will have higher correlation to similar references and will eventually group together. For classification into N classes we will need N initial references and N initially identical tables.Follow these steps to run the MRA:

# Create a new project by typing “drun2” in the project name of the alignment GUI.
# Set number of references to 2.
# Activate the ''Swap particles'' button.
# Go to ''particles'' and add <tt>data_classification/data</tt> to the particle data. Click ok.
# Go to ''table'' and type <tt>data_classification/real.tbl</tt> into the field ''clone this'' and press ''copy''. Click ok.
# Go to ''template'' and clone <tt>data_classification/original_template.em</tt> with addition of some extra noise with amplitude 1.
# Click on ''masks'' and click on ''use default masks''. Click ok.
# Click on ''numerical parameters'' and set the following parameters. Click ok.

[[File:StartersGuideResultsClassification2.png|thumb|center|400px|]]

Choose the same computing environment as in the previous alignment project and run the project in the same way too. MRA projects usually run longer, because each particle will be aligned to two references. Here, however, we chose the parameters in a way that the process is still fast (e.g., small dimensions). Monitor the progress of the project same as before:

<tt>dvstatus drun2</tt>

And visualize the results using the command:

<tt>ddb drun2:a:ref=* -j c5</tt>

You should get two averages with particle in one slightly class larger than in the other.

[[File:StartersGuideResultsClassification.png|thumb|center|600px| Results of classification.]]

User:Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)

2025-12-11T14:54:00Z

Miguel Sanchez: /* Alignment projects */

[[Category:WalkthroughsSpecific]]

This tutorial shows how to manually pick particles in a tomogram, extract them, align and classify them. This tutorial is a shortened version of the original [[Starters_guide | starters guide]] that was adapted for the use in ''Dynamo'' workshops.

=Manual particle picking and ''Dynamo'' catalogues=
The ''Dynamo'' catalogues are databases that manage tomograms and link the tomographic data to the extracted particles. Start the catalogue manager by typing the command:

<tt>dcm</tt>
After the catalogue manager opens, we create 3 synthetic tomograms that include our particles (thermosomes) in the following way:

[[File:StartersGuideFigure1.png|thumb|center|600px| Figure 1: creating a set of synthetic tomograms with ''Dynamo'' Catalogue Manager]]

You can see the list of your tomograms and their metadata in a table in the bottom of your catalogue manager. When workin on your own projects, you can add tomograms to the catalogue by ''Catalogue -> Browse for new volume''. The tomograms are situated in the directory <tt>testCatalogue</tt>. They contain a small amount of noise and a missing wedge associated to rotation around Y-axis. We added the information about location of the particles in the tomograms in an additional catalogue called <tt>testCatalogue_withmodels</tt>. If needed, it can be opened from the current folder with ''Catalogue -> look for local catalogues'' in the catalogue manager window.

==Viewing tomograms==
Select the first tomogram in the list and go to ''View volume>Full tomogram file in tomoslice''.

[[ File:StartersSelectTomoSliceInCatalogue.png |thumb| center |600px| Figure 2: Selecting a volume in the catalogue manager to be inspected in <tt>dpreview</tt>]]

The volume browser tomoslicer loads the entire tomograms into memory and allows making annotations to the regions of interest. The tomograms in this tutorial are small, and you can load them directly into memory. For real life tomograms, bear in mind that you will need to [[Prebinned tomograms| prebin]] the files before loading them into memory. Tomoslice has a simple set of controls and is suitable for visualization tasks that require oblique sections through the tomogram. It uses the same tool as other ''Dynamo'' browsers to keep track of your annotations: a pool of models. You might need to adjust the contrast (blue arrow). To move through the tomogram slices, you can either use the mouse wheel, click and drag the tomogram slice up and down (orange arrows), or move the position control left and right (orange box).

[[ File:StartersTomoSlice.png |thumb| center |600px|]]

==Picking and extracting particles in tomograms==
Coordinates of picked particles are represented by data types called models. In the tomoslicer window go to ''Model Pool -> Create new model in pool (choose type) -> General''. This is the simplest type of [[model]] where each clicked/model point corresponds to a single isolated particle. Now you can navigate up and down the tomogram, place the mouse on the center of a particle and press the [c] key on your keyboard to add a new model point. (Note the ''Help -> all hot keys'' options that lists the different the actions of the different keystrokes). Backspace button deletes the last clicked point (you can also use the right-click to delete single points).

[[File:StartersGuideFigure4.png|thumb|center|600px| Generating a new model]]

After you are done clicking about 10 particles click on ''Active model > Update Crop points'' in the tomoslice window.

[[File:StartersGuideUpdate.png|thumb|center|600px|]]

Save the model into the catalogue by ''Active model -> Save active model into catalogue (disk)'' and close the slicer window.

[[File:StartersGuideFigure6.png|thumb|center|600px| ]]

Pick particles for tomograms 2 and 3. In total, there are around 30-40 particles in the generated dataset. When you open a new tomogram, make sure that you delete the pool of models from memory when asked. This will have no effect onto the models stored in disk, and it is necessary in order to ensure that you are not mixing models from different tomograms.

==An alternate visualization: orthogonal projections==

Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen where the x-y projection of the tomogram is shown. Use the secondary click on it to launch the orthogonal views of x-z and y-z planes that traverse that point. These views can also be used to click particles, in case the standard view is not sufficient.

{|style="margin: 0 auto;"
| [[File:orthoPickMain.png|thumb|upright|250px| click on the main projection determines two orthogonal slices]]
| [[File:orthoPickX.png|thumb|upright|250px| Slice xz ]]
| [[File:orthoPickY.png|thumb|upright|250px| Slice xy]]
|}

=Extracting particles from tomograms=
In the catalogue manager window select the rows for tomograms from which you want to extract particles from. You can either select them one by one with a mouse click and holding the [ctrl] key or by clicking the ''Select all'' button. Then, go to ''Crop Particles -> Open Volume List Manager''.

[[File:StartersGuideopenVolumeList.png|thumb|center|600px|]]

A new window opens with all the models in the catalogue listed in the bottom. Pick (by checking boxes) the models of type ''general'' that you have just clicked. Click ''Create list'' and then ''Crop particle''.

[[File:StartersGuideSelectModels.png|thumb|center|600px|]]

In the new window, change the data name to something meaningful, such as ''thermosomeParticles'', change the sidelength from 32 to 48 and click start cropping.

[[File:StartersGuideCrop.png|thumb|center|600px|]]

After cropping is done, explore your cropped particles by clicking ''ddbrowse'' (in the window above). A new window opens where you can simply click on ''show''.

[[File:StartersGuideShow.png|thumb|center|500px|]]

You see a 2D representation (projections) of all cropped 3D subtomograms. Make sure your particles are well centered and fit the box.

[[File:StartersGuideParticles.png|thumb|center|500px|]]

We also introduce the concept of the ''dynamo'' table: The information about each particle is stored in tables. Each particle has an entry in the table that contains shifts and rotations to describe its orientation (by default these values are initialized as zeroes). It also contains the particle ID (tag), the orientation of the missing wedge and others. For full info type the command <tt>dthelp</tt>. The ''Dynamo'' catalogue generates an initial table during particle extraction. Its location is in <tt>particles/crop.tbl </tt>.

=Subtomogram alignment and averaging=

==Initial reference generation==
We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually aligning a few particles and averaging them. We use the command <tt>dpkdata.montage</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all open ''Dynamo'' windows and type into the ''Dynamo'' command line:

<tt> gui = dpkdata.montage('thermosomeParticles.Data', 't', 'thermosomeParticles.Data/crop.tbl'); </tt>

''Attention''': only if you find an error in the Matlab version running the command above, please try instead this version of the command:
<nowiki>slt = dpktbl.star.FullTable();
tbl = dread('thermosomeParticles.Data/crop.tbl');
slt.fillFromClassicalTable(tbl);
gui = dpkdata.montage('thermosomeParticles.Data', 't', slt);
</nowiki>

The gui opens. Click the bottons below to show more or fewer images.

[[File:DpkdataMontage.png|thumb|center|600px|]]

To manually align the particles, do the following for about 10 particles:
# Place the mouse over the particle center and press the key [c] (this centers the particle).
# Place the mouse over its top (or bottom) part and press the key [n] (this aligns the particle).
This is just done to create an initial reference, so orientations don't need to be very exact.

[[File:DpkdataMontage Aligned.png|thumb|center|500px|]]

Save the corresponding table by clicking ''Table'' and ''save edited table'' button in the top and save. It saves an editedTable.tbl that will be used later. To generate the average you need to apply the table on the particles. For this, type

<tt> oa = daverage('thermosomeParticles.Data', 't', 'editedTable.tbl'); </tt>

and save the result with

<tt> dwrite(oa.average, 'my_average.em') </tt>

You can see the result by typing

<tt> dview('my_average.em');</tt>

==Alignment projects==
Iterative alignment of subtomograms to their average is performed by ''dynamo'' projects that you can run in various high-performance computational environments. To run an alignment project you need the particles, an initial reference and a table. All of these files we generated before. Start the alignment project GUI by typing

<tt> dcp</tt>

In thw new window, do the following:
# Add the project name ''drun1'', press the ''enter'' key and select ''create a new project'' in the pop-up window.
# Click on ''particles'' and provide the particle folder name ''thermosomeParticles.Data''. Click ok.
# Click on ''table'' and provide the table name ''thermosomeParticles.Data/crop.tbl''. Click ok.
# Click on ''template'' and provide the initial reference name ''my_average.em''. Click ok.
# Click on ''masks'' and simply click on ''use default masks''. Click ok. You could also specify the semi-axis of the ellipsoid masks or go to “Mask editor” to make more sophisticated masks. Note that ''Dynamo'' by default uses Rossman correlation which eliminates the artefacts associated with hard (non-soft) mask.

[[File:StartersGuideAli1.png|thumb|center|500px|]]

Click on ''numerical parameters'' to set all parameters and details about the different iterations of the alignment project. You can select any parameter in the table with a mouse and click the ''?'' button on the top right of the parameter window to see a description of the parameters. The most important parameters to consider are:

* ''Number of iterations'': Make 3 rounds with 2 iterations each. The first round will be a global search with a coarse angular step and the following rounds will be used for refinement.
* ''Angular search ranges'': Cone aperture is the scan range for the first two Euler angles around the initial orientation defined in the table. 360 degrees is the full scan range. Azimuth rotation range defines the rotation range around the new vertical axis of the particle.
* ''High- and lowpass values'': Fourier voxels to limit the used frequency range.
*''Particle dimensions'': Defined as sidelength of your subvolume. If you put a lower value, the particles will be downsampled for the particular round. This will speed up the process.
* ''Refine'': After each angular scan, the search step is reduced by the ''refine factor''. This is repeated ''refine'' times. I.e., if your cone sampling is 10 degrees, ''refine'' is 3 and ''refine factor'' is 2, then 10, 5, 2.5 and 1.25 degrees will be sampled. This is the optimization of angular search space.
*''Shift limits'': Limits the translation of particles from the center of the box (if shifts limiting way is 1) or from the previously estimated center (if shifts limiting way is 2). The previous estimates for the shifts and rotations are taken from input tables and are updated at the end of each iteration.
*''Symmetry'': If you know the symmetry of your protein it will speed up the convergence and result in higher resolution.

Set the parameters as follows and click ''ok'':

[[File:StartersGuideFigure10.png|thumb|center|600px|]]

Click on ''Computing environment'' and select your computing environment (choose ''standalone'' if you are working on the standalone version or GPU standalone if you are working in the AWS Machine). Set ''CPU cores'' and ''parallelize averaging step'' to the maximum available (e.g., 4). Leave the rest as it is and click ''ok''. In the alignment GUI click ''check'' and ''unfold''. To run the project

* in a Matlab session, you can just click on “run”.
* in a standalone project it is more convenient to write in the terminal <tt>"dynamo_execute_project drun1.exe"</tt> or to open a new terminal, load ''Dynamo'' (but do not run it) and run the project by typing <tt>./drun1.exe</tt>.

While the project is running, open another Matlab window (or in standalone open another terminal with ''Dynamo'' running) and you can monitor the progress of the alignment project by typing:

<tt>dvstatus drun1</tt>

While the project is running, you can look at projections of the intermediate results by typing:

<tt>ddb drun1:a:ite=* -j c10</tt>

or at the latest average by typing:

<tt>ddb drun1:a -v </tt>

The final result should look similar to:

[[File:StartersGuideResultsAlignment.png|thumb|center|400px| Results of alignment.]]

=Subtomogram classification=
To demonstrate a classification example we provide particles with 2 slightly different sizes. We can then classify them with a simple Multi-reference Analysis (MRA). To do that, we first generate a dataset which has 2 populations of particles. For this, type:

<tt>dynamo_tutorial('data_classification','M',8,'N',8);</tt>

It generates two sets of particles, 8 particles in each including their table. The idea behind [[Multireference Analysis|MRA]] is the following: The particles are aligned to several references (here only 2). After each iteration, each particle is assigned to only one single reference where it fits the best. This procedure is repeated iteratively. Similar particles will have higher correlation to similar references and will eventually group together. For classification into N classes we will need N initial references and N initially identical tables.Follow these steps to run the MRA:

# Create a new project by typing “drun2” in the project name of the alignment GUI.
# Set number of references to 2.
# Activate the ''Swap particles'' button.
# Go to ''particles'' and add <tt>data_classification/data</tt> to the particle data. Click ok.
# Go to ''table'' and type <tt>data_classification/real.tbl</tt> into the field ''clone this'' and press ''copy''. Click ok.
# Go to ''template'' and clone <tt>data_classification/original_template.em</tt> with addition of some extra noise with amplitude 1.
# Click on ''masks'' and click on ''use default masks''. Click ok.
# Click on ''numerical parameters'' and set the following parameters. Click ok.

[[File:StartersGuideResultsClassification2.png|thumb|center|400px|]]

Choose the same computing environment as in the previous alignment project and run the project in the same way too. MRA projects usually run longer, because each particle will be aligned to two references. Here, however, we chose the parameters in a way that the process is still fast (e.g., small dimensions). Monitor the progress of the project same as before:

<tt>dvstatus drun2</tt>

And visualize the results using the command:

<tt>ddb drun2:a:ref=* -j c5</tt>

You should get two averages with particle in one slightly class larger than in the other.

[[File:StartersGuideResultsClassification.png|thumb|center|600px| Results of classification.]]

User:Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)

2025-12-10T16:20:04Z

Miguel Sanchez: /* Subtomogram alignment and averaging */

[[Category:WalkthroughsSpecific]]

This tutorial shows how to manually pick particles in a tomogram, extract them, align and classify them. This tutorial is a shortened version of the original [[Starters_guide | starters guide]] that was adapted for the use in ''Dynamo'' workshops.

=Manual particle picking and ''Dynamo'' catalogues=
The ''Dynamo'' catalogues are databases that manage tomograms and link the tomographic data to the extracted particles. Start the catalogue manager by typing the command:

<tt>dcm</tt>
After the catalogue manager opens, we create 3 synthetic tomograms that include our particles (thermosomes) in the following way:

[[File:StartersGuideFigure1.png|thumb|center|600px| Figure 1: creating a set of synthetic tomograms with ''Dynamo'' Catalogue Manager]]

You can see the list of your tomograms and their metadata in a table in the bottom of your catalogue manager. When workin on your own projects, you can add tomograms to the catalogue by ''Catalogue -> Browse for new volume''. The tomograms are situated in the directory <tt>testCatalogue</tt>. They contain a small amount of noise and a missing wedge associated to rotation around Y-axis. We added the information about location of the particles in the tomograms in an additional catalogue called <tt>testCatalogue_withmodels</tt>. If needed, it can be opened from the current folder with ''Catalogue -> look for local catalogues'' in the catalogue manager window.

==Viewing tomograms==
Select the first tomogram in the list and go to ''View volume>Full tomogram file in tomoslice''.

[[ File:StartersSelectTomoSliceInCatalogue.png |thumb| center |600px| Figure 2: Selecting a volume in the catalogue manager to be inspected in <tt>dpreview</tt>]]

The volume browser tomoslicer loads the entire tomograms into memory and allows making annotations to the regions of interest. The tomograms in this tutorial are small, and you can load them directly into memory. For real life tomograms, bear in mind that you will need to [[Prebinned tomograms| prebin]] the files before loading them into memory. Tomoslice has a simple set of controls and is suitable for visualization tasks that require oblique sections through the tomogram. It uses the same tool as other ''Dynamo'' browsers to keep track of your annotations: a pool of models. You might need to adjust the contrast (blue arrow). To move through the tomogram slices, you can either use the mouse wheel, click and drag the tomogram slice up and down (orange arrows), or move the position control left and right (orange box).

[[ File:StartersTomoSlice.png |thumb| center |600px|]]

==Picking and extracting particles in tomograms==
Coordinates of picked particles are represented by data types called models. In the tomoslicer window go to ''Model Pool -> Create new model in pool (choose type) -> General''. This is the simplest type of [[model]] where each clicked/model point corresponds to a single isolated particle. Now you can navigate up and down the tomogram, place the mouse on the center of a particle and press the [c] key on your keyboard to add a new model point. (Note the ''Help -> all hot keys'' options that lists the different the actions of the different keystrokes). Backspace button deletes the last clicked point (you can also use the right-click to delete single points).

[[File:StartersGuideFigure4.png|thumb|center|600px| Generating a new model]]

After you are done clicking about 10 particles click on ''Active model > Update Crop points'' in the tomoslice window.

[[File:StartersGuideUpdate.png|thumb|center|600px|]]

Save the model into the catalogue by ''Active model -> Save active model into catalogue (disk)'' and close the slicer window.

[[File:StartersGuideFigure6.png|thumb|center|600px| ]]

Pick particles for tomograms 2 and 3. In total, there are around 30-40 particles in the generated dataset. When you open a new tomogram, make sure that you delete the pool of models from memory when asked. This will have no effect onto the models stored in disk, and it is necessary in order to ensure that you are not mixing models from different tomograms.

==An alternate visualization: orthogonal projections==

Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen where the x-y projection of the tomogram is shown. Use the secondary click on it to launch the orthogonal views of x-z and y-z planes that traverse that point. These views can also be used to click particles, in case the standard view is not sufficient.

{|style="margin: 0 auto;"
| [[File:orthoPickMain.png|thumb|upright|250px| click on the main projection determines two orthogonal slices]]
| [[File:orthoPickX.png|thumb|upright|250px| Slice xz ]]
| [[File:orthoPickY.png|thumb|upright|250px| Slice xy]]
|}

=Extracting particles from tomograms=
In the catalogue manager window select the rows for tomograms from which you want to extract particles from. You can either select them one by one with a mouse click and holding the [ctrl] key or by clicking the ''Select all'' button. Then, go to ''Crop Particles -> Open Volume List Manager''.

[[File:StartersGuideopenVolumeList.png|thumb|center|600px|]]

A new window opens with all the models in the catalogue listed in the bottom. Pick (by checking boxes) the models of type ''general'' that you have just clicked. Click ''Create list'' and then ''Crop particle''.

[[File:StartersGuideSelectModels.png|thumb|center|600px|]]

In the new window, change the data name to something meaningful, such as ''thermosomeParticles'', change the sidelength from 32 to 48 and click start cropping.

[[File:StartersGuideCrop.png|thumb|center|600px|]]

After cropping is done, explore your cropped particles by clicking ''ddbrowse'' (in the window above). A new window opens where you can simply click on ''show''.

[[File:StartersGuideShow.png|thumb|center|500px|]]

You see a 2D representation (projections) of all cropped 3D subtomograms. Make sure your particles are well centered and fit the box.

[[File:StartersGuideParticles.png|thumb|center|500px|]]

We also introduce the concept of the ''dynamo'' table: The information about each particle is stored in tables. Each particle has an entry in the table that contains shifts and rotations to describe its orientation (by default these values are initialized as zeroes). It also contains the particle ID (tag), the orientation of the missing wedge and others. For full info type the command <tt>dthelp</tt>. The ''Dynamo'' catalogue generates an initial table during particle extraction. Its location is in <tt>particles/crop.tbl </tt>.

=Subtomogram alignment and averaging=

==Initial reference generation==
We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually aligning a few particles and averaging them. We use the command <tt>dpkdata.montage</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all open ''Dynamo'' windows and type into the ''Dynamo'' command line:

<tt> gui = dpkdata.montage('thermosomeParticles.Data', 't', 'thermosomeParticles.Data/crop.tbl') </tt>

The gui opens. Click the bottons below to show more or fewer images.

[[File:DpkdataMontage.png|thumb|center|600px|]]

To manually align the particles, do the following for about 10 particles:
# Place the mouse over the particle center and press the key [c] (this centers the particle).
# Place the mouse over its top (or bottom) part and press the key [n] (this aligns the particle).
This is just done to create an initial reference, so orientations don't need to be very exact.

[[File:DpkdataMontage Aligned.png|thumb|center|500px|]]

Save the corresponding table by clicking ''Table'' and ''save edited table'' button in the top and save. It saves an editedTable.tbl that will be used later. To generate the average you need to apply the table on the particles. For this, type

<tt> oa = daverage('thermosomeParticles.Data', 't', 'editedTable.tbl'); </tt>

and save the result with

<tt> dwrite(oa.average, 'my_average.em') </tt>

You can see the result by typing

<tt> dview('my_average.em');</tt>

==Alignment projects==
Iterative alignment of subtomograms to their average is performed by ''dynamo'' projects that you can run in various high-performance computational environments. To run an alignment project you need the particles, an initial reference and a table. All of these files we generated before. Start the alignment project GUI by typing

<tt> dcp</tt>

In thw new window, do the following:
# Add the project name ''drun1'', press the ''enter'' key and select ''create a new project'' in the pop-up window.
# Click on ''particles'' and provide the particle folder name ''thermosomeParticles.Data''. Click ok.
# Click on ''table'' and provide the table name ''thermosomeParticles.Data/crop.tbl''. Click ok.
# Click on ''template'' and provide the initial reference name ''my_average.em''. Click ok.
# Click on ''masks'' and simply click on ''use default masks''. Click ok. You could also specify the semi-axis of the ellipsoid masks or go to “Mask editor” to make more sophisticated masks. Note that ''Dynamo'' by default uses Rossman correlation which eliminates the artefacts associated with hard (non-soft) mask.

[[File:StartersGuideAli1.png|thumb|center|500px|]]

Click on ''numerical parameters'' to set all parameters and details about the different iterations of the alignment project. You can select any parameter in the table with a mouse and click the ''?'' button on the top right of the parameter window to see a description of the parameters. The most important parameters to consider are:

* ''Number of iterations'': Make 3 rounds with 2 iterations each. The first round will be a global search with a coarse angular step and the following rounds will be used for refinement.
* ''Angular search ranges'': Cone aperture is the scan range for the first two Euler angles around the initial orientation defined in the table. 360 degrees is the full scan range. Azimuth rotation range defines the rotation range around the new vertical axis of the particle.
* ''High- and lowpass values'': Fourier voxels to limit the used frequency range.
*''Particle dimensions'': Defined as sidelength of your subvolume. If you put a lower value, the particles will be downsampled for the particular round. This will speed up the process.
* ''Refine'': After each angular scan, the search step is reduced by the ''refine factor''. This is repeated ''refine'' times. I.e., if your cone sampling is 10 degrees, ''refine'' is 3 and ''refine factor'' is 2, then 10, 5, 2.5 and 1.25 degrees will be sampled. This is the optimization of angular search space.
*''Shift limits'': Limits the translation of particles from the center of the box (if shifts limiting way is 1) or from the previously estimated center (if shifts limiting way is 2). The previous estimates for the shifts and rotations are taken from input tables and are updated at the end of each iteration.
*''Symmetry'': If you know the symmetry of your protein it will speed up the convergence and result in higher resolution.

Set the parameters as follows and click ''ok'':

[[File:StartersGuideFigure10.png|thumb|center|600px|]]

Click on ''Computing environment'' and select your computing environment (choose ''standalone'' if you are working on the standalone version or GPU standalone if you are working in the AWS Machine). Set ''CPU cores'' and ''parallelize averaging step'' to the maximum available (e.g., 4). Leave the rest as it is and click ''ok''. In the alignment GUI click ''check'' and ''unfold''. To run the project

* in a Matlab session, you can just click on “run”.
* in a standalone project it is more convenient to open a new terminal, load ''Dynamo'' (but do not run it) and run the project by typing <tt>./drun1.exe</tt>.

While the project is running, open another Matlab window (or in standalone open another terminal with ''Dynamo'' running) and you can monitor the progress of the alignment project by typing:

<tt>dvstatus drun1</tt>

While the project is running, you can look at projections of the intermediate results by typing:

<tt>ddb drun1:a:ite=* -j c10</tt>

or at the latest average by typing:

<tt>ddb drun1:a -v </tt>

The final result should look similar to:

[[File:StartersGuideResultsAlignment.png|thumb|center|400px| Results of alignment.]]

=Subtomogram classification=
To demonstrate a classification example we provide particles with 2 slightly different sizes. We can then classify them with a simple Multi-reference Analysis (MRA). To do that, we first generate a dataset which has 2 populations of particles. For this, type:

<tt>dynamo_tutorial('data_classification','M',8,'N',8);</tt>

It generates two sets of particles, 8 particles in each including their table. The idea behind [[Multireference Analysis|MRA]] is the following: The particles are aligned to several references (here only 2). After each iteration, each particle is assigned to only one single reference where it fits the best. This procedure is repeated iteratively. Similar particles will have higher correlation to similar references and will eventually group together. For classification into N classes we will need N initial references and N initially identical tables.Follow these steps to run the MRA:

# Create a new project by typing “drun2” in the project name of the alignment GUI.
# Set number of references to 2.
# Activate the ''Swap particles'' button.
# Go to ''particles'' and add <tt>data_classification/data</tt> to the particle data. Click ok.
# Go to ''table'' and type <tt>data_classification/real.tbl</tt> into the field ''clone this'' and press ''copy''. Click ok.
# Go to ''template'' and clone <tt>data_classification/original_template.em</tt> with addition of some extra noise with amplitude 1.
# Click on ''masks'' and click on ''use default masks''. Click ok.
# Click on ''numerical parameters'' and set the following parameters. Click ok.

[[File:StartersGuideResultsClassification2.png|thumb|center|400px|]]

Choose the same computing environment as in the previous alignment project and run the project in the same way too. MRA projects usually run longer, because each particle will be aligned to two references. Here, however, we chose the parameters in a way that the process is still fast (e.g., small dimensions). Monitor the progress of the project same as before:

<tt>dvstatus drun2</tt>

And visualize the results using the command:

<tt>ddb drun2:a:ref=* -j c5</tt>

You should get two averages with particle in one slightly class larger than in the other.

[[File:StartersGuideResultsClassification.png|thumb|center|600px| Results of classification.]]

User:Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)

2025-12-10T16:17:50Z

Miguel Sanchez: /* Subtomogram alignment and averaging */

[[Category:WalkthroughsSpecific]]

This tutorial shows how to manually pick particles in a tomogram, extract them, align and classify them. This tutorial is a shortened version of the original [[Starters_guide | starters guide]] that was adapted for the use in ''Dynamo'' workshops.

=Manual particle picking and ''Dynamo'' catalogues=
The ''Dynamo'' catalogues are databases that manage tomograms and link the tomographic data to the extracted particles. Start the catalogue manager by typing the command:

<tt>dcm</tt>
After the catalogue manager opens, we create 3 synthetic tomograms that include our particles (thermosomes) in the following way:

[[File:StartersGuideFigure1.png|thumb|center|600px| Figure 1: creating a set of synthetic tomograms with ''Dynamo'' Catalogue Manager]]

You can see the list of your tomograms and their metadata in a table in the bottom of your catalogue manager. When workin on your own projects, you can add tomograms to the catalogue by ''Catalogue -> Browse for new volume''. The tomograms are situated in the directory <tt>testCatalogue</tt>. They contain a small amount of noise and a missing wedge associated to rotation around Y-axis. We added the information about location of the particles in the tomograms in an additional catalogue called <tt>testCatalogue_withmodels</tt>. If needed, it can be opened from the current folder with ''Catalogue -> look for local catalogues'' in the catalogue manager window.

==Viewing tomograms==
Select the first tomogram in the list and go to ''View volume>Full tomogram file in tomoslice''.

[[ File:StartersSelectTomoSliceInCatalogue.png |thumb| center |600px| Figure 2: Selecting a volume in the catalogue manager to be inspected in <tt>dpreview</tt>]]

The volume browser tomoslicer loads the entire tomograms into memory and allows making annotations to the regions of interest. The tomograms in this tutorial are small, and you can load them directly into memory. For real life tomograms, bear in mind that you will need to [[Prebinned tomograms| prebin]] the files before loading them into memory. Tomoslice has a simple set of controls and is suitable for visualization tasks that require oblique sections through the tomogram. It uses the same tool as other ''Dynamo'' browsers to keep track of your annotations: a pool of models. You might need to adjust the contrast (blue arrow). To move through the tomogram slices, you can either use the mouse wheel, click and drag the tomogram slice up and down (orange arrows), or move the position control left and right (orange box).

[[ File:StartersTomoSlice.png |thumb| center |600px|]]

==Picking and extracting particles in tomograms==
Coordinates of picked particles are represented by data types called models. In the tomoslicer window go to ''Model Pool -> Create new model in pool (choose type) -> General''. This is the simplest type of [[model]] where each clicked/model point corresponds to a single isolated particle. Now you can navigate up and down the tomogram, place the mouse on the center of a particle and press the [c] key on your keyboard to add a new model point. (Note the ''Help -> all hot keys'' options that lists the different the actions of the different keystrokes). Backspace button deletes the last clicked point (you can also use the right-click to delete single points).

[[File:StartersGuideFigure4.png|thumb|center|600px| Generating a new model]]

After you are done clicking about 10 particles click on ''Active model > Update Crop points'' in the tomoslice window.

[[File:StartersGuideUpdate.png|thumb|center|600px|]]

Save the model into the catalogue by ''Active model -> Save active model into catalogue (disk)'' and close the slicer window.

[[File:StartersGuideFigure6.png|thumb|center|600px| ]]

Pick particles for tomograms 2 and 3. In total, there are around 30-40 particles in the generated dataset. When you open a new tomogram, make sure that you delete the pool of models from memory when asked. This will have no effect onto the models stored in disk, and it is necessary in order to ensure that you are not mixing models from different tomograms.

==An alternate visualization: orthogonal projections==

Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen where the x-y projection of the tomogram is shown. Use the secondary click on it to launch the orthogonal views of x-z and y-z planes that traverse that point. These views can also be used to click particles, in case the standard view is not sufficient.

{|style="margin: 0 auto;"
| [[File:orthoPickMain.png|thumb|upright|250px| click on the main projection determines two orthogonal slices]]
| [[File:orthoPickX.png|thumb|upright|250px| Slice xz ]]
| [[File:orthoPickY.png|thumb|upright|250px| Slice xy]]
|}

=Extracting particles from tomograms=
In the catalogue manager window select the rows for tomograms from which you want to extract particles from. You can either select them one by one with a mouse click and holding the [ctrl] key or by clicking the ''Select all'' button. Then, go to ''Crop Particles -> Open Volume List Manager''.

[[File:StartersGuideopenVolumeList.png|thumb|center|600px|]]

A new window opens with all the models in the catalogue listed in the bottom. Pick (by checking boxes) the models of type ''general'' that you have just clicked. Click ''Create list'' and then ''Crop particle''.

[[File:StartersGuideSelectModels.png|thumb|center|600px|]]

In the new window, change the data name to something meaningful, such as ''thermosomeParticles'', change the sidelength from 32 to 48 and click start cropping.

[[File:StartersGuideCrop.png|thumb|center|600px|]]

After cropping is done, explore your cropped particles by clicking ''ddbrowse'' (in the window above). A new window opens where you can simply click on ''show''.

[[File:StartersGuideShow.png|thumb|center|500px|]]

You see a 2D representation (projections) of all cropped 3D subtomograms. Make sure your particles are well centered and fit the box.

[[File:StartersGuideParticles.png|thumb|center|500px|]]

We also introduce the concept of the ''dynamo'' table: The information about each particle is stored in tables. Each particle has an entry in the table that contains shifts and rotations to describe its orientation (by default these values are initialized as zeroes). It also contains the particle ID (tag), the orientation of the missing wedge and others. For full info type the command <tt>dthelp</tt>. The ''Dynamo'' catalogue generates an initial table during particle extraction. Its location is in <tt>particles/crop.tbl </tt>.

=Subtomogram alignment and averaging=

==Initial reference generation==
We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually aligning a few particles and averaging them. We use the command <tt>dpkdata.montage</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all open ''Dynamo'' windows and type into the ''Dynamo'' command line:

<tt> gui = dpkdata.montage('thermosomeParticles.Data', 't', 'thermosomeParticles.Data/crop.tbl') </tt>

The gui opens. Click the bottons below to show more or fewer images.

[[File:DpkdataMontage.png|thumb|center|600px|]]

To manually align the particles, do the following for about 10 particles:
# Place the mouse over the particle center and press the key [c] (this centers the particle).
# Place the mouse over its top (or bottom) part and press the key [n] (this aligns the particle).
This is just done to create an initial reference, so orientations don't need to be very exact.

[[File:DpkdataMontage Aligned.png|thumb|center|500px|]]

Save the corresponding table by clicking ''Selection'' button in the top and save. It saves an editedTable.tbl that will be used later. To generate the average you need to apply the table on the particles. For this, type

<tt> oa = daverage('thermosomeParticles.Data', 't', 'editedTable.tbl'); </tt>

and save the result with

<tt> dwrite(oa.average, 'my_average.em') </tt>

You can see the result by typing

<tt> dview('my_average.em');</tt>

==Alignment projects==
Iterative alignment of subtomograms to their average is performed by ''dynamo'' projects that you can run in various high-performance computational environments. To run an alignment project you need the particles, an initial reference and a table. All of these files we generated before. Start the alignment project GUI by typing

<tt> dcp</tt>

In thw new window, do the following:
# Add the project name ''drun1'', press the ''enter'' key and select ''create a new project'' in the pop-up window.
# Click on ''particles'' and provide the particle folder name ''thermosomeParticles.Data''. Click ok.
# Click on ''table'' and provide the table name ''thermosomeParticles.Data/crop.tbl''. Click ok.
# Click on ''template'' and provide the initial reference name ''my_average.em''. Click ok.
# Click on ''masks'' and simply click on ''use default masks''. Click ok. You could also specify the semi-axis of the ellipsoid masks or go to “Mask editor” to make more sophisticated masks. Note that ''Dynamo'' by default uses Rossman correlation which eliminates the artefacts associated with hard (non-soft) mask.

[[File:StartersGuideAli1.png|thumb|center|500px|]]

Click on ''numerical parameters'' to set all parameters and details about the different iterations of the alignment project. You can select any parameter in the table with a mouse and click the ''?'' button on the top right of the parameter window to see a description of the parameters. The most important parameters to consider are:

* ''Number of iterations'': Make 3 rounds with 2 iterations each. The first round will be a global search with a coarse angular step and the following rounds will be used for refinement.
* ''Angular search ranges'': Cone aperture is the scan range for the first two Euler angles around the initial orientation defined in the table. 360 degrees is the full scan range. Azimuth rotation range defines the rotation range around the new vertical axis of the particle.
* ''High- and lowpass values'': Fourier voxels to limit the used frequency range.
*''Particle dimensions'': Defined as sidelength of your subvolume. If you put a lower value, the particles will be downsampled for the particular round. This will speed up the process.
* ''Refine'': After each angular scan, the search step is reduced by the ''refine factor''. This is repeated ''refine'' times. I.e., if your cone sampling is 10 degrees, ''refine'' is 3 and ''refine factor'' is 2, then 10, 5, 2.5 and 1.25 degrees will be sampled. This is the optimization of angular search space.
*''Shift limits'': Limits the translation of particles from the center of the box (if shifts limiting way is 1) or from the previously estimated center (if shifts limiting way is 2). The previous estimates for the shifts and rotations are taken from input tables and are updated at the end of each iteration.
*''Symmetry'': If you know the symmetry of your protein it will speed up the convergence and result in higher resolution.

Set the parameters as follows and click ''ok'':

[[File:StartersGuideFigure10.png|thumb|center|600px|]]

Click on ''Computing environment'' and select your computing environment (choose ''standalone'' if you are working on the standalone version or GPU standalone if you are working in the AWS Machine). Set ''CPU cores'' and ''parallelize averaging step'' to the maximum available (e.g., 4). Leave the rest as it is and click ''ok''. In the alignment GUI click ''check'' and ''unfold''. To run the project

* in a Matlab session, you can just click on “run”.
* in a standalone project it is more convenient to open a new terminal, load ''Dynamo'' (but do not run it) and run the project by typing <tt>./drun1.exe</tt>.

While the project is running, open another Matlab window (or in standalone open another terminal with ''Dynamo'' running) and you can monitor the progress of the alignment project by typing:

<tt>dvstatus drun1</tt>

While the project is running, you can look at projections of the intermediate results by typing:

<tt>ddb drun1:a:ite=* -j c10</tt>

or at the latest average by typing:

<tt>ddb drun1:a -v </tt>

The final result should look similar to:

[[File:StartersGuideResultsAlignment.png|thumb|center|400px| Results of alignment.]]

=Subtomogram classification=
To demonstrate a classification example we provide particles with 2 slightly different sizes. We can then classify them with a simple Multi-reference Analysis (MRA). To do that, we first generate a dataset which has 2 populations of particles. For this, type:

<tt>dynamo_tutorial('data_classification','M',8,'N',8);</tt>

It generates two sets of particles, 8 particles in each including their table. The idea behind [[Multireference Analysis|MRA]] is the following: The particles are aligned to several references (here only 2). After each iteration, each particle is assigned to only one single reference where it fits the best. This procedure is repeated iteratively. Similar particles will have higher correlation to similar references and will eventually group together. For classification into N classes we will need N initial references and N initially identical tables.Follow these steps to run the MRA:

# Create a new project by typing “drun2” in the project name of the alignment GUI.
# Set number of references to 2.
# Activate the ''Swap particles'' button.
# Go to ''particles'' and add <tt>data_classification/data</tt> to the particle data. Click ok.
# Go to ''table'' and type <tt>data_classification/real.tbl</tt> into the field ''clone this'' and press ''copy''. Click ok.
# Go to ''template'' and clone <tt>data_classification/original_template.em</tt> with addition of some extra noise with amplitude 1.
# Click on ''masks'' and click on ''use default masks''. Click ok.
# Click on ''numerical parameters'' and set the following parameters. Click ok.

[[File:StartersGuideResultsClassification2.png|thumb|center|400px|]]

Choose the same computing environment as in the previous alignment project and run the project in the same way too. MRA projects usually run longer, because each particle will be aligned to two references. Here, however, we chose the parameters in a way that the process is still fast (e.g., small dimensions). Monitor the progress of the project same as before:

<tt>dvstatus drun2</tt>

And visualize the results using the command:

<tt>ddb drun2:a:ref=* -j c5</tt>

You should get two averages with particle in one slightly class larger than in the other.

[[File:StartersGuideResultsClassification.png|thumb|center|600px| Results of classification.]]

User:Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)

2025-12-10T16:16:33Z

Miguel Sanchez: /* Initial reference generation */

[[Category:WalkthroughsSpecific]]

This tutorial shows how to manually pick particles in a tomogram, extract them, align and classify them. This tutorial is a shortened version of the original [[Starters_guide | starters guide]] that was adapted for the use in ''Dynamo'' workshops.

=Manual particle picking and ''Dynamo'' catalogues=
The ''Dynamo'' catalogues are databases that manage tomograms and link the tomographic data to the extracted particles. Start the catalogue manager by typing the command:

<tt>dcm</tt>
After the catalogue manager opens, we create 3 synthetic tomograms that include our particles (thermosomes) in the following way:

[[File:StartersGuideFigure1.png|thumb|center|600px| Figure 1: creating a set of synthetic tomograms with ''Dynamo'' Catalogue Manager]]

You can see the list of your tomograms and their metadata in a table in the bottom of your catalogue manager. When workin on your own projects, you can add tomograms to the catalogue by ''Catalogue -> Browse for new volume''. The tomograms are situated in the directory <tt>testCatalogue</tt>. They contain a small amount of noise and a missing wedge associated to rotation around Y-axis. We added the information about location of the particles in the tomograms in an additional catalogue called <tt>testCatalogue_withmodels</tt>. If needed, it can be opened from the current folder with ''Catalogue -> look for local catalogues'' in the catalogue manager window.

==Viewing tomograms==
Select the first tomogram in the list and go to ''View volume>Full tomogram file in tomoslice''.

[[ File:StartersSelectTomoSliceInCatalogue.png |thumb| center |600px| Figure 2: Selecting a volume in the catalogue manager to be inspected in <tt>dpreview</tt>]]

The volume browser tomoslicer loads the entire tomograms into memory and allows making annotations to the regions of interest. The tomograms in this tutorial are small, and you can load them directly into memory. For real life tomograms, bear in mind that you will need to [[Prebinned tomograms| prebin]] the files before loading them into memory. Tomoslice has a simple set of controls and is suitable for visualization tasks that require oblique sections through the tomogram. It uses the same tool as other ''Dynamo'' browsers to keep track of your annotations: a pool of models. You might need to adjust the contrast (blue arrow). To move through the tomogram slices, you can either use the mouse wheel, click and drag the tomogram slice up and down (orange arrows), or move the position control left and right (orange box).

[[ File:StartersTomoSlice.png |thumb| center |600px|]]

==Picking and extracting particles in tomograms==
Coordinates of picked particles are represented by data types called models. In the tomoslicer window go to ''Model Pool -> Create new model in pool (choose type) -> General''. This is the simplest type of [[model]] where each clicked/model point corresponds to a single isolated particle. Now you can navigate up and down the tomogram, place the mouse on the center of a particle and press the [c] key on your keyboard to add a new model point. (Note the ''Help -> all hot keys'' options that lists the different the actions of the different keystrokes). Backspace button deletes the last clicked point (you can also use the right-click to delete single points).

[[File:StartersGuideFigure4.png|thumb|center|600px| Generating a new model]]

After you are done clicking about 10 particles click on ''Active model > Update Crop points'' in the tomoslice window.

[[File:StartersGuideUpdate.png|thumb|center|600px|]]

Save the model into the catalogue by ''Active model -> Save active model into catalogue (disk)'' and close the slicer window.

[[File:StartersGuideFigure6.png|thumb|center|600px| ]]

Pick particles for tomograms 2 and 3. In total, there are around 30-40 particles in the generated dataset. When you open a new tomogram, make sure that you delete the pool of models from memory when asked. This will have no effect onto the models stored in disk, and it is necessary in order to ensure that you are not mixing models from different tomograms.

==An alternate visualization: orthogonal projections==

Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen where the x-y projection of the tomogram is shown. Use the secondary click on it to launch the orthogonal views of x-z and y-z planes that traverse that point. These views can also be used to click particles, in case the standard view is not sufficient.

{|style="margin: 0 auto;"
| [[File:orthoPickMain.png|thumb|upright|250px| click on the main projection determines two orthogonal slices]]
| [[File:orthoPickX.png|thumb|upright|250px| Slice xz ]]
| [[File:orthoPickY.png|thumb|upright|250px| Slice xy]]
|}

=Extracting particles from tomograms=
In the catalogue manager window select the rows for tomograms from which you want to extract particles from. You can either select them one by one with a mouse click and holding the [ctrl] key or by clicking the ''Select all'' button. Then, go to ''Crop Particles -> Open Volume List Manager''.

[[File:StartersGuideopenVolumeList.png|thumb|center|600px|]]

A new window opens with all the models in the catalogue listed in the bottom. Pick (by checking boxes) the models of type ''general'' that you have just clicked. Click ''Create list'' and then ''Crop particle''.

[[File:StartersGuideSelectModels.png|thumb|center|600px|]]

In the new window, change the data name to something meaningful, such as ''thermosomeParticles'', change the sidelength from 32 to 48 and click start cropping.

[[File:StartersGuideCrop.png|thumb|center|600px|]]

After cropping is done, explore your cropped particles by clicking ''ddbrowse'' (in the window above). A new window opens where you can simply click on ''show''.

[[File:StartersGuideShow.png|thumb|center|500px|]]

You see a 2D representation (projections) of all cropped 3D subtomograms. Make sure your particles are well centered and fit the box.

[[File:StartersGuideParticles.png|thumb|center|500px|]]

We also introduce the concept of the ''dynamo'' table: The information about each particle is stored in tables. Each particle has an entry in the table that contains shifts and rotations to describe its orientation (by default these values are initialized as zeroes). It also contains the particle ID (tag), the orientation of the missing wedge and others. For full info type the command <tt>dthelp</tt>. The ''Dynamo'' catalogue generates an initial table during particle extraction. Its location is in <tt>particles/crop.tbl </tt>.

=Subtomogram alignment and averaging=

==Initial reference generation==
We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually aligning a few particles and averaging them. We use the command <tt>dpkdata.montage</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all open ''Dynamo'' windows and type into the ''Dynamo'' command line:

<tt> gui = dpkdata.montage('ThermosomeParticles.Data', 't', 'ThermosomeParticles.Data/crop.tbl') </tt>

The gui opens. Click the bottons below to show more or fewer images.

[[File:DpkdataMontage.png|thumb|center|600px|]]

To manually align the particles, do the following for about 10 particles:
# Place the mouse over the particle center and press the key [c] (this centers the particle).
# Place the mouse over its top (or bottom) part and press the key [n] (this aligns the particle).
This is just done to create an initial reference, so orientations don't need to be very exact.

[[File:DpkdataMontage Aligned.png|thumb|center|500px|]]

Save the corresponding table by clicking ''Selection'' button in the top and save. It saves an editedTable.tbl that will be used later. To generate the average you need to apply the table on the particles. For this, type

<tt> oa = daverage('thermosomeParticles.Data', 't', 'editedTable.tbl'); </tt>

and save the result with

<tt> dwrite(oa.average, 'my_average.em') </tt>

You can see the result by typing

<tt> dview('my_average.em');</tt>

==Alignment projects==
Iterative alignment of subtomograms to their average is performed by ''dynamo'' projects that you can run in various high-performance computational environments. To run an alignment project you need the particles, an initial reference and a table. All of these files we generated before. Start the alignment project GUI by typing

<tt> dcp</tt>

In thw new window, do the following:
# Add the project name ''drun1'', press the ''enter'' key and select ''create a new project'' in the pop-up window.
# Click on ''particles'' and provide the particle folder name ''thermosomeParticles.Data''. Click ok.
# Click on ''table'' and provide the table name ''thermosomeParticles.Data/crop.tbl''. Click ok.
# Click on ''template'' and provide the initial reference name ''my_average.em''. Click ok.
# Click on ''masks'' and simply click on ''use default masks''. Click ok. You could also specify the semi-axis of the ellipsoid masks or go to “Mask editor” to make more sophisticated masks. Note that ''Dynamo'' by default uses Rossman correlation which eliminates the artefacts associated with hard (non-soft) mask.

[[File:StartersGuideAli1.png|thumb|center|500px|]]

Click on ''numerical parameters'' to set all parameters and details about the different iterations of the alignment project. You can select any parameter in the table with a mouse and click the ''?'' button on the top right of the parameter window to see a description of the parameters. The most important parameters to consider are:

* ''Number of iterations'': Make 3 rounds with 2 iterations each. The first round will be a global search with a coarse angular step and the following rounds will be used for refinement.
* ''Angular search ranges'': Cone aperture is the scan range for the first two Euler angles around the initial orientation defined in the table. 360 degrees is the full scan range. Azimuth rotation range defines the rotation range around the new vertical axis of the particle.
* ''High- and lowpass values'': Fourier voxels to limit the used frequency range.
*''Particle dimensions'': Defined as sidelength of your subvolume. If you put a lower value, the particles will be downsampled for the particular round. This will speed up the process.
* ''Refine'': After each angular scan, the search step is reduced by the ''refine factor''. This is repeated ''refine'' times. I.e., if your cone sampling is 10 degrees, ''refine'' is 3 and ''refine factor'' is 2, then 10, 5, 2.5 and 1.25 degrees will be sampled. This is the optimization of angular search space.
*''Shift limits'': Limits the translation of particles from the center of the box (if shifts limiting way is 1) or from the previously estimated center (if shifts limiting way is 2). The previous estimates for the shifts and rotations are taken from input tables and are updated at the end of each iteration.
*''Symmetry'': If you know the symmetry of your protein it will speed up the convergence and result in higher resolution.

Set the parameters as follows and click ''ok'':

[[File:StartersGuideFigure10.png|thumb|center|600px|]]

Click on ''Computing environment'' and select your computing environment (choose ''standalone'' if you are working on the standalone version or GPU standalone if you are working in the AWS Machine). Set ''CPU cores'' and ''parallelize averaging step'' to the maximum available (e.g., 4). Leave the rest as it is and click ''ok''. In the alignment GUI click ''check'' and ''unfold''. To run the project

* in a Matlab session, you can just click on “run”.
* in a standalone project it is more convenient to open a new terminal, load ''Dynamo'' (but do not run it) and run the project by typing <tt>./drun1.exe</tt>.

While the project is running, open another Matlab window (or in standalone open another terminal with ''Dynamo'' running) and you can monitor the progress of the alignment project by typing:

<tt>dvstatus drun1</tt>

While the project is running, you can look at projections of the intermediate results by typing:

<tt>ddb drun1:a:ite=* -j c10</tt>

or at the latest average by typing:

<tt>ddb drun1:a -v </tt>

The final result should look similar to:

[[File:StartersGuideResultsAlignment.png|thumb|center|400px| Results of alignment.]]

=Subtomogram classification=
To demonstrate a classification example we provide particles with 2 slightly different sizes. We can then classify them with a simple Multi-reference Analysis (MRA). To do that, we first generate a dataset which has 2 populations of particles. For this, type:

<tt>dynamo_tutorial('data_classification','M',8,'N',8);</tt>

It generates two sets of particles, 8 particles in each including their table. The idea behind [[Multireference Analysis|MRA]] is the following: The particles are aligned to several references (here only 2). After each iteration, each particle is assigned to only one single reference where it fits the best. This procedure is repeated iteratively. Similar particles will have higher correlation to similar references and will eventually group together. For classification into N classes we will need N initial references and N initially identical tables.Follow these steps to run the MRA:

# Create a new project by typing “drun2” in the project name of the alignment GUI.
# Set number of references to 2.
# Activate the ''Swap particles'' button.
# Go to ''particles'' and add <tt>data_classification/data</tt> to the particle data. Click ok.
# Go to ''table'' and type <tt>data_classification/real.tbl</tt> into the field ''clone this'' and press ''copy''. Click ok.
# Go to ''template'' and clone <tt>data_classification/original_template.em</tt> with addition of some extra noise with amplitude 1.
# Click on ''masks'' and click on ''use default masks''. Click ok.
# Click on ''numerical parameters'' and set the following parameters. Click ok.

[[File:StartersGuideResultsClassification2.png|thumb|center|400px|]]

Choose the same computing environment as in the previous alignment project and run the project in the same way too. MRA projects usually run longer, because each particle will be aligned to two references. Here, however, we chose the parameters in a way that the process is still fast (e.g., small dimensions). Monitor the progress of the project same as before:

<tt>dvstatus drun2</tt>

And visualize the results using the command:

<tt>ddb drun2:a:ref=* -j c5</tt>

You should get two averages with particle in one slightly class larger than in the other.

[[File:StartersGuideResultsClassification.png|thumb|center|600px| Results of classification.]]

User:Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)

2025-12-10T12:01:39Z

Miguel Sanchez: /* Initial reference generation */

[[Category:WalkthroughsSpecific]]

This tutorial shows how to manually pick particles in a tomogram, extract them, align and classify them. This tutorial is a shortened version of the original [[Starters_guide | starters guide]] that was adapted for the use in ''Dynamo'' workshops.

=Manual particle picking and ''Dynamo'' catalogues=
The ''Dynamo'' catalogues are databases that manage tomograms and link the tomographic data to the extracted particles. Start the catalogue manager by typing the command:

<tt>dcm</tt>
After the catalogue manager opens, we create 3 synthetic tomograms that include our particles (thermosomes) in the following way:

[[File:StartersGuideFigure1.png|thumb|center|600px| Figure 1: creating a set of synthetic tomograms with ''Dynamo'' Catalogue Manager]]

You can see the list of your tomograms and their metadata in a table in the bottom of your catalogue manager. When workin on your own projects, you can add tomograms to the catalogue by ''Catalogue -> Browse for new volume''. The tomograms are situated in the directory <tt>testCatalogue</tt>. They contain a small amount of noise and a missing wedge associated to rotation around Y-axis. We added the information about location of the particles in the tomograms in an additional catalogue called <tt>testCatalogue_withmodels</tt>. If needed, it can be opened from the current folder with ''Catalogue -> look for local catalogues'' in the catalogue manager window.

==Viewing tomograms==
Select the first tomogram in the list and go to ''View volume>Full tomogram file in tomoslice''.

[[ File:StartersSelectTomoSliceInCatalogue.png |thumb| center |600px| Figure 2: Selecting a volume in the catalogue manager to be inspected in <tt>dpreview</tt>]]

The volume browser tomoslicer loads the entire tomograms into memory and allows making annotations to the regions of interest. The tomograms in this tutorial are small, and you can load them directly into memory. For real life tomograms, bear in mind that you will need to [[Prebinned tomograms| prebin]] the files before loading them into memory. Tomoslice has a simple set of controls and is suitable for visualization tasks that require oblique sections through the tomogram. It uses the same tool as other ''Dynamo'' browsers to keep track of your annotations: a pool of models. You might need to adjust the contrast (blue arrow). To move through the tomogram slices, you can either use the mouse wheel, click and drag the tomogram slice up and down (orange arrows), or move the position control left and right (orange box).

[[ File:StartersTomoSlice.png |thumb| center |600px|]]

==Picking and extracting particles in tomograms==
Coordinates of picked particles are represented by data types called models. In the tomoslicer window go to ''Model Pool -> Create new model in pool (choose type) -> General''. This is the simplest type of [[model]] where each clicked/model point corresponds to a single isolated particle. Now you can navigate up and down the tomogram, place the mouse on the center of a particle and press the [c] key on your keyboard to add a new model point. (Note the ''Help -> all hot keys'' options that lists the different the actions of the different keystrokes). Backspace button deletes the last clicked point (you can also use the right-click to delete single points).

[[File:StartersGuideFigure4.png|thumb|center|600px| Generating a new model]]

After you are done clicking about 10 particles click on ''Active model > Update Crop points'' in the tomoslice window.

[[File:StartersGuideUpdate.png|thumb|center|600px|]]

Save the model into the catalogue by ''Active model -> Save active model into catalogue (disk)'' and close the slicer window.

[[File:StartersGuideFigure6.png|thumb|center|600px| ]]

Pick particles for tomograms 2 and 3. In total, there are around 30-40 particles in the generated dataset. When you open a new tomogram, make sure that you delete the pool of models from memory when asked. This will have no effect onto the models stored in disk, and it is necessary in order to ensure that you are not mixing models from different tomograms.

==An alternate visualization: orthogonal projections==

Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen where the x-y projection of the tomogram is shown. Use the secondary click on it to launch the orthogonal views of x-z and y-z planes that traverse that point. These views can also be used to click particles, in case the standard view is not sufficient.

{|style="margin: 0 auto;"
| [[File:orthoPickMain.png|thumb|upright|250px| click on the main projection determines two orthogonal slices]]
| [[File:orthoPickX.png|thumb|upright|250px| Slice xz ]]
| [[File:orthoPickY.png|thumb|upright|250px| Slice xy]]
|}

=Extracting particles from tomograms=
In the catalogue manager window select the rows for tomograms from which you want to extract particles from. You can either select them one by one with a mouse click and holding the [ctrl] key or by clicking the ''Select all'' button. Then, go to ''Crop Particles -> Open Volume List Manager''.

[[File:StartersGuideopenVolumeList.png|thumb|center|600px|]]

A new window opens with all the models in the catalogue listed in the bottom. Pick (by checking boxes) the models of type ''general'' that you have just clicked. Click ''Create list'' and then ''Crop particle''.

[[File:StartersGuideSelectModels.png|thumb|center|600px|]]

In the new window, change the data name to something meaningful, such as ''thermosomeParticles'', change the sidelength from 32 to 48 and click start cropping.

[[File:StartersGuideCrop.png|thumb|center|600px|]]

After cropping is done, explore your cropped particles by clicking ''ddbrowse'' (in the window above). A new window opens where you can simply click on ''show''.

[[File:StartersGuideShow.png|thumb|center|500px|]]

You see a 2D representation (projections) of all cropped 3D subtomograms. Make sure your particles are well centered and fit the box.

[[File:StartersGuideParticles.png|thumb|center|500px|]]

We also introduce the concept of the ''dynamo'' table: The information about each particle is stored in tables. Each particle has an entry in the table that contains shifts and rotations to describe its orientation (by default these values are initialized as zeroes). It also contains the particle ID (tag), the orientation of the missing wedge and others. For full info type the command <tt>dthelp</tt>. The ''Dynamo'' catalogue generates an initial table during particle extraction. Its location is in <tt>particles/crop.tbl </tt>.

=Subtomogram alignment and averaging=

==Initial reference generation==
We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually aligning a few particles and averaging them. We use the command <tt>dpkdata.montage</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all open ''Dynamo'' windows and type into the ''Dynamo'' command line:

<tt> gui = dpkdata.montage('thermosomeParticles.Data', 't', 'thermosomeParticles.Data/crop.tbl') </tt>

The gui opens. Click the bottons below to show more or fewer images.

[[File:DpkdataMontage.png|thumb|center|600px|]]

To manually align the particles, do the following for about 10 particles:
# Place the mouse over the particle center and press the key [c] (this centers the particle).
# Place the mouse over its top (or bottom) part and press the key [n] (this aligns the particle).
This is just done to create an initial reference, so orientations don't need to be very exact.

[[File:DpkdataMontage Aligned.png|thumb|center|500px|]]

Save the corresponding table by clicking ''Selection'' button in the top and save. It saves an editedTable.tbl that will be used later. To generate the average you need to apply the table on the particles. For this, type

<tt> oa = daverage('thermosomeParticles.Data', 't', 'editedTable.tbl'); </tt>

and save the result with

<tt> dwrite(oa.average, 'my_average.em') </tt>

You can see the result by typing

<tt> dview('my_average.em');</tt>

==Alignment projects==
Iterative alignment of subtomograms to their average is performed by ''dynamo'' projects that you can run in various high-performance computational environments. To run an alignment project you need the particles, an initial reference and a table. All of these files we generated before. Start the alignment project GUI by typing

<tt> dcp</tt>

In thw new window, do the following:
# Add the project name ''drun1'', press the ''enter'' key and select ''create a new project'' in the pop-up window.
# Click on ''particles'' and provide the particle folder name ''thermosomeParticles.Data''. Click ok.
# Click on ''table'' and provide the table name ''thermosomeParticles.Data/crop.tbl''. Click ok.
# Click on ''template'' and provide the initial reference name ''my_average.em''. Click ok.
# Click on ''masks'' and simply click on ''use default masks''. Click ok. You could also specify the semi-axis of the ellipsoid masks or go to “Mask editor” to make more sophisticated masks. Note that ''Dynamo'' by default uses Rossman correlation which eliminates the artefacts associated with hard (non-soft) mask.

[[File:StartersGuideAli1.png|thumb|center|500px|]]

Click on ''numerical parameters'' to set all parameters and details about the different iterations of the alignment project. You can select any parameter in the table with a mouse and click the ''?'' button on the top right of the parameter window to see a description of the parameters. The most important parameters to consider are:

* ''Number of iterations'': Make 3 rounds with 2 iterations each. The first round will be a global search with a coarse angular step and the following rounds will be used for refinement.
* ''Angular search ranges'': Cone aperture is the scan range for the first two Euler angles around the initial orientation defined in the table. 360 degrees is the full scan range. Azimuth rotation range defines the rotation range around the new vertical axis of the particle.
* ''High- and lowpass values'': Fourier voxels to limit the used frequency range.
*''Particle dimensions'': Defined as sidelength of your subvolume. If you put a lower value, the particles will be downsampled for the particular round. This will speed up the process.
* ''Refine'': After each angular scan, the search step is reduced by the ''refine factor''. This is repeated ''refine'' times. I.e., if your cone sampling is 10 degrees, ''refine'' is 3 and ''refine factor'' is 2, then 10, 5, 2.5 and 1.25 degrees will be sampled. This is the optimization of angular search space.
*''Shift limits'': Limits the translation of particles from the center of the box (if shifts limiting way is 1) or from the previously estimated center (if shifts limiting way is 2). The previous estimates for the shifts and rotations are taken from input tables and are updated at the end of each iteration.
*''Symmetry'': If you know the symmetry of your protein it will speed up the convergence and result in higher resolution.

Set the parameters as follows and click ''ok'':

[[File:StartersGuideFigure10.png|thumb|center|600px|]]

Click on ''Computing environment'' and select your computing environment (choose ''standalone'' if you are working on the standalone version or GPU standalone if you are working in the AWS Machine). Set ''CPU cores'' and ''parallelize averaging step'' to the maximum available (e.g., 4). Leave the rest as it is and click ''ok''. In the alignment GUI click ''check'' and ''unfold''. To run the project

* in a Matlab session, you can just click on “run”.
* in a standalone project it is more convenient to open a new terminal, load ''Dynamo'' (but do not run it) and run the project by typing <tt>./drun1.exe</tt>.

While the project is running, open another Matlab window (or in standalone open another terminal with ''Dynamo'' running) and you can monitor the progress of the alignment project by typing:

<tt>dvstatus drun1</tt>

While the project is running, you can look at projections of the intermediate results by typing:

<tt>ddb drun1:a:ite=* -j c10</tt>

or at the latest average by typing:

<tt>ddb drun1:a -v </tt>

The final result should look similar to:

[[File:StartersGuideResultsAlignment.png|thumb|center|400px| Results of alignment.]]

=Subtomogram classification=
To demonstrate a classification example we provide particles with 2 slightly different sizes. We can then classify them with a simple Multi-reference Analysis (MRA). To do that, we first generate a dataset which has 2 populations of particles. For this, type:

<tt>dynamo_tutorial('data_classification','M',8,'N',8);</tt>

It generates two sets of particles, 8 particles in each including their table. The idea behind [[Multireference Analysis|MRA]] is the following: The particles are aligned to several references (here only 2). After each iteration, each particle is assigned to only one single reference where it fits the best. This procedure is repeated iteratively. Similar particles will have higher correlation to similar references and will eventually group together. For classification into N classes we will need N initial references and N initially identical tables.Follow these steps to run the MRA:

# Create a new project by typing “drun2” in the project name of the alignment GUI.
# Set number of references to 2.
# Activate the ''Swap particles'' button.
# Go to ''particles'' and add <tt>data_classification/data</tt> to the particle data. Click ok.
# Go to ''table'' and type <tt>data_classification/real.tbl</tt> into the field ''clone this'' and press ''copy''. Click ok.
# Go to ''template'' and clone <tt>data_classification/original_template.em</tt> with addition of some extra noise with amplitude 1.
# Click on ''masks'' and click on ''use default masks''. Click ok.
# Click on ''numerical parameters'' and set the following parameters. Click ok.

[[File:StartersGuideResultsClassification2.png|thumb|center|400px|]]

Choose the same computing environment as in the previous alignment project and run the project in the same way too. MRA projects usually run longer, because each particle will be aligned to two references. Here, however, we chose the parameters in a way that the process is still fast (e.g., small dimensions). Monitor the progress of the project same as before:

<tt>dvstatus drun2</tt>

And visualize the results using the command:

<tt>ddb drun2:a:ref=* -j c5</tt>

You should get two averages with particle in one slightly class larger than in the other.

[[File:StartersGuideResultsClassification.png|thumb|center|600px| Results of classification.]]

User:Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)

2025-12-10T11:58:31Z

Miguel Sanchez: /* Subtomogram alignment and averaging */

[[Category:WalkthroughsSpecific]]

This tutorial shows how to manually pick particles in a tomogram, extract them, align and classify them. This tutorial is a shortened version of the original [[Starters_guide | starters guide]] that was adapted for the use in ''Dynamo'' workshops.

=Manual particle picking and ''Dynamo'' catalogues=
The ''Dynamo'' catalogues are databases that manage tomograms and link the tomographic data to the extracted particles. Start the catalogue manager by typing the command:

<tt>dcm</tt>
After the catalogue manager opens, we create 3 synthetic tomograms that include our particles (thermosomes) in the following way:

[[File:StartersGuideFigure1.png|thumb|center|600px| Figure 1: creating a set of synthetic tomograms with ''Dynamo'' Catalogue Manager]]

You can see the list of your tomograms and their metadata in a table in the bottom of your catalogue manager. When workin on your own projects, you can add tomograms to the catalogue by ''Catalogue -> Browse for new volume''. The tomograms are situated in the directory <tt>testCatalogue</tt>. They contain a small amount of noise and a missing wedge associated to rotation around Y-axis. We added the information about location of the particles in the tomograms in an additional catalogue called <tt>testCatalogue_withmodels</tt>. If needed, it can be opened from the current folder with ''Catalogue -> look for local catalogues'' in the catalogue manager window.

==Viewing tomograms==
Select the first tomogram in the list and go to ''View volume>Full tomogram file in tomoslice''.

[[ File:StartersSelectTomoSliceInCatalogue.png |thumb| center |600px| Figure 2: Selecting a volume in the catalogue manager to be inspected in <tt>dpreview</tt>]]

The volume browser tomoslicer loads the entire tomograms into memory and allows making annotations to the regions of interest. The tomograms in this tutorial are small, and you can load them directly into memory. For real life tomograms, bear in mind that you will need to [[Prebinned tomograms| prebin]] the files before loading them into memory. Tomoslice has a simple set of controls and is suitable for visualization tasks that require oblique sections through the tomogram. It uses the same tool as other ''Dynamo'' browsers to keep track of your annotations: a pool of models. You might need to adjust the contrast (blue arrow). To move through the tomogram slices, you can either use the mouse wheel, click and drag the tomogram slice up and down (orange arrows), or move the position control left and right (orange box).

[[ File:StartersTomoSlice.png |thumb| center |600px|]]

==Picking and extracting particles in tomograms==
Coordinates of picked particles are represented by data types called models. In the tomoslicer window go to ''Model Pool -> Create new model in pool (choose type) -> General''. This is the simplest type of [[model]] where each clicked/model point corresponds to a single isolated particle. Now you can navigate up and down the tomogram, place the mouse on the center of a particle and press the [c] key on your keyboard to add a new model point. (Note the ''Help -> all hot keys'' options that lists the different the actions of the different keystrokes). Backspace button deletes the last clicked point (you can also use the right-click to delete single points).

[[File:StartersGuideFigure4.png|thumb|center|600px| Generating a new model]]

After you are done clicking about 10 particles click on ''Active model > Update Crop points'' in the tomoslice window.

[[File:StartersGuideUpdate.png|thumb|center|600px|]]

Save the model into the catalogue by ''Active model -> Save active model into catalogue (disk)'' and close the slicer window.

[[File:StartersGuideFigure6.png|thumb|center|600px| ]]

Pick particles for tomograms 2 and 3. In total, there are around 30-40 particles in the generated dataset. When you open a new tomogram, make sure that you delete the pool of models from memory when asked. This will have no effect onto the models stored in disk, and it is necessary in order to ensure that you are not mixing models from different tomograms.

==An alternate visualization: orthogonal projections==

Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen where the x-y projection of the tomogram is shown. Use the secondary click on it to launch the orthogonal views of x-z and y-z planes that traverse that point. These views can also be used to click particles, in case the standard view is not sufficient.

{|style="margin: 0 auto;"
| [[File:orthoPickMain.png|thumb|upright|250px| click on the main projection determines two orthogonal slices]]
| [[File:orthoPickX.png|thumb|upright|250px| Slice xz ]]
| [[File:orthoPickY.png|thumb|upright|250px| Slice xy]]
|}

=Extracting particles from tomograms=
In the catalogue manager window select the rows for tomograms from which you want to extract particles from. You can either select them one by one with a mouse click and holding the [ctrl] key or by clicking the ''Select all'' button. Then, go to ''Crop Particles -> Open Volume List Manager''.

[[File:StartersGuideopenVolumeList.png|thumb|center|600px|]]

A new window opens with all the models in the catalogue listed in the bottom. Pick (by checking boxes) the models of type ''general'' that you have just clicked. Click ''Create list'' and then ''Crop particle''.

[[File:StartersGuideSelectModels.png|thumb|center|600px|]]

In the new window, change the data name to something meaningful, such as ''thermosomeParticles'', change the sidelength from 32 to 48 and click start cropping.

[[File:StartersGuideCrop.png|thumb|center|600px|]]

After cropping is done, explore your cropped particles by clicking ''ddbrowse'' (in the window above). A new window opens where you can simply click on ''show''.

[[File:StartersGuideShow.png|thumb|center|500px|]]

You see a 2D representation (projections) of all cropped 3D subtomograms. Make sure your particles are well centered and fit the box.

[[File:StartersGuideParticles.png|thumb|center|500px|]]

We also introduce the concept of the ''dynamo'' table: The information about each particle is stored in tables. Each particle has an entry in the table that contains shifts and rotations to describe its orientation (by default these values are initialized as zeroes). It also contains the particle ID (tag), the orientation of the missing wedge and others. For full info type the command <tt>dthelp</tt>. The ''Dynamo'' catalogue generates an initial table during particle extraction. Its location is in <tt>particles/crop.tbl </tt>.

=Subtomogram alignment and averaging=

==Initial reference generation==
We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually align a few particles and average them. We use the command <tt>dpkdata.montage</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all open ''Dynamo'' windows and type into the ''Dynamo'' command line:

<tt> gui = dpkdata.montage('thermosomeParticles.Data', 't', 'thermosomeParticles.Data/crop.tbl') </tt>

The gui opens. Click the bottons below to show more or fewer images.

[[File:DpkdataMontage.png|thumb|center|600px|]]

To manually align the particles, do the following for about 10 particles:
# Place the mouse over the particle center and press the key [c] (this centers the particle).
# Place the mouse over its top (or bottom) part and press the key [n] (this aligns the particle).
This is just done to create an initial reference, so orientations don't need to be very exact.

[[File:DpkdataMontage Aligned.png|thumb|center|500px|]]

Save the corresponding table by clicking ''Selection'' button in the top and save. It saves an editedTable.tbl that will be used later. To generate the average you need to apply the table on the particles. For this, type

<tt> oa = daverage('thermosomeParticles.Data', 't', 'editedTable.tbl'); </tt>

and save the result with

<tt> dwrite(oa.average, 'my_average.em') </tt>

You can see the result by typing

<tt> dview('my_average.em');</tt>

==Alignment projects==
Iterative alignment of subtomograms to their average is performed by ''dynamo'' projects that you can run in various high-performance computational environments. To run an alignment project you need the particles, an initial reference and a table. All of these files we generated before. Start the alignment project GUI by typing

<tt> dcp</tt>

In thw new window, do the following:
# Add the project name ''drun1'', press the ''enter'' key and select ''create a new project'' in the pop-up window.
# Click on ''particles'' and provide the particle folder name ''thermosomeParticles.Data''. Click ok.
# Click on ''table'' and provide the table name ''thermosomeParticles.Data/crop.tbl''. Click ok.
# Click on ''template'' and provide the initial reference name ''my_average.em''. Click ok.
# Click on ''masks'' and simply click on ''use default masks''. Click ok. You could also specify the semi-axis of the ellipsoid masks or go to “Mask editor” to make more sophisticated masks. Note that ''Dynamo'' by default uses Rossman correlation which eliminates the artefacts associated with hard (non-soft) mask.

[[File:StartersGuideAli1.png|thumb|center|500px|]]

Click on ''numerical parameters'' to set all parameters and details about the different iterations of the alignment project. You can select any parameter in the table with a mouse and click the ''?'' button on the top right of the parameter window to see a description of the parameters. The most important parameters to consider are:

* ''Number of iterations'': Make 3 rounds with 2 iterations each. The first round will be a global search with a coarse angular step and the following rounds will be used for refinement.
* ''Angular search ranges'': Cone aperture is the scan range for the first two Euler angles around the initial orientation defined in the table. 360 degrees is the full scan range. Azimuth rotation range defines the rotation range around the new vertical axis of the particle.
* ''High- and lowpass values'': Fourier voxels to limit the used frequency range.
*''Particle dimensions'': Defined as sidelength of your subvolume. If you put a lower value, the particles will be downsampled for the particular round. This will speed up the process.
* ''Refine'': After each angular scan, the search step is reduced by the ''refine factor''. This is repeated ''refine'' times. I.e., if your cone sampling is 10 degrees, ''refine'' is 3 and ''refine factor'' is 2, then 10, 5, 2.5 and 1.25 degrees will be sampled. This is the optimization of angular search space.
*''Shift limits'': Limits the translation of particles from the center of the box (if shifts limiting way is 1) or from the previously estimated center (if shifts limiting way is 2). The previous estimates for the shifts and rotations are taken from input tables and are updated at the end of each iteration.
*''Symmetry'': If you know the symmetry of your protein it will speed up the convergence and result in higher resolution.

Set the parameters as follows and click ''ok'':

[[File:StartersGuideFigure10.png|thumb|center|600px|]]

Click on ''Computing environment'' and select your computing environment (choose ''standalone'' if you are working on the standalone version or GPU standalone if you are working in the AWS Machine). Set ''CPU cores'' and ''parallelize averaging step'' to the maximum available (e.g., 4). Leave the rest as it is and click ''ok''. In the alignment GUI click ''check'' and ''unfold''. To run the project

* in a Matlab session, you can just click on “run”.
* in a standalone project it is more convenient to open a new terminal, load ''Dynamo'' (but do not run it) and run the project by typing <tt>./drun1.exe</tt>.

While the project is running, open another Matlab window (or in standalone open another terminal with ''Dynamo'' running) and you can monitor the progress of the alignment project by typing:

<tt>dvstatus drun1</tt>

While the project is running, you can look at projections of the intermediate results by typing:

<tt>ddb drun1:a:ite=* -j c10</tt>

or at the latest average by typing:

<tt>ddb drun1:a -v </tt>

The final result should look similar to:

[[File:StartersGuideResultsAlignment.png|thumb|center|400px| Results of alignment.]]

=Subtomogram classification=
To demonstrate a classification example we provide particles with 2 slightly different sizes. We can then classify them with a simple Multi-reference Analysis (MRA). To do that, we first generate a dataset which has 2 populations of particles. For this, type:

<tt>dynamo_tutorial('data_classification','M',8,'N',8);</tt>

It generates two sets of particles, 8 particles in each including their table. The idea behind [[Multireference Analysis|MRA]] is the following: The particles are aligned to several references (here only 2). After each iteration, each particle is assigned to only one single reference where it fits the best. This procedure is repeated iteratively. Similar particles will have higher correlation to similar references and will eventually group together. For classification into N classes we will need N initial references and N initially identical tables.Follow these steps to run the MRA:

# Create a new project by typing “drun2” in the project name of the alignment GUI.
# Set number of references to 2.
# Activate the ''Swap particles'' button.
# Go to ''particles'' and add <tt>data_classification/data</tt> to the particle data. Click ok.
# Go to ''table'' and type <tt>data_classification/real.tbl</tt> into the field ''clone this'' and press ''copy''. Click ok.
# Go to ''template'' and clone <tt>data_classification/original_template.em</tt> with addition of some extra noise with amplitude 1.
# Click on ''masks'' and click on ''use default masks''. Click ok.
# Click on ''numerical parameters'' and set the following parameters. Click ok.

[[File:StartersGuideResultsClassification2.png|thumb|center|400px|]]

Choose the same computing environment as in the previous alignment project and run the project in the same way too. MRA projects usually run longer, because each particle will be aligned to two references. Here, however, we chose the parameters in a way that the process is still fast (e.g., small dimensions). Monitor the progress of the project same as before:

<tt>dvstatus drun2</tt>

And visualize the results using the command:

<tt>ddb drun2:a:ref=* -j c5</tt>

You should get two averages with particle in one slightly class larger than in the other.

[[File:StartersGuideResultsClassification.png|thumb|center|600px| Results of classification.]]

File:DpkdataMontage.png

2025-12-10T11:54:16Z

Miguel Sanchez:

File:DpkdataMontage Aligned.png

2025-12-10T11:53:30Z

Miguel Sanchez:

User:Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)

2025-12-10T11:44:26Z

Miguel Sanchez: /* Subtomogram alignment and averaging */

[[Category:WalkthroughsSpecific]]

This tutorial shows how to manually pick particles in a tomogram, extract them, align and classify them. This tutorial is a shortened version of the original [[Starters_guide | starters guide]] that was adapted for the use in ''Dynamo'' workshops.

=Manual particle picking and ''Dynamo'' catalogues=
The ''Dynamo'' catalogues are databases that manage tomograms and link the tomographic data to the extracted particles. Start the catalogue manager by typing the command:

<tt>dcm</tt>
After the catalogue manager opens, we create 3 synthetic tomograms that include our particles (thermosomes) in the following way:

[[File:StartersGuideFigure1.png|thumb|center|600px| Figure 1: creating a set of synthetic tomograms with ''Dynamo'' Catalogue Manager]]

You can see the list of your tomograms and their metadata in a table in the bottom of your catalogue manager. When workin on your own projects, you can add tomograms to the catalogue by ''Catalogue -> Browse for new volume''. The tomograms are situated in the directory <tt>testCatalogue</tt>. They contain a small amount of noise and a missing wedge associated to rotation around Y-axis. We added the information about location of the particles in the tomograms in an additional catalogue called <tt>testCatalogue_withmodels</tt>. If needed, it can be opened from the current folder with ''Catalogue -> look for local catalogues'' in the catalogue manager window.

==Viewing tomograms==
Select the first tomogram in the list and go to ''View volume>Full tomogram file in tomoslice''.

[[ File:StartersSelectTomoSliceInCatalogue.png |thumb| center |600px| Figure 2: Selecting a volume in the catalogue manager to be inspected in <tt>dpreview</tt>]]

The volume browser tomoslicer loads the entire tomograms into memory and allows making annotations to the regions of interest. The tomograms in this tutorial are small, and you can load them directly into memory. For real life tomograms, bear in mind that you will need to [[Prebinned tomograms| prebin]] the files before loading them into memory. Tomoslice has a simple set of controls and is suitable for visualization tasks that require oblique sections through the tomogram. It uses the same tool as other ''Dynamo'' browsers to keep track of your annotations: a pool of models. You might need to adjust the contrast (blue arrow). To move through the tomogram slices, you can either use the mouse wheel, click and drag the tomogram slice up and down (orange arrows), or move the position control left and right (orange box).

[[ File:StartersTomoSlice.png |thumb| center |600px|]]

==Picking and extracting particles in tomograms==
Coordinates of picked particles are represented by data types called models. In the tomoslicer window go to ''Model Pool -> Create new model in pool (choose type) -> General''. This is the simplest type of [[model]] where each clicked/model point corresponds to a single isolated particle. Now you can navigate up and down the tomogram, place the mouse on the center of a particle and press the [c] key on your keyboard to add a new model point. (Note the ''Help -> all hot keys'' options that lists the different the actions of the different keystrokes). Backspace button deletes the last clicked point (you can also use the right-click to delete single points).

[[File:StartersGuideFigure4.png|thumb|center|600px| Generating a new model]]

After you are done clicking about 10 particles click on ''Active model > Update Crop points'' in the tomoslice window.

[[File:StartersGuideUpdate.png|thumb|center|600px|]]

Save the model into the catalogue by ''Active model -> Save active model into catalogue (disk)'' and close the slicer window.

[[File:StartersGuideFigure6.png|thumb|center|600px| ]]

Pick particles for tomograms 2 and 3. In total, there are around 30-40 particles in the generated dataset. When you open a new tomogram, make sure that you delete the pool of models from memory when asked. This will have no effect onto the models stored in disk, and it is necessary in order to ensure that you are not mixing models from different tomograms.

==An alternate visualization: orthogonal projections==

Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen where the x-y projection of the tomogram is shown. Use the secondary click on it to launch the orthogonal views of x-z and y-z planes that traverse that point. These views can also be used to click particles, in case the standard view is not sufficient.

{|style="margin: 0 auto;"
| [[File:orthoPickMain.png|thumb|upright|250px| click on the main projection determines two orthogonal slices]]
| [[File:orthoPickX.png|thumb|upright|250px| Slice xz ]]
| [[File:orthoPickY.png|thumb|upright|250px| Slice xy]]
|}

=Extracting particles from tomograms=
In the catalogue manager window select the rows for tomograms from which you want to extract particles from. You can either select them one by one with a mouse click and holding the [ctrl] key or by clicking the ''Select all'' button. Then, go to ''Crop Particles -> Open Volume List Manager''.

[[File:StartersGuideopenVolumeList.png|thumb|center|600px|]]

A new window opens with all the models in the catalogue listed in the bottom. Pick (by checking boxes) the models of type ''general'' that you have just clicked. Click ''Create list'' and then ''Crop particle''.

[[File:StartersGuideSelectModels.png|thumb|center|600px|]]

In the new window, change the data name to something meaningful, such as ''thermosomeParticles'', change the sidelength from 32 to 48 and click start cropping.

[[File:StartersGuideCrop.png|thumb|center|600px|]]

After cropping is done, explore your cropped particles by clicking ''ddbrowse'' (in the window above). A new window opens where you can simply click on ''show''.

[[File:StartersGuideShow.png|thumb|center|500px|]]

You see a 2D representation (projections) of all cropped 3D subtomograms. Make sure your particles are well centered and fit the box.

[[File:StartersGuideParticles.png|thumb|center|500px|]]

We also introduce the concept of the ''dynamo'' table: The information about each particle is stored in tables. Each particle has an entry in the table that contains shifts and rotations to describe its orientation (by default these values are initialized as zeroes). It also contains the particle ID (tag), the orientation of the missing wedge and others. For full info type the command <tt>dthelp</tt>. The ''Dynamo'' catalogue generates an initial table during particle extraction. Its location is in <tt>particles/crop.tbl </tt>.

=Subtomogram alignment and averaging=

==Initial reference generation==
We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually align a few particles and average them. We use the command <tt>dpkdata.montage</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all open ''Dynamo'' windows and type into the ''Dynamo'' command line:

<tt> gui = dpkdata.montage('thermosomeParticles.Data', 't', 'thermosomeParticles.Data/crop.tbl') </tt>

The gui opens. Click the bottons below to show more or fewer images.

[[File:StartersGuideGallery.png|thumb|center|600px|]]

To manually align the particles, do the following for about 10 particles:
# Place the mouse over the particle center and press the key [c] (this centers the particle).
# Place the mouse over its top (or bottom) part and press the key [n] (this aligns the particle).
This is just done to create an initial reference, so orientations don't need to be very exact.

[[File:StartersGuideGallery2.png|thumb|center|500px|]]

Save the selected tags and corresponding table by clicking ''Selection'' button in the top and save. It saves an editedTable.tbl that will be used later. To generate the average you need to apply the table on the particles. For this, type

<tt> oa = daverage('thermosomeParticles.Data', 't', 'editedTable.tbl'); </tt>

and save the result with

<tt> dwrite(oa.average, 'my_average.em') </tt>

You can see the result by typing

<tt> dview('my_average.em');</tt>

==Alignment projects==
Iterative alignment of subtomograms to their average is performed by ''dynamo'' projects that you can run in various high-performance computational environments. To run an alignment project you need the particles, an initial reference and a table. All of these files we generated before. Start the alignment project GUI by typing

<tt> dcp</tt>

In thw new window, do the following:
# Add the project name ''drun1'', press the ''enter'' key and select ''create a new project'' in the pop-up window.
# Click on ''particles'' and provide the particle folder name ''thermosomeParticles.Data''. Click ok.
# Click on ''table'' and provide the table name ''thermosomeParticles.Data/crop.tbl''. Click ok.
# Click on ''template'' and provide the initial reference name ''my_average.em''. Click ok.
# Click on ''masks'' and simply click on ''use default masks''. Click ok. You could also specify the semi-axis of the ellipsoid masks or go to “Mask editor” to make more sophisticated masks. Note that ''Dynamo'' by default uses Rossman correlation which eliminates the artefacts associated with hard (non-soft) mask.

[[File:StartersGuideAli1.png|thumb|center|500px|]]

Click on ''numerical parameters'' to set all parameters and details about the different iterations of the alignment project. You can select any parameter in the table with a mouse and click the ''?'' button on the top right of the parameter window to see a description of the parameters. The most important parameters to consider are:

* ''Number of iterations'': Make 3 rounds with 2 iterations each. The first round will be a global search with a coarse angular step and the following rounds will be used for refinement.
* ''Angular search ranges'': Cone aperture is the scan range for the first two Euler angles around the initial orientation defined in the table. 360 degrees is the full scan range. Azimuth rotation range defines the rotation range around the new vertical axis of the particle.
* ''High- and lowpass values'': Fourier voxels to limit the used frequency range.
*''Particle dimensions'': Defined as sidelength of your subvolume. If you put a lower value, the particles will be downsampled for the particular round. This will speed up the process.
* ''Refine'': After each angular scan, the search step is reduced by the ''refine factor''. This is repeated ''refine'' times. I.e., if your cone sampling is 10 degrees, ''refine'' is 3 and ''refine factor'' is 2, then 10, 5, 2.5 and 1.25 degrees will be sampled. This is the optimization of angular search space.
*''Shift limits'': Limits the translation of particles from the center of the box (if shifts limiting way is 1) or from the previously estimated center (if shifts limiting way is 2). The previous estimates for the shifts and rotations are taken from input tables and are updated at the end of each iteration.
*''Symmetry'': If you know the symmetry of your protein it will speed up the convergence and result in higher resolution.

Set the parameters as follows and click ''ok'':

[[File:StartersGuideFigure10.png|thumb|center|600px|]]

Click on ''Computing environment'' and select your computing environment (choose ''standalone'' if you are working on the standalone version or GPU standalone if you are working in the AWS Machine). Set ''CPU cores'' and ''parallelize averaging step'' to the maximum available (e.g., 4). Leave the rest as it is and click ''ok''. In the alignment GUI click ''check'' and ''unfold''. To run the project

* in a Matlab session, you can just click on “run”.
* in a standalone project it is more convenient to open a new terminal, load ''Dynamo'' (but do not run it) and run the project by typing <tt>./drun1.exe</tt>.

While the project is running, open another Matlab window (or in standalone open another terminal with ''Dynamo'' running) and you can monitor the progress of the alignment project by typing:

<tt>dvstatus drun1</tt>

While the project is running, you can look at projections of the intermediate results by typing:

<tt>ddb drun1:a:ite=* -j c10</tt>

or at the latest average by typing:

<tt>ddb drun1:a -v </tt>

The final result should look similar to:

[[File:StartersGuideResultsAlignment.png|thumb|center|400px| Results of alignment.]]

=Subtomogram classification=
To demonstrate a classification example we provide particles with 2 slightly different sizes. We can then classify them with a simple Multi-reference Analysis (MRA). To do that, we first generate a dataset which has 2 populations of particles. For this, type:

<tt>dynamo_tutorial('data_classification','M',8,'N',8);</tt>

It generates two sets of particles, 8 particles in each including their table. The idea behind [[Multireference Analysis|MRA]] is the following: The particles are aligned to several references (here only 2). After each iteration, each particle is assigned to only one single reference where it fits the best. This procedure is repeated iteratively. Similar particles will have higher correlation to similar references and will eventually group together. For classification into N classes we will need N initial references and N initially identical tables.Follow these steps to run the MRA:

# Create a new project by typing “drun2” in the project name of the alignment GUI.
# Set number of references to 2.
# Activate the ''Swap particles'' button.
# Go to ''particles'' and add <tt>data_classification/data</tt> to the particle data. Click ok.
# Go to ''table'' and type <tt>data_classification/real.tbl</tt> into the field ''clone this'' and press ''copy''. Click ok.
# Go to ''template'' and clone <tt>data_classification/original_template.em</tt> with addition of some extra noise with amplitude 1.
# Click on ''masks'' and click on ''use default masks''. Click ok.
# Click on ''numerical parameters'' and set the following parameters. Click ok.

[[File:StartersGuideResultsClassification2.png|thumb|center|400px|]]

Choose the same computing environment as in the previous alignment project and run the project in the same way too. MRA projects usually run longer, because each particle will be aligned to two references. Here, however, we chose the parameters in a way that the process is still fast (e.g., small dimensions). Monitor the progress of the project same as before:

<tt>dvstatus drun2</tt>

And visualize the results using the command:

<tt>ddb drun2:a:ref=* -j c5</tt>

You should get two averages with particle in one slightly class larger than in the other.

[[File:StartersGuideResultsClassification.png|thumb|center|600px| Results of classification.]]

I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025

2025-12-09T16:35:10Z

Miguel Sanchez: /* Entering in the AWS Machine */

[[Category:WalkthroughsSpecific]]
= The course =
== The venue ==
This page describes the contents of the ''Dynamo''-specific part of the course "I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025", which will take part at the premises of the Centro Nacional de Biotecnología in Madrid, from the 9th to the 12th of December 2025.
== Contents ==
Whole pipelines for cryo-ET processing will be covered in the Scipion-related area of the course (days 1 and 2). The ''Dynamo'' part will covered selected parts of the pipeline.

= Installation of Dynamo and Matlab =
== Dynamo on your own laptop ==
To follow the course in your own laptop, please install '''[https://drive.google.com/file/d/1x5he7ctkC4BUCNFhfXLk6heggGohELoM/view?usp=drive_link the Dynamo for Matlab version]''' as explain in [[ Downloads ]] page.

= Computing resources =

== Laptops ==
Participants can use their own laptops to complete the Dynamo part of the course. For this, participants need to have and active '''Matlab installation''' and an Dynamo installation.
* For Matlab, we advise the (R2025b version). If you don't have a license through your home institution, a [https://ch.mathworks.com/campaigns/products/trials.html licence free trial version is available] from the Mathworks company.
* '''The Dynamo Download link is currently down''', we will update it later today (17:00 ECT): prior to installation make sure you have a compiler. On Linux you probably have one by default. On Mac, Xcode needs to be installed. On Windows, the recommended option is to install it via Matlab:

https://es.mathworks.com/help/matlab/matlab_external/install-mingw-support-package.html

''Dynamo'' is delivered as a single .tar file. To install it, move the file to the location where you want to install ''Dynamo'', then open a Matlab session and type after the Matlab prompt:

<tt> >> tar -xvf dynamo_temp_1.1.579.tar </tt>

to untar the installation file. ''Dynamo'' will be installed in the folder that contained the .tar. If we call this folder <DYNAMO_ROOT>, you can activate ''Dynamo'' in your MATLAB session by typing:

<tt> >> run dynamo_activate.m </tt>

when you are in that folder, or with

<tt> >> run <DYNAMO_ROOT>/dynamo_activate.m </tt>

if you are in some other folder. Wait while some packages are compiled. Activate it again.

== Amazon machines ==

If you want to follow the course with virtual machines provided by the course, follow this instructions.

=== Entering in the AWS Machine ===

Access the link of your AWS Machine provided by the organizers, that appears in the [https://docs.google.com/spreadsheets/d/15o8IUOSsNjGHxK0Bmi1QBfI9KCCWCpX603R4l_rn6KA/edit?gid=653170857#gid=653170857 Google Sheet]. After introducing your password (also given in the same google sheet), you will have entered in the AWS Machine.

Before accessing, it may be helpful to set the browser zoom to 50% or less and refresh the website. This will help later to visualize some GUIs in a friendlier way.

=== Activating Dynamo Standalone ===

Once you have accessed the AWS Machine, you need to activate Dynamo Standalone. Open the terminal emulator and type the next command:

<pre>
source /home/student/dynamo-v-1.1.579/dynamo_activate_linux_shipped_MCR.sh
</pre>

After some lines asserting the correct addition of several paths and tests, it should appear as the last line: "Dynamo is ready for standalone use in your Linux system".

=== Initializing Dynamo Standalone ===

For a specific explanation of the Standalone see [https://www.dynamo-em.org//w/index.php?title=Standalone].
Once dynamo has been initialized, you can enter in dynamo by typing

<pre>
dynamo
</pre>

You can also type

<pre>
dynamo x
</pre>

so dynamo will open a GUI console, instead of using the terminal, nevertheless the first option is strongly reccommended for some Walkthroughs.

=== Solution of some possible minor cons of working in a laptop ====

Working with AWS Machine in the Work Shop may entails some minor cons that you may encounter. Here we present the most common ones so you can solve them quickly.

==== Problem opening a GUI Window ====

If you are working on a small laptop screen, opening a GUI window, for example when typing the "dcp" command to start a project, may make appear it with the header of the window hidden on the top of the screen:

[[File:Problem GUI Window Hidden.png|thumb|center|600px|The open GUI Window appears hidden in the AWS Machine. Pressing Alt+Click will make it possible to move it so it is possible to access to the header of the window.]]

A quick way of solving it is pressing Alt+Click on the window and move it down until the header appears so it is possible to change its size.

==== Problem pressing right click in a MAC laptop with no external mouse ====

For some walkthroughs, like "Walkthrough on GUI based tilt series alignment", you need to press the right click on the "View" botton:

[[File:View Button.png|thumb|center|450px|Necessity of right clicking view button]]

If you are working on a MAC laptop with no external mouse, just press with two fingers on the trackpad at the same time.

== Workshop data ==

The data that will be used during the workshop can be downloaded through the SACO server of CSIC. In detail, the data for the respective modules is as follows (for a total of about 61 Gb ):
{| class="wikitable"
|+ Module and data source
|-
! Module !! Data source
|-
| Starters Guide: subtomogram averaging || Data generated locally by Dynamo
|-
| Models: Filaments || Data generated locally by Dynamo
|-
| Models: Vesicles || Data generated locally by Dynamo
|-
| Models: Surfaces || Data generated locally by Dynamo
|-
| Template Matching || {{Template:DownloadLinkTemplateMatchingBasic}} (750MB)
|-
| Template Matching (GUI) || {{Template:DownloadLinkTemplateMCP}} (7.6GB)
|-
| Alignment of tilt series || {{Template:DownloadLinkAWFHIV1TS}} (600MB)
|-
| Virus like particles || {{Template:DownloadLinkVLPs}} (4.6GB)
|-
| Spherical geometries || {{Template:DownloadLinkBasicHIVTomo}} (64 MB)
|-
| Principal Component Analysis || Data generated locally by Dynamo
|-
| Complete walkthrough on FHV virus || {{Template:DownloadLinkFHV}} (2GB)
|-
| Walkthrough on hexagonal lattice coherence through neighborhood analysis || {{Template:DownloadLinkNeighborhoodData}}
|-
| High-resolution HIV1 || {{Template:DownloadLinkHighResHIV1}} (48Gb)
|}

= Time schedule =

{| class="wikitable"
|+ Day 3 (Morning) 11th of December
|-
! Module !! Time !! Subject
|-
| 1 || 09:30 - 10:00|| Hands-on tutorial. First steps and formats.
|-
| 2 || 10:00 - 11:00|| [[Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Starters Guide: subtomogram averaging]]
|-
| coffee || 11:00 - 11:30 || Coffee Break
|-
| 2 || 11:30 - 12:30|| Starters Guide: subtomogram averaging (continuation).
|-
| 3 || 12:30 - 13:00 || General modeling
|}

{| class="wikitable"
|+ Day 3 (Afternoon) 11th of December
|-
| 3a ||14:00 - 14:30 || [[Walkthrough_on_filament_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Filaments]] Additional material: [[Walkthrough model workflow reuse (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Coordinated extraction from several filaments]]
|-
| 3b || 15:00 - 15:30 || [[Walkthrough_on_vesicle_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Vesicles ]]
|-
| 3c || 15:30 - 16:00 || [[Walkthrough_on_membrane_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Models: Surfaces ]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 4 || 16:30 - 17:30 || [[Getting a Structure from Multiple Tomograms of HIV Capsids (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Virus like particles]] or [[Walkthrough for lattices on vesicles (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Spherical geometries]]
|}

{| class="wikitable"
|+ Day 4, Morning: 12th of December (Friday)
|-
| 5a || 09:30 - 09:45 || Presentation of FHV: Advanced starters guide
|-
| 5b || 09:45 - 11:00 || [[Complete walkthrough on FHV virus (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Hands-on tutorial: Advanced starters guide ]]
|-
| coffee || 11:00 - 11:30 || Coffee break
|-
| 5b || 11:30 - 12:00 || Hands-on tutorial: Advanced starters guide (continued)
|-
| 6a || 12:00 - 12:20 || [[Walkthrough on manual marker clicking (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: Manual]]
|-
| 6b || 12:20 - 12:40 || [[Walkthrough on GUI based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: GUI ]]
|-
| 6c || 12:40 - 13:00 || [[Walkthrough on command line based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: command line]]
|}

{| class="wikitable"
|+ Day 4, Afternoon session: 12th of December (Friday)
|-
! Module !! Time !! Subject
|-
| 7a || 14:00 - 15:00 || [[Walkthrough for template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Template Matching]]
|-
| 7b || 15:00 - 16:00 || [[Walkthrough for GUI-based template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Geometry aware template Matching]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 8 || 16:30- 17:30 || [[Walkthrough on PCA through the command line (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Principal Component Analysis ]]
|}

= Instructors =
* Daniel Castano-Diez (CSIC Bilbao, Spain).
* Raffaele Coray (CSIC Bilbao, Spain).
* Laura García-Cornejo (CSIC Bilbao, Spain).
* Andrés Molina (CSIC Bilbao, Spain).
* Miguel Sánchez López-Cuervo (CSIC Bilbao, Spain).

I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025

2025-12-09T13:10:29Z

Miguel Sanchez: /* Amazon machines */

[[Category:WalkthroughsSpecific]]
= The course =
== The venue ==
This page describes the contents of the ''Dynamo''-specific part of the course "I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025", which will take part at the premises of the Centro Nacional de Biotecnología in Madrid, from the 9th to the 12th of December 2025.
== Contents ==
Whole pipelines for cryo-ET processing will be covered in the Scipion-related area of the course (days 1 and 2). The ''Dynamo'' part will covered selected parts of the pipeline.

= Installation of Dynamo and Matlab =
== Dynamo on your own laptop ==
To follow the course in your own laptop, please install '''[https://drive.google.com/file/d/1x5he7ctkC4BUCNFhfXLk6heggGohELoM/view?usp=drive_link the Dynamo for Matlab version]''' as explain in [[ Downloads ]] page.

= Computing resources =

== Laptops ==
Participants can use their own laptops to complete the Dynamo part of the course. For this, participants need to have and active '''Matlab installation''' and an Dynamo installation.
* For Matlab, we advise the (R2025b version). If you don't have a license through your home institution, a [https://ch.mathworks.com/campaigns/products/trials.html licence free trial version is available] from the Mathworks company.
* '''The Dynamo Download link is currently down''', we will update it later today (17:00 ECT): prior to installation make sure you have a compiler. On Linux you probably have one by default. On Mac, Xcode needs to be installed. On Windows, the recommended option is to install it via Matlab:

https://es.mathworks.com/help/matlab/matlab_external/install-mingw-support-package.html

''Dynamo'' is delivered as a single .tar file. To install it, move the file to the location where you want to install ''Dynamo'', then open a Matlab session and type after the Matlab prompt:

<tt> >> tar -xvf dynamo_temp_1.1.579.tar </tt>

to untar the installation file. ''Dynamo'' will be installed in the folder that contained the .tar. If we call this folder <DYNAMO_ROOT>, you can activate ''Dynamo'' in your MATLAB session by typing:

<tt> >> run dynamo_activate.m </tt>

when you are in that folder, or with

<tt> >> run <DYNAMO_ROOT>/dynamo_activate.m </tt>

if you are in some other folder. Wait while some packages are compiled. Activate it again.

== Amazon machines ==

If you want to follow the course with virtual machines provided by the course, follow this instructions.

=== Entering in the AWS Machine ===

Access the link of your AWS Machine provided by the organizers, that appears in the [https://docs.google.com/spreadsheets/d/15o8IUOSsNjGHxK0Bmi1QBfI9KCCWCpX603R4l_rn6KA/edit?gid=653170857#gid=653170857 Google Sheet]. After introducing your password (also given in the same google sheet), you will have entered in the AWS Machine.

=== Activating Dynamo Standalone ===

Once you have accessed the AWS Machine, you need to activate Dynamo Standalone. Open the terminal emulator and type the next command:

<pre>
source /home/student/dynamo-v-1.1.579/dynamo_activate_linux_shipped_MCR.sh
</pre>

After some lines asserting the correct addition of several paths and tests, it should appear as the last line: "Dynamo is ready for standalone use in your Linux system".

=== Initializing Dynamo Standalone ===

For a specific explanation of the Standalone see [https://www.dynamo-em.org//w/index.php?title=Standalone].
Once dynamo has been initialized, you can enter in dynamo by typing

<pre>
dynamo
</pre>

You can also type

<pre>
dynamo x
</pre>

so dynamo will open a GUI console, instead of using the terminal, nevertheless the first option is strongly reccommended for some Walkthroughs.

=== Solution of some possible minor cons of working in a laptop ====

Working with AWS Machine in the Work Shop may entails some minor cons that you may encounter. Here we present the most common ones so you can solve them quickly.

==== Problem opening a GUI Window ====

If you are working on a small laptop screen, opening a GUI window, for example when typing the "dcp" command to start a project, may make appear it with the header of the window hidden on the top of the screen:

[[File:Problem GUI Window Hidden.png|thumb|center|600px|The open GUI Window appears hidden in the AWS Machine. Pressing Alt+Click will make it possible to move it so it is possible to access to the header of the window.]]

A quick way of solving it is pressing Alt+Click on the window and move it down until the header appears so it is possible to change its size.

==== Problem pressing right click in a MAC laptop with no external mouse ====

For some walkthroughs, like "Walkthrough on GUI based tilt series alignment", you need to press the right click on the "View" botton:

[[File:View Button.png|thumb|center|450px|Necessity of right clicking view button]]

If you are working on a MAC laptop with no external mouse, just press with two fingers on the trackpad at the same time.

== Workshop data ==

The data that will be used during the workshop can be downloaded through the SACO server of CSIC. In detail, the data for the respective modules is as follows (for a total of about 61 Gb ):
{| class="wikitable"
|+ Module and data source
|-
! Module !! Data source
|-
| Starters Guide: subtomogram averaging || Data generated locally by Dynamo
|-
| Models: Filaments || Data generated locally by Dynamo
|-
| Models: Vesicles || Data generated locally by Dynamo
|-
| Models: Surfaces || Data generated locally by Dynamo
|-
| Template Matching || {{Template:DownloadLinkTemplateMatchingBasic}} (750MB)
|-
| Template Matching (GUI) || {{Template:DownloadLinkTemplateMCP}} (7.6GB)
|-
| Alignment of tilt series || {{Template:DownloadLinkAWFHIV1TS}} (600MB)
|-
| Virus like particles || {{Template:DownloadLinkVLPs}} (4.6GB)
|-
| Spherical geometries || {{Template:DownloadLinkBasicHIVTomo}} (64 MB)
|-
| Principal Component Analysis || Data generated locally by Dynamo
|-
| Complete walkthrough on FHV virus || {{Template:DownloadLinkFHV}} (2GB)
|-
| Walkthrough on hexagonal lattice coherence through neighborhood analysis || {{Template:DownloadLinkNeighborhoodData}}
|-
| High-resolution HIV1 || {{Template:DownloadLinkHighResHIV1}} (48Gb)
|}

= Time schedule =

{| class="wikitable"
|+ Day 3 (Morning) 11th of December
|-
! Module !! Time !! Subject
|-
| 1 || 09:30 - 10:00|| Hands-on tutorial. First steps and formats.
|-
| 2 || 10:00 - 11:00|| [[Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Starters Guide: subtomogram averaging]]
|-
| coffee || 11:00 - 11:30 || Coffee Break
|-
| 2 || 11:30 - 12:30|| Starters Guide: subtomogram averaging (continuation).
|-
| 3 || 12:30 - 13:00 || General modeling
|}

{| class="wikitable"
|+ Day 3 (Afternoon) 11th of December
|-
| 3a ||14:00 - 14:30 || [[Walkthrough_on_filament_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Filaments]] Additional material: [[Walkthrough model workflow reuse (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Coordinated extraction from several filaments]]
|-
| 3b || 15:00 - 15:30 || [[Walkthrough_on_vesicle_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Vesicles ]]
|-
| 3c || 15:30 - 16:00 || [[Walkthrough_on_membrane_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Models: Surfaces ]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 4 || 16:30 - 17:30 || [[Getting a Structure from Multiple Tomograms of HIV Capsids (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Virus like particles]] or [[Walkthrough for lattices on vesicles (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Spherical geometries]]
|}

{| class="wikitable"
|+ Day 4, Morning: 12th of December (Friday)
|-
| 5a || 09:30 - 09:45 || Presentation of FHV: Advanced starters guide
|-
| 5b || 09:45 - 11:00 || [[Complete walkthrough on FHV virus (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Hands-on tutorial: Advanced starters guide ]]
|-
| coffee || 11:00 - 11:30 || Coffee break
|-
| 5b || 11:30 - 12:00 || Hands-on tutorial: Advanced starters guide (continued)
|-
| 6a || 12:00 - 12:20 || [[Walkthrough on manual marker clicking (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: Manual]]
|-
| 6b || 12:20 - 12:40 || [[Walkthrough on GUI based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: GUI ]]
|-
| 6c || 12:40 - 13:00 || [[Walkthrough on command line based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: command line]]
|}

{| class="wikitable"
|+ Day 4, Afternoon session: 12th of December (Friday)
|-
! Module !! Time !! Subject
|-
| 7a || 14:00 - 15:00 || [[Walkthrough for template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Template Matching]]
|-
| 7b || 15:00 - 16:00 || [[Walkthrough for GUI-based template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Geometry aware template Matching]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 8 || 16:30- 17:30 || [[Walkthrough on PCA through the command line (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Principal Component Analysis ]]
|}

= Instructors =
* Daniel Castano-Diez (CSIC Bilbao, Spain).
* Raffaele Coray (CSIC Bilbao, Spain).
* Laura García-Cornejo (CSIC Bilbao, Spain).
* Andrés Molina (CSIC Bilbao, Spain).
* Miguel Sánchez López-Cuervo (CSIC Bilbao, Spain).

I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025

2025-12-09T13:09:24Z

Miguel Sanchez: /* Amazon machines */

[[Category:WalkthroughsSpecific]]
= The course =
== The venue ==
This page describes the contents of the ''Dynamo''-specific part of the course "I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025", which will take part at the premises of the Centro Nacional de Biotecnología in Madrid, from the 9th to the 12th of December 2025.
== Contents ==
Whole pipelines for cryo-ET processing will be covered in the Scipion-related area of the course (days 1 and 2). The ''Dynamo'' part will covered selected parts of the pipeline.

= Installation of Dynamo and Matlab =
== Dynamo on your own laptop ==
To follow the course in your own laptop, please install '''[https://drive.google.com/file/d/1x5he7ctkC4BUCNFhfXLk6heggGohELoM/view?usp=drive_link the Dynamo for Matlab version]''' as explain in [[ Downloads ]] page.

= Computing resources =

== Laptops ==
Participants can use their own laptops to complete the Dynamo part of the course. For this, participants need to have and active '''Matlab installation''' and an Dynamo installation.
* For Matlab, we advise the (R2025b version). If you don't have a license through your home institution, a [https://ch.mathworks.com/campaigns/products/trials.html licence free trial version is available] from the Mathworks company.
* '''The Dynamo Download link is currently down''', we will update it later today (17:00 ECT): prior to installation make sure you have a compiler. On Linux you probably have one by default. On Mac, Xcode needs to be installed. On Windows, the recommended option is to install it via Matlab:

https://es.mathworks.com/help/matlab/matlab_external/install-mingw-support-package.html

''Dynamo'' is delivered as a single .tar file. To install it, move the file to the location where you want to install ''Dynamo'', then open a Matlab session and type after the Matlab prompt:

<tt> >> tar -xvf dynamo_temp_1.1.579.tar </tt>

to untar the installation file. ''Dynamo'' will be installed in the folder that contained the .tar. If we call this folder <DYNAMO_ROOT>, you can activate ''Dynamo'' in your MATLAB session by typing:

<tt> >> run dynamo_activate.m </tt>

when you are in that folder, or with

<tt> >> run <DYNAMO_ROOT>/dynamo_activate.m </tt>

if you are in some other folder. Wait while some packages are compiled. Activate it again.

== Amazon machines ==

If you want to follow the course with virtual machines provided by the course, follow this instructions.

=== Entering in the AWS Machine ===

Access the link of your AWS Machine provided by the organizers, that appears in the [https://docs.google.com/spreadsheets/d/15o8IUOSsNjGHxK0Bmi1QBfI9KCCWCpX603R4l_rn6KA/edit?gid=653170857#gid=653170857 Google Sheet]. After introducing your password (also given in the same google sheet), you will have entered in the AWS Machine.

=== Activating Dynamo Standalone ===

Once you have accessed the AWS Machine, you need to activate Dynamo Standalone. Open the terminal emulator and type the next command:

<pre>
source /home/student/dynamo-v-1.1.579/dynamo_activate_linux_shipped_MCR.sh
</pre>

After some lines asserting the correct addition of several paths and tests, it should appear as the last line: "Dynamo is ready for standalone use in your Linux system".

=== Initializing Dynamo Standalone ===

For a specific explanation of the Standalone see [https://www.dynamo-em.org//w/index.php?title=Standalone].
Once dynamo has been initialized, you can enter in dynamo by typing

<pre>
dynamo
</pre>

You can also type

<pre>
dynamo x
</pre>

so dynamo will open a GUI console, instead of using the terminal, nevertheless the first option is strongly reccommended for some Walkthroughs.

=== Solution of some possible minor cons of working in a laptop ====

Working with AWS Machine in the Work Shop may entails some minor cons that you may encounter. Here we present the most common ones so you can solve them quickly.

==== Problem opening a GUI Window ====

If you are working on a small laptop screen, opening a GUI window, for example when typing the "dcp" command to start a project, may make appear it with the header of the window hidden on the top of the screen:

[[File:Problem GUI Window Hidden.png|thumb|center|600px|The open GUI Window appears hidden in the AWS Machine. Pressing Alt+Click will make it possible to move it so it is possible to access to the header of the window.]]

A quick way of solving it is pressing Alt+Click on the window and move it down until the header appears so it is possible to change its size.

==== Problem pressing right click in a MAC laptop with no external mouse ====

For some walkthroughs, like "Walkthrough on GUI based tilt series alignment", you need to press the right click on the "View" botton:

[[File:View Button.png|thumb|center|550px|Necessity of right clicking view button]]

If you are working on a MAC laptop with no external mouse, just press with two fingers on the trackpad at the same time.

== Workshop data ==

The data that will be used during the workshop can be downloaded through the SACO server of CSIC. In detail, the data for the respective modules is as follows (for a total of about 61 Gb ):
{| class="wikitable"
|+ Module and data source
|-
! Module !! Data source
|-
| Starters Guide: subtomogram averaging || Data generated locally by Dynamo
|-
| Models: Filaments || Data generated locally by Dynamo
|-
| Models: Vesicles || Data generated locally by Dynamo
|-
| Models: Surfaces || Data generated locally by Dynamo
|-
| Template Matching || {{Template:DownloadLinkTemplateMatchingBasic}} (750MB)
|-
| Template Matching (GUI) || {{Template:DownloadLinkTemplateMCP}} (7.6GB)
|-
| Alignment of tilt series || {{Template:DownloadLinkAWFHIV1TS}} (600MB)
|-
| Virus like particles || {{Template:DownloadLinkVLPs}} (4.6GB)
|-
| Spherical geometries || {{Template:DownloadLinkBasicHIVTomo}} (64 MB)
|-
| Principal Component Analysis || Data generated locally by Dynamo
|-
| Complete walkthrough on FHV virus || {{Template:DownloadLinkFHV}} (2GB)
|-
| Walkthrough on hexagonal lattice coherence through neighborhood analysis || {{Template:DownloadLinkNeighborhoodData}}
|-
| High-resolution HIV1 || {{Template:DownloadLinkHighResHIV1}} (48Gb)
|}

= Time schedule =

{| class="wikitable"
|+ Day 3 (Morning) 11th of December
|-
! Module !! Time !! Subject
|-
| 1 || 09:30 - 10:00|| Hands-on tutorial. First steps and formats.
|-
| 2 || 10:00 - 11:00|| [[Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Starters Guide: subtomogram averaging]]
|-
| coffee || 11:00 - 11:30 || Coffee Break
|-
| 2 || 11:30 - 12:30|| Starters Guide: subtomogram averaging (continuation).
|-
| 3 || 12:30 - 13:00 || General modeling
|}

{| class="wikitable"
|+ Day 3 (Afternoon) 11th of December
|-
| 3a ||14:00 - 14:30 || [[Walkthrough_on_filament_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Filaments]] Additional material: [[Walkthrough model workflow reuse (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Coordinated extraction from several filaments]]
|-
| 3b || 15:00 - 15:30 || [[Walkthrough_on_vesicle_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Vesicles ]]
|-
| 3c || 15:30 - 16:00 || [[Walkthrough_on_membrane_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Models: Surfaces ]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 4 || 16:30 - 17:30 || [[Getting a Structure from Multiple Tomograms of HIV Capsids (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Virus like particles]] or [[Walkthrough for lattices on vesicles (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Spherical geometries]]
|}

{| class="wikitable"
|+ Day 4, Morning: 12th of December (Friday)
|-
| 5a || 09:30 - 09:45 || Presentation of FHV: Advanced starters guide
|-
| 5b || 09:45 - 11:00 || [[Complete walkthrough on FHV virus (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Hands-on tutorial: Advanced starters guide ]]
|-
| coffee || 11:00 - 11:30 || Coffee break
|-
| 5b || 11:30 - 12:00 || Hands-on tutorial: Advanced starters guide (continued)
|-
| 6a || 12:00 - 12:20 || [[Walkthrough on manual marker clicking (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: Manual]]
|-
| 6b || 12:20 - 12:40 || [[Walkthrough on GUI based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: GUI ]]
|-
| 6c || 12:40 - 13:00 || [[Walkthrough on command line based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: command line]]
|}

{| class="wikitable"
|+ Day 4, Afternoon session: 12th of December (Friday)
|-
! Module !! Time !! Subject
|-
| 7a || 14:00 - 15:00 || [[Walkthrough for template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Template Matching]]
|-
| 7b || 15:00 - 16:00 || [[Walkthrough for GUI-based template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Geometry aware template Matching]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 8 || 16:30- 17:30 || [[Walkthrough on PCA through the command line (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Principal Component Analysis ]]
|}

= Instructors =
* Daniel Castano-Diez (CSIC Bilbao, Spain).
* Raffaele Coray (CSIC Bilbao, Spain).
* Laura García-Cornejo (CSIC Bilbao, Spain).
* Andrés Molina (CSIC Bilbao, Spain).
* Miguel Sánchez López-Cuervo (CSIC Bilbao, Spain).

I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025

2025-12-09T12:13:59Z

Miguel Sanchez: /* Amazon machines */

[[Category:WalkthroughsSpecific]]
= The course =
== The venue ==
This page describes the contents of the ''Dynamo''-specific part of the course "I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025", which will take part at the premises of the Centro Nacional de Biotecnología in Madrid, from the 9th to the 12th of December 2025.
== Contents ==
Whole pipelines for cryo-ET processing will be covered in the Scipion-related area of the course (days 1 and 2). The ''Dynamo'' part will covered selected parts of the pipeline.

= Installation of Dynamo and Matlab =
== Dynamo on your own laptop ==
To follow the course in your own laptop, please install '''[https://drive.google.com/file/d/1x5he7ctkC4BUCNFhfXLk6heggGohELoM/view?usp=drive_link the Dynamo for Matlab version]''' as explain in [[ Downloads ]] page.

= Computing resources =

== Laptops ==
Participants can use their own laptops to complete the Dynamo part of the course. For this, participants need to have and active '''Matlab installation''' and an Dynamo installation.
* For Matlab, we advise the (R2025b version). If you don't have a license through your home institution, a [https://ch.mathworks.com/campaigns/products/trials.html licence free trial version is available] from the Mathworks company.
* '''The Dynamo Download link is currently down''', we will update it later today (17:00 ECT): prior to installation make sure you have a compiler. On Linux you probably have one by default. On Mac, Xcode needs to be installed. On Windows, the recommended option is to install it via Matlab:

https://es.mathworks.com/help/matlab/matlab_external/install-mingw-support-package.html

''Dynamo'' is delivered as a single .tar file. To install it, move the file to the location where you want to install ''Dynamo'', then open a Matlab session and type after the Matlab prompt:

<tt> >> tar -xvf dynamo_temp_1.1.579.tar </tt>

to untar the installation file. ''Dynamo'' will be installed in the folder that contained the .tar. If we call this folder <DYNAMO_ROOT>, you can activate ''Dynamo'' in your MATLAB session by typing:

<tt> >> run dynamo_activate.m </tt>

when you are in that folder, or with

<tt> >> run <DYNAMO_ROOT>/dynamo_activate.m </tt>

if you are in some other folder. Wait while some packages are compiled. Activate it again.

== Amazon machines ==

If you want to follow the course with virtual machines provided by the course, follow this instructions.

=== Entering in the AWS Machine ===

Access the link of your AWS Machine provided by the organizers, that appears in the [https://docs.google.com/spreadsheets/d/15o8IUOSsNjGHxK0Bmi1QBfI9KCCWCpX603R4l_rn6KA/edit?gid=653170857#gid=653170857 Google Sheet]. After introducing your password (also given in the same google sheet), you will have entered in the AWS Machine.

=== Activating Dynamo Standalone ===

Once you have accessed the AWS Machine, you need to activate Dynamo Standalone. Open the terminal emulator and type the next command:

<pre>
source /home/student/dynamo-v-1.1.579/dynamo_activate_linux_shipped_MCR.sh
</pre>

After some lines asserting the correct addition of several paths and tests, it should appear as the last line: "Dynamo is ready for standalone use in your Linux system".

=== Initializing Dynamo Standalone ===

For a specific explanation of the Standalone see [https://www.dynamo-em.org//w/index.php?title=Standalone].
Once dynamo has been initialized, you can enter in dynamo by typing

<pre>
dynamo
</pre>

You can also type

<pre>
dynamo x
</pre>

so dynamo will open a GUI console, instead of using the terminal, nevertheless the first option is strongly reccommended for some Walkthroughs.

=== Solution of some possible minor cons of working in a laptop ====

Working with AWS Machine in the Work Shop may entails some minor cons that you may encounter. Here we present the most common ones so you can solve them quickly.

==== Problem opening a GUI Window ====

If you are working on a small laptop screen, opening a GUI window, for example when typing the "dcp" command to start a project, may make appear it with the header of the window hidden on the top of the screen:

[[File:Problem GUI Window Hidden.png|thumb|center|600px|The open GUI Window appears hidden in the AWS Machine. Pressing Alt+Click will make it possible to move it so it is possible to access to the header of the window.]]

A quick way of solving it is pressing Alt+Click on the window and move it down until the header appears so it is possible to change its size.

==== Problem pressing right click in a MAC laptop with no external mouse ====

For some walkthroughs, like "Walkthrough on GUI based tilt series alignment", you need to press the right click on the "View" botton:

[[File:View Button.png|thumb|center|600px|Necessity of right clicking view button]]

If you are working on a MAC laptop with no external mouse, just press with two fingers on the trackpad at the same time.

== Workshop data ==

The data that will be used during the workshop can be downloaded through the SACO server of CSIC. In detail, the data for the respective modules is as follows (for a total of about 61 Gb ):
{| class="wikitable"
|+ Module and data source
|-
! Module !! Data source
|-
| Starters Guide: subtomogram averaging || Data generated locally by Dynamo
|-
| Models: Filaments || Data generated locally by Dynamo
|-
| Models: Vesicles || Data generated locally by Dynamo
|-
| Models: Surfaces || Data generated locally by Dynamo
|-
| Template Matching || {{Template:DownloadLinkTemplateMatchingBasic}} (750MB)
|-
| Template Matching (GUI) || {{Template:DownloadLinkTemplateMCP}} (7.6GB)
|-
| Alignment of tilt series || {{Template:DownloadLinkAWFHIV1TS}} (600MB)
|-
| Virus like particles || {{Template:DownloadLinkVLPs}} (4.6GB)
|-
| Spherical geometries || {{Template:DownloadLinkBasicHIVTomo}} (64 MB)
|-
| Principal Component Analysis || Data generated locally by Dynamo
|-
| Complete walkthrough on FHV virus || {{Template:DownloadLinkFHV}} (2GB)
|-
| Walkthrough on hexagonal lattice coherence through neighborhood analysis || {{Template:DownloadLinkNeighborhoodData}}
|-
| High-resolution HIV1 || {{Template:DownloadLinkHighResHIV1}} (48Gb)
|}

= Time schedule =

{| class="wikitable"
|+ Day 3 (Morning) 11th of December
|-
! Module !! Time !! Subject
|-
| 1 || 09:30 - 10:00|| Hands-on tutorial. First steps and formats.
|-
| 2 || 10:00 - 11:00|| [[Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Starters Guide: subtomogram averaging]]
|-
| coffee || 11:00 - 11:30 || Coffee Break
|-
| 2 || 11:30 - 12:30|| Starters Guide: subtomogram averaging (continuation).
|-
| 3 || 12:30 - 13:00 || General modeling
|}

{| class="wikitable"
|+ Day 3 (Afternoon) 11th of December
|-
| 3a ||14:00 - 14:30 || [[Walkthrough_on_filament_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Filaments]] Additional material: [[Walkthrough model workflow reuse (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Coordinated extraction from several filaments]]
|-
| 3b || 15:00 - 15:30 || [[Walkthrough_on_vesicle_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Vesicles ]]
|-
| 3c || 15:30 - 16:00 || [[Walkthrough_on_membrane_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Models: Surfaces ]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 4 || 16:30 - 17:30 || [[Getting a Structure from Multiple Tomograms of HIV Capsids (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Virus like particles]] or [[Walkthrough for lattices on vesicles (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Spherical geometries]]
|}

{| class="wikitable"
|+ Day 4, Morning: 12th of December (Friday)
|-
| 5a || 09:30 - 09:45 || Presentation of FHV: Advanced starters guide
|-
| 5b || 09:45 - 11:00 || [[Complete walkthrough on FHV virus (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Hands-on tutorial: Advanced starters guide ]]
|-
| coffee || 11:00 - 11:30 || Coffee break
|-
| 5b || 11:30 - 12:00 || Hands-on tutorial: Advanced starters guide (continued)
|-
| 6a || 12:00 - 12:20 || [[Walkthrough on manual marker clicking (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: Manual]]
|-
| 6b || 12:20 - 12:40 || [[Walkthrough on GUI based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: GUI ]]
|-
| 6c || 12:40 - 13:00 || [[Walkthrough on command line based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: command line]]
|}

{| class="wikitable"
|+ Day 4, Afternoon session: 12th of December (Friday)
|-
! Module !! Time !! Subject
|-
| 7a || 14:00 - 15:00 || [[Walkthrough for template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Template Matching]]
|-
| 7b || 15:00 - 16:00 || [[Walkthrough for GUI-based template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Geometry aware template Matching]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 8 || 16:30- 17:30 || [[Walkthrough on PCA through the command line (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Principal Component Analysis ]]
|}

= Instructors =
* Daniel Castano-Diez (CSIC Bilbao, Spain).
* Raffaele Coray (CSIC Bilbao, Spain).
* Laura García-Cornejo (CSIC Bilbao, Spain).
* Andrés Molina (CSIC Bilbao, Spain).
* Miguel Sánchez López-Cuervo (CSIC Bilbao, Spain).

I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025

2025-12-09T12:11:53Z

Miguel Sanchez: /* Amazon machines */

[[Category:WalkthroughsSpecific]]
= The course =
== The venue ==
This page describes the contents of the ''Dynamo''-specific part of the course "I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025", which will take part at the premises of the Centro Nacional de Biotecnología in Madrid, from the 9th to the 12th of December 2025.
== Contents ==
Whole pipelines for cryo-ET processing will be covered in the Scipion-related area of the course (days 1 and 2). The ''Dynamo'' part will covered selected parts of the pipeline.

= Installation of Dynamo and Matlab =
== Dynamo on your own laptop ==
To follow the course in your own laptop, please install '''[https://drive.google.com/file/d/1x5he7ctkC4BUCNFhfXLk6heggGohELoM/view?usp=drive_link the Dynamo for Matlab version]''' as explain in [[ Downloads ]] page.

= Computing resources =

== Laptops ==
Participants can use their own laptops to complete the Dynamo part of the course. For this, participants need to have and active '''Matlab installation''' and an Dynamo installation.
* For Matlab, we advise the (R2025b version). If you don't have a license through your home institution, a [https://ch.mathworks.com/campaigns/products/trials.html licence free trial version is available] from the Mathworks company.
* '''The Dynamo Download link is currently down''', we will update it later today (17:00 ECT): prior to installation make sure you have a compiler. On Linux you probably have one by default. On Mac, Xcode needs to be installed. On Windows, the recommended option is to install it via Matlab:

https://es.mathworks.com/help/matlab/matlab_external/install-mingw-support-package.html

''Dynamo'' is delivered as a single .tar file. To install it, move the file to the location where you want to install ''Dynamo'', then open a Matlab session and type after the Matlab prompt:

<tt> >> tar -xvf dynamo_temp_1.1.579.tar </tt>

to untar the installation file. ''Dynamo'' will be installed in the folder that contained the .tar. If we call this folder <DYNAMO_ROOT>, you can activate ''Dynamo'' in your MATLAB session by typing:

<tt> >> run dynamo_activate.m </tt>

when you are in that folder, or with

<tt> >> run <DYNAMO_ROOT>/dynamo_activate.m </tt>

if you are in some other folder. Wait while some packages are compiled. Activate it again.

== Amazon machines ==

If you want to follow the course with virtual machines provided by the course, follow this instructions.

=== Entering in the AWS Machine ===

Access the link of your AWS Machine provided by the organizers, that appears in the [https://docs.google.com/spreadsheets/d/15o8IUOSsNjGHxK0Bmi1QBfI9KCCWCpX603R4l_rn6KA/edit?gid=653170857#gid=653170857 Google Sheet]. After introducing your password (also given in the same google sheet), you will have entered in the AWS Machine.

=== Activating Dynamo Standalone ===

Once you have accessed the AWS Machine, you need to activate Dynamo Standalone. Open the terminal emulator and type the next command:

<pre>
source /home/student/dynamo-v-1.1.579/dynamo_activate_linux_shipped_MCR.sh
</pre>

After some lines asserting the correct addition of several paths and tests, it should appear as the last line: "Dynamo is ready for standalone use in your Linux system".

=== Initializing Dynamo Standalone ===

For a specific explanation of the Standalone see [https://www.dynamo-em.org//w/index.php?title=Standalone].
Once dynamo has been initialized, you can enter in dynamo by typing

<pre>
dynamo
</pre>

You can also type

<pre>
dynamo x
</pre>

so dynamo will open a GUI console, instead of using the terminal, nevertheless the first option is strongly reccommended for some Walkthroughs.

=== Solution of some possible minor cons of working in a laptop ====

Working with AWS Machine in the Work Shop may entails some minor cons that you may encounter. Here we present the most common ones so you can solve them quickly.

==== Problem opening a GUI Window ====

If you are working on a small laptop screen, opening a GUI window, for example when typing the "dcp" command to start a project, may make appear it with the header of the window hidden on the top of the screen:

[[File:Problem GUI Window Hidden.png|thumb|center|600px|The open GUI Window appears hidden in the AWS Machine. Pressing Alt+Click will make it possible to move it so it is possible to access to the header of the window.]]

A quick way of solving it is pressing Alt+Click on the window and move it down until the header appears so it is possible to change its size.

==== Problem pressing right click in a MAC laptop with no external mouse ====

For some walkthroughs, like "Walkthrough on GUI based tilt series alignment", you need to press the right click on the "View" botton:

[[File:View Button.png|thumb|center|600px|Necessity of right clicking view button]]

If you are working on a MAC laptop with no external mouse

== Workshop data ==

The data that will be used during the workshop can be downloaded through the SACO server of CSIC. In detail, the data for the respective modules is as follows (for a total of about 61 Gb ):
{| class="wikitable"
|+ Module and data source
|-
! Module !! Data source
|-
| Starters Guide: subtomogram averaging || Data generated locally by Dynamo
|-
| Models: Filaments || Data generated locally by Dynamo
|-
| Models: Vesicles || Data generated locally by Dynamo
|-
| Models: Surfaces || Data generated locally by Dynamo
|-
| Template Matching || {{Template:DownloadLinkTemplateMatchingBasic}} (750MB)
|-
| Template Matching (GUI) || {{Template:DownloadLinkTemplateMCP}} (7.6GB)
|-
| Alignment of tilt series || {{Template:DownloadLinkAWFHIV1TS}} (600MB)
|-
| Virus like particles || {{Template:DownloadLinkVLPs}} (4.6GB)
|-
| Spherical geometries || {{Template:DownloadLinkBasicHIVTomo}} (64 MB)
|-
| Principal Component Analysis || Data generated locally by Dynamo
|-
| Complete walkthrough on FHV virus || {{Template:DownloadLinkFHV}} (2GB)
|-
| Walkthrough on hexagonal lattice coherence through neighborhood analysis || {{Template:DownloadLinkNeighborhoodData}}
|-
| High-resolution HIV1 || {{Template:DownloadLinkHighResHIV1}} (48Gb)
|}

= Time schedule =

{| class="wikitable"
|+ Day 3 (Morning) 11th of December
|-
! Module !! Time !! Subject
|-
| 1 || 09:30 - 10:00|| Hands-on tutorial. First steps and formats.
|-
| 2 || 10:00 - 11:00|| [[Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Starters Guide: subtomogram averaging]]
|-
| coffee || 11:00 - 11:30 || Coffee Break
|-
| 2 || 11:30 - 12:30|| Starters Guide: subtomogram averaging (continuation).
|-
| 3 || 12:30 - 13:00 || General modeling
|}

{| class="wikitable"
|+ Day 3 (Afternoon) 11th of December
|-
| 3a ||14:00 - 14:30 || [[Walkthrough_on_filament_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Filaments]] Additional material: [[Walkthrough model workflow reuse (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Coordinated extraction from several filaments]]
|-
| 3b || 15:00 - 15:30 || [[Walkthrough_on_vesicle_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Vesicles ]]
|-
| 3c || 15:30 - 16:00 || [[Walkthrough_on_membrane_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Models: Surfaces ]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 4 || 16:30 - 17:30 || [[Getting a Structure from Multiple Tomograms of HIV Capsids (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Virus like particles]] or [[Walkthrough for lattices on vesicles (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Spherical geometries]]
|}

{| class="wikitable"
|+ Day 4, Morning: 12th of December (Friday)
|-
| 5a || 09:30 - 09:45 || Presentation of FHV: Advanced starters guide
|-
| 5b || 09:45 - 11:00 || [[Complete walkthrough on FHV virus (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Hands-on tutorial: Advanced starters guide ]]
|-
| coffee || 11:00 - 11:30 || Coffee break
|-
| 5b || 11:30 - 12:00 || Hands-on tutorial: Advanced starters guide (continued)
|-
| 6a || 12:00 - 12:20 || [[Walkthrough on manual marker clicking (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: Manual]]
|-
| 6b || 12:20 - 12:40 || [[Walkthrough on GUI based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: GUI ]]
|-
| 6c || 12:40 - 13:00 || [[Walkthrough on command line based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: command line]]
|}

{| class="wikitable"
|+ Day 4, Afternoon session: 12th of December (Friday)
|-
! Module !! Time !! Subject
|-
| 7a || 14:00 - 15:00 || [[Walkthrough for template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Template Matching]]
|-
| 7b || 15:00 - 16:00 || [[Walkthrough for GUI-based template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Geometry aware template Matching]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 8 || 16:30- 17:30 || [[Walkthrough on PCA through the command line (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Principal Component Analysis ]]
|}

= Instructors =
* Daniel Castano-Diez (CSIC Bilbao, Spain).
* Raffaele Coray (CSIC Bilbao, Spain).
* Laura García-Cornejo (CSIC Bilbao, Spain).
* Andrés Molina (CSIC Bilbao, Spain).
* Miguel Sánchez López-Cuervo (CSIC Bilbao, Spain).

File:View Button.png

2025-12-09T12:08:55Z

Miguel Sanchez: Need to press right button with the mouse

== Summary ==
Need to press right button with the mouse

File:Problem GUI Window Hidden.png

2025-12-09T11:52:33Z

Miguel Sanchez: The open GUI Window appears hidden in the AWS Machine. Pressing Alt+Click will make it possible to move it so it is possible to access to the header of the window.

== Summary ==
The open GUI Window appears hidden in the AWS Machine. Pressing Alt+Click will make it possible to move it so it is possible to access to the header of the window.

I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025

2025-12-09T11:50:28Z

Miguel Sanchez: /* Amazon machines */

[[Category:WalkthroughsSpecific]]
= The course =
== The venue ==
This page describes the contents of the ''Dynamo''-specific part of the course "I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025", which will take part at the premises of the Centro Nacional de Biotecnología in Madrid, from the 9th to the 12th of December 2025.
== Contents ==
Whole pipelines for cryo-ET processing will be covered in the Scipion-related area of the course (days 1 and 2). The ''Dynamo'' part will covered selected parts of the pipeline.

= Installation of Dynamo and Matlab =
== Dynamo on your own laptop ==
To follow the course in your own laptop, please install '''[https://drive.google.com/file/d/1x5he7ctkC4BUCNFhfXLk6heggGohELoM/view?usp=drive_link the Dynamo for Matlab version]''' as explain in [[ Downloads ]] page.

= Computing resources =

== Laptops ==
Participants can use their own laptops to complete the Dynamo part of the course. For this, participants need to have and active '''Matlab installation''' and an Dynamo installation.
* For Matlab, we advise the (R2025b version). If you don't have a license through your home institution, a [https://ch.mathworks.com/campaigns/products/trials.html licence free trial version is available] from the Mathworks company.
* '''The Dynamo Download link is currently down''', we will update it later today (17:00 ECT): prior to installation make sure you have a compiler. On Linux you probably have one by default. On Mac, Xcode needs to be installed. On Windows, the recommended option is to install it via Matlab:

https://es.mathworks.com/help/matlab/matlab_external/install-mingw-support-package.html

''Dynamo'' is delivered as a single .tar file. To install it, move the file to the location where you want to install ''Dynamo'', then open a Matlab session and type after the Matlab prompt:

<tt> >> tar -xvf dynamo_temp_1.1.579.tar </tt>

to untar the installation file. ''Dynamo'' will be installed in the folder that contained the .tar. If we call this folder <DYNAMO_ROOT>, you can activate ''Dynamo'' in your MATLAB session by typing:

<tt> >> run dynamo_activate.m </tt>

when you are in that folder, or with

<tt> >> run <DYNAMO_ROOT>/dynamo_activate.m </tt>

if you are in some other folder. Wait while some packages are compiled. Activate it again.

== Amazon machines ==

If you want to follow the course with virtual machines provided by the course, follow this instructions.

=== Entering in the AWS Machine ===

Access the link of your AWS Machine provided by the organizers, that appears in the [https://docs.google.com/spreadsheets/d/15o8IUOSsNjGHxK0Bmi1QBfI9KCCWCpX603R4l_rn6KA/edit?gid=653170857#gid=653170857 Google Sheet]. After introducing your password (also given in the same google sheet), you will have entered in the AWS Machine.

=== Activating Dynamo Standalone ===

Once you have accessed the AWS Machine, you need to activate Dynamo Standalone. Open the terminal emulator and type the next command:

<pre>
source /home/student/dynamo-v-1.1.579/dynamo_activate_linux_shipped_MCR.sh
</pre>

After some lines asserting the correct addition of several paths and tests, it should appear as the last line: "Dynamo is ready for standalone use in your Linux system".

=== Initializing Dynamo Standalone ===

For a specific explanation of the Standalone see [https://www.dynamo-em.org//w/index.php?title=Standalone].
Once dynamo has been initialized, you can enter in dynamo by typing

<pre>
dynamo
</pre>

You can also type

<pre>
dynamo x
</pre>

so dynamo will open a GUI console, instead of using the terminal, nevertheless the first option is strongly reccommended for some Walkthroughs.

=== Solution of some possible minor cons of working in a laptop ====

Working with AWS Machine in the Work Shop may entails some minor cons that you may encounter. Here we present the most common ones so you can solve them quickly.

==== Problem opening a GUI Window ====

If you are working on a small laptop screen, opening a GUI window, for example when typing the "dcp" command to start a project, may make appear with the header of the window hidden on the top of the screen

==== Problem pressing right click in a MAC laptop with no external mouse ====

Walkthrough on GUI based tilt series alignment

== Workshop data ==

The data that will be used during the workshop can be downloaded through the SACO server of CSIC. In detail, the data for the respective modules is as follows (for a total of about 61 Gb ):
{| class="wikitable"
|+ Module and data source
|-
! Module !! Data source
|-
| Starters Guide: subtomogram averaging || Data generated locally by Dynamo
|-
| Models: Filaments || Data generated locally by Dynamo
|-
| Models: Vesicles || Data generated locally by Dynamo
|-
| Models: Surfaces || Data generated locally by Dynamo
|-
| Template Matching || {{Template:DownloadLinkTemplateMatchingBasic}} (750MB)
|-
| Template Matching (GUI) || {{Template:DownloadLinkTemplateMCP}} (7.6GB)
|-
| Alignment of tilt series || {{Template:DownloadLinkAWFHIV1TS}} (600MB)
|-
| Virus like particles || {{Template:DownloadLinkVLPs}} (4.6GB)
|-
| Spherical geometries || {{Template:DownloadLinkBasicHIVTomo}} (64 MB)
|-
| Principal Component Analysis || Data generated locally by Dynamo
|-
| Complete walkthrough on FHV virus || {{Template:DownloadLinkFHV}} (2GB)
|-
| Walkthrough on hexagonal lattice coherence through neighborhood analysis || {{Template:DownloadLinkNeighborhoodData}}
|-
| High-resolution HIV1 || {{Template:DownloadLinkHighResHIV1}} (48Gb)
|}

= Time schedule =

{| class="wikitable"
|+ Day 3 (Morning) 11th of December
|-
! Module !! Time !! Subject
|-
| 1 || 09:30 - 10:00|| Hands-on tutorial. First steps and formats.
|-
| 2 || 10:00 - 11:00|| [[Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Starters Guide: subtomogram averaging]]
|-
| coffee || 11:00 - 11:30 || Coffee Break
|-
| 2 || 11:30 - 12:30|| Starters Guide: subtomogram averaging (continuation).
|-
| 3 || 12:30 - 13:00 || General modeling
|}

{| class="wikitable"
|+ Day 3 (Afternoon) 11th of December
|-
| 3a ||14:00 - 14:30 || [[Walkthrough_on_filament_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Filaments]] Additional material: [[Walkthrough model workflow reuse (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Coordinated extraction from several filaments]]
|-
| 3b || 15:00 - 15:30 || [[Walkthrough_on_vesicle_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Vesicles ]]
|-
| 3c || 15:30 - 16:00 || [[Walkthrough_on_membrane_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Models: Surfaces ]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 4 || 16:30 - 17:30 || [[Getting a Structure from Multiple Tomograms of HIV Capsids (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Virus like particles]] or [[Walkthrough for lattices on vesicles (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Spherical geometries]]
|}

{| class="wikitable"
|+ Day 4, Morning: 12th of December (Friday)
|-
| 5a || 09:30 - 09:45 || Presentation of FHV: Advanced starters guide
|-
| 5b || 09:45 - 11:00 || [[Complete walkthrough on FHV virus (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Hands-on tutorial: Advanced starters guide ]]
|-
| coffee || 11:00 - 11:30 || Coffee break
|-
| 5b || 11:30 - 12:00 || Hands-on tutorial: Advanced starters guide (continued)
|-
| 6a || 12:00 - 12:20 || [[Walkthrough on manual marker clicking (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: Manual]]
|-
| 6b || 12:20 - 12:40 || [[Walkthrough on GUI based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: GUI ]]
|-
| 6c || 12:40 - 13:00 || [[Walkthrough on command line based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: command line]]
|}

{| class="wikitable"
|+ Day 4, Afternoon session: 12th of December (Friday)
|-
! Module !! Time !! Subject
|-
| 7a || 14:00 - 15:00 || [[Walkthrough for template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Template Matching]]
|-
| 7b || 15:00 - 16:00 || [[Walkthrough for GUI-based template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Geometry aware template Matching]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 8 || 16:30- 17:30 || [[Walkthrough on PCA through the command line (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Principal Component Analysis ]]
|}

= Instructors =
* Daniel Castano-Diez (CSIC Bilbao, Spain).
* Raffaele Coray (CSIC Bilbao, Spain).
* Laura García-Cornejo (CSIC Bilbao, Spain).
* Andrés Molina (CSIC Bilbao, Spain).
* Miguel Sánchez López-Cuervo (CSIC Bilbao, Spain).

I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025

2025-12-09T11:31:27Z

Miguel Sanchez: /* Amazon machines */

[[Category:WalkthroughsSpecific]]
= The course =
== The venue ==
This page describes the contents of the ''Dynamo''-specific part of the course "I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025", which will take part at the premises of the Centro Nacional de Biotecnología in Madrid, from the 9th to the 12th of December 2025.
== Contents ==
Whole pipelines for cryo-ET processing will be covered in the Scipion-related area of the course (days 1 and 2). The ''Dynamo'' part will covered selected parts of the pipeline.

= Installation of Dynamo and Matlab =
== Dynamo on your own laptop ==
To follow the course in your own laptop, please install '''[https://drive.google.com/file/d/1x5he7ctkC4BUCNFhfXLk6heggGohELoM/view?usp=drive_link the Dynamo for Matlab version]''' as explain in [[ Downloads ]] page.

= Computing resources =

== Laptops ==
Participants can use their own laptops to complete the Dynamo part of the course. For this, participants need to have and active '''Matlab installation''' and an Dynamo installation.
* For Matlab, we advise the (R2025b version). If you don't have a license through your home institution, a [https://ch.mathworks.com/campaigns/products/trials.html licence free trial version is available] from the Mathworks company.
* '''The Dynamo Download link is currently down''', we will update it later today (17:00 ECT): prior to installation make sure you have a compiler. On Linux you probably have one by default. On Mac, Xcode needs to be installed. On Windows, the recommended option is to install it via Matlab:

https://es.mathworks.com/help/matlab/matlab_external/install-mingw-support-package.html

''Dynamo'' is delivered as a single .tar file. To install it, move the file to the location where you want to install ''Dynamo'', then open a Matlab session and type after the Matlab prompt:

<tt> >> tar -xvf dynamo_temp_1.1.579.tar </tt>

to untar the installation file. ''Dynamo'' will be installed in the folder that contained the .tar. If we call this folder <DYNAMO_ROOT>, you can activate ''Dynamo'' in your MATLAB session by typing:

<tt> >> run dynamo_activate.m </tt>

when you are in that folder, or with

<tt> >> run <DYNAMO_ROOT>/dynamo_activate.m </tt>

if you are in some other folder. Wait while some packages are compiled. Activate it again.

== Amazon machines ==

If you want to follow the course with virtual machines provided by the course, follow this instructions.

=== Entering in the AWS Machine ===

Access the link of your AWS Machine provided by the organizers, that appears in the [https://docs.google.com/spreadsheets/d/15o8IUOSsNjGHxK0Bmi1QBfI9KCCWCpX603R4l_rn6KA/edit?gid=653170857#gid=653170857 Google Sheet]. After introducing your password (also given in the same google sheet), you will have entered in the AWS Machine.

=== Initializating Dynamo Standalone ===

Once you have accessed the AWS Machine, you need to initialize Dynamo Standalone. Open the terminal emulator and type the next command:

<pre>
source dynamo-v-1.1.579/dynamo_activate_linux_shipped_MCR.sh
</pre>

After some lines asserting the correct addition of several paths and tests, it should appear as the last line: "Dynamo is ready for standalone use in your Linux system".

=== Working with the Dynamo Standalone ===

For a specific explanation of the Standalone see [https://www.dynamo-em.org//w/index.php?title=Standalone].
Once dynamo has been initialized, you can enter in dynamo by typing

<pre>
dynamo
</pre>

You can also type

<pre>
dynamo x
</pre>

so dynamo will open a GUI console, instead of using the terminal, nevertheless the first option is strongly reccommended for some Walkthroughs.

=== Solution of some possible minor cons of working in a laptop ====

Since

== Workshop data ==

The data that will be used during the workshop can be downloaded through the SACO server of CSIC. In detail, the data for the respective modules is as follows (for a total of about 61 Gb ):
{| class="wikitable"
|+ Module and data source
|-
! Module !! Data source
|-
| Starters Guide: subtomogram averaging || Data generated locally by Dynamo
|-
| Models: Filaments || Data generated locally by Dynamo
|-
| Models: Vesicles || Data generated locally by Dynamo
|-
| Models: Surfaces || Data generated locally by Dynamo
|-
| Template Matching || {{Template:DownloadLinkTemplateMatchingBasic}} (750MB)
|-
| Template Matching (GUI) || {{Template:DownloadLinkTemplateMCP}} (7.6GB)
|-
| Alignment of tilt series || {{Template:DownloadLinkAWFHIV1TS}} (600MB)
|-
| Virus like particles || {{Template:DownloadLinkVLPs}} (4.6GB)
|-
| Spherical geometries || {{Template:DownloadLinkBasicHIVTomo}} (64 MB)
|-
| Principal Component Analysis || Data generated locally by Dynamo
|-
| Complete walkthrough on FHV virus || {{Template:DownloadLinkFHV}} (2GB)
|-
| Walkthrough on hexagonal lattice coherence through neighborhood analysis || {{Template:DownloadLinkNeighborhoodData}}
|-
| High-resolution HIV1 || {{Template:DownloadLinkHighResHIV1}} (48Gb)
|}

= Time schedule =

{| class="wikitable"
|+ Day 3 (Morning) 11th of December
|-
! Module !! Time !! Subject
|-
| 1 || 09:30 - 10:00|| Hands-on tutorial. First steps and formats.
|-
| 2 || 10:00 - 11:00|| [[Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Starters Guide: subtomogram averaging]]
|-
| coffee || 11:00 - 11:30 || Coffee Break
|-
| 2 || 11:30 - 12:30|| Starters Guide: subtomogram averaging (continuation).
|-
| 3 || 12:30 - 13:00 || General modeling
|}

{| class="wikitable"
|+ Day 3 (Afternoon) 11th of December
|-
| 3a ||14:00 - 14:30 || [[Walkthrough_on_filament_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Filaments]] Additional material: [[Walkthrough model workflow reuse (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Coordinated extraction from several filaments]]
|-
| 3b || 15:00 - 15:30 || [[Walkthrough_on_vesicle_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Vesicles ]]
|-
| 3c || 15:30 - 16:00 || [[Walkthrough_on_membrane_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Models: Surfaces ]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 4 || 16:30 - 17:30 || [[Getting a Structure from Multiple Tomograms of HIV Capsids (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Virus like particles]] or [[Walkthrough for lattices on vesicles (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Spherical geometries]]
|}

{| class="wikitable"
|+ Day 4, Morning: 12th of December (Friday)
|-
| 5a || 09:30 - 09:45 || Presentation of FHV: Advanced starters guide
|-
| 5b || 09:45 - 11:00 || [[Complete walkthrough on FHV virus (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Hands-on tutorial: Advanced starters guide ]]
|-
| coffee || 11:00 - 11:30 || Coffee break
|-
| 5b || 11:30 - 12:00 || Hands-on tutorial: Advanced starters guide (continued)
|-
| 6a || 12:00 - 12:20 || [[Walkthrough on manual marker clicking (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: Manual]]
|-
| 6b || 12:20 - 12:40 || [[Walkthrough on GUI based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: GUI ]]
|-
| 6c || 12:40 - 13:00 || [[Walkthrough on command line based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: command line]]
|}

{| class="wikitable"
|+ Day 4, Afternoon session: 12th of December (Friday)
|-
! Module !! Time !! Subject
|-
| 7a || 14:00 - 15:00 || [[Walkthrough for template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Template Matching]]
|-
| 7b || 15:00 - 16:00 || [[Walkthrough for GUI-based template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Geometry aware template Matching]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 8 || 16:30- 17:30 || [[Walkthrough on PCA through the command line (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Principal Component Analysis ]]
|}

= Instructors =
* Daniel Castano-Diez (CSIC Bilbao, Spain).
* Raffaele Coray (CSIC Bilbao, Spain).
* Laura García-Cornejo (CSIC Bilbao, Spain).
* Andrés Molina (CSIC Bilbao, Spain).
* Miguel Sánchez López-Cuervo (CSIC Bilbao, Spain).

I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025

2025-12-09T11:16:17Z

Miguel Sanchez: /* Amazon machines */

[[Category:WalkthroughsSpecific]]
= The course =
== The venue ==
This page describes the contents of the ''Dynamo''-specific part of the course "I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025", which will take part at the premises of the Centro Nacional de Biotecnología in Madrid, from the 9th to the 12th of December 2025.
== Contents ==
Whole pipelines for cryo-ET processing will be covered in the Scipion-related area of the course (days 1 and 2). The ''Dynamo'' part will covered selected parts of the pipeline.

= Installation of Dynamo and Matlab =
== Dynamo on your own laptop ==
To follow the course in your own laptop, please install '''[https://drive.google.com/file/d/1x5he7ctkC4BUCNFhfXLk6heggGohELoM/view?usp=drive_link the Dynamo for Matlab version]''' as explain in [[ Downloads ]] page.

= Computing resources =

== Laptops ==
Participants can use their own laptops to complete the Dynamo part of the course. For this, participants need to have and active '''Matlab installation''' and an Dynamo installation.
* For Matlab, we advise the (R2025b version). If you don't have a license through your home institution, a [https://ch.mathworks.com/campaigns/products/trials.html licence free trial version is available] from the Mathworks company.
* '''The Dynamo Download link is currently down''', we will update it later today (17:00 ECT): prior to installation make sure you have a compiler. On Linux you probably have one by default. On Mac, Xcode needs to be installed. On Windows, the recommended option is to install it via Matlab:

https://es.mathworks.com/help/matlab/matlab_external/install-mingw-support-package.html

''Dynamo'' is delivered as a single .tar file. To install it, move the file to the location where you want to install ''Dynamo'', then open a Matlab session and type after the Matlab prompt:

<tt> >> tar -xvf dynamo_temp_1.1.579.tar </tt>

to untar the installation file. ''Dynamo'' will be installed in the folder that contained the .tar. If we call this folder <DYNAMO_ROOT>, you can activate ''Dynamo'' in your MATLAB session by typing:

<tt> >> run dynamo_activate.m </tt>

when you are in that folder, or with

<tt> >> run <DYNAMO_ROOT>/dynamo_activate.m </tt>

if you are in some other folder. Wait while some packages are compiled. Activate it again.

== Amazon machines ==

If you want to follow the course with virtual machines provided by the course, follow this instructions.

=== Entering in the AWS Machine ===

Access the link of your AWS Machine provided by the organizers, that appears in the [https://docs.google.com/spreadsheets/d/15o8IUOSsNjGHxK0Bmi1QBfI9KCCWCpX603R4l_rn6KA/edit?gid=653170857#gid=653170857 Google Sheet]. After introducing your password (also given in the same google sheet), you will have entered in the AWS Machine.

=== Initializating Dynamo Standalone ===

Once you have accessed the AWS Machine, you need to initialize Dynamo Standalone. Open the terminal emulator and type the next command:

<pre>
source dynamo-v-1.1.579/dynamo_activate_linux_shipped_MCR.sh
</pre>

After some lines asserting the correct addition of several paths and tests, it should appear as the last line: "Dynamo is ready for standalone use in your Linux system".

=== Working with the Dynamo Standalone ===

The complete

== Workshop data ==

The data that will be used during the workshop can be downloaded through the SACO server of CSIC. In detail, the data for the respective modules is as follows (for a total of about 61 Gb ):
{| class="wikitable"
|+ Module and data source
|-
! Module !! Data source
|-
| Starters Guide: subtomogram averaging || Data generated locally by Dynamo
|-
| Models: Filaments || Data generated locally by Dynamo
|-
| Models: Vesicles || Data generated locally by Dynamo
|-
| Models: Surfaces || Data generated locally by Dynamo
|-
| Template Matching || {{Template:DownloadLinkTemplateMatchingBasic}} (750MB)
|-
| Template Matching (GUI) || {{Template:DownloadLinkTemplateMCP}} (7.6GB)
|-
| Alignment of tilt series || {{Template:DownloadLinkAWFHIV1TS}} (600MB)
|-
| Virus like particles || {{Template:DownloadLinkVLPs}} (4.6GB)
|-
| Spherical geometries || {{Template:DownloadLinkBasicHIVTomo}} (64 MB)
|-
| Principal Component Analysis || Data generated locally by Dynamo
|-
| Complete walkthrough on FHV virus || {{Template:DownloadLinkFHV}} (2GB)
|-
| Walkthrough on hexagonal lattice coherence through neighborhood analysis || {{Template:DownloadLinkNeighborhoodData}}
|-
| High-resolution HIV1 || {{Template:DownloadLinkHighResHIV1}} (48Gb)
|}

= Time schedule =

{| class="wikitable"
|+ Day 3 (Morning) 11th of December
|-
! Module !! Time !! Subject
|-
| 1 || 09:30 - 10:00|| Hands-on tutorial. First steps and formats.
|-
| 2 || 10:00 - 11:00|| [[Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Starters Guide: subtomogram averaging]]
|-
| coffee || 11:00 - 11:30 || Coffee Break
|-
| 2 || 11:30 - 12:30|| Starters Guide: subtomogram averaging (continuation).
|-
| 3 || 12:30 - 13:00 || General modeling
|}

{| class="wikitable"
|+ Day 3 (Afternoon) 11th of December
|-
| 3a ||14:00 - 14:30 || [[Walkthrough_on_filament_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Filaments]] Additional material: [[Walkthrough model workflow reuse (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Coordinated extraction from several filaments]]
|-
| 3b || 15:00 - 15:30 || [[Walkthrough_on_vesicle_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Vesicles ]]
|-
| 3c || 15:30 - 16:00 || [[Walkthrough_on_membrane_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Models: Surfaces ]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 4 || 16:30 - 17:30 || [[Getting a Structure from Multiple Tomograms of HIV Capsids (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Virus like particles]] or [[Walkthrough for lattices on vesicles (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Spherical geometries]]
|}

{| class="wikitable"
|+ Day 4, Morning: 12th of December (Friday)
|-
| 5a || 09:30 - 09:45 || Presentation of FHV: Advanced starters guide
|-
| 5b || 09:45 - 11:00 || [[Complete walkthrough on FHV virus (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Hands-on tutorial: Advanced starters guide ]]
|-
| coffee || 11:00 - 11:30 || Coffee break
|-
| 5b || 11:30 - 12:00 || Hands-on tutorial: Advanced starters guide (continued)
|-
| 6a || 12:00 - 12:20 || [[Walkthrough on manual marker clicking (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: Manual]]
|-
| 6b || 12:20 - 12:40 || [[Walkthrough on GUI based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: GUI ]]
|-
| 6c || 12:40 - 13:00 || [[Walkthrough on command line based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: command line]]
|}

{| class="wikitable"
|+ Day 4, Afternoon session: 12th of December (Friday)
|-
! Module !! Time !! Subject
|-
| 7a || 14:00 - 15:00 || [[Walkthrough for template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Template Matching]]
|-
| 7b || 15:00 - 16:00 || [[Walkthrough for GUI-based template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Geometry aware template Matching]]
|-
| coffee || 16:00 - 16:30 || Coffee Break
|-
| 8 || 16:30- 17:30 || [[Walkthrough on PCA through the command line (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Principal Component Analysis ]]
|}

= Instructors =
* Daniel Castano-Diez (CSIC Bilbao, Spain).
* Raffaele Coray (CSIC Bilbao, Spain).
* Laura García-Cornejo (CSIC Bilbao, Spain).
* Andrés Molina (CSIC Bilbao, Spain).
* Miguel Sánchez López-Cuervo (CSIC Bilbao, Spain).

Standalone

2025-12-05T13:32:26Z

Miguel Sanchez: /* Testing your standalone */

{{DISPLAYTITLE:''Dynamo'' standalone}}

The ''Dynamo standalone'' is the version of ''Dynamo'' that runs without any Matlab installation. A ''standalone'' package carries its own "Matlab" version in the form of [[MCR libraries]].

==Activating the standalone==
To use ''Dynamo'' is standalone modus in a shell, you need to activate first that shell, typically with:

<tt>source <DYNAMO_ROOT>/dynamo_activate_linux_shipped_MCR.sh</tt>

==Using the standalone==

Our advice to work with the ''Dynamo'' standalone is to use at least two linux shells. You would use one shell (let's call it ''console shell'') to run an interactive [[Dynamo console]], where you can create projects, view tomograms or analyse results. In a second linux shell (let's call it ''computing shell''), you can launch the projects edited on the first shell.

''Dynamo'' must be active in both shells!

=== On the Console shell===
A console shell can be launched through typing <tt>dynamo</tt> or <tt>dynamo x</tt>.

*Using the Wizard GUI
*:Make certain that when you create a project, you use the <tt>standalone</tt> option in the [[Computing environment GUI]]. Each "core" will be handled by a different openMP process. You can also run alignment projects in the GPU, in which case you also have to mark the set of [[GPU identifiers]].
*Using the command line
*: In case that you are designing your project from the command line, the parameter that controls the environment is called {{t|destination}}. To use the standalone, it should be tuned to {{t|system_omp}} for multicore projects, or to {{t|system_gpu}} for GPU projects.

In both cases you can check and unfold the project in the GUI handled by the [[Dynamo console]] to produce an [[execution script]]. A project called {{t|myProject}} will generate an standalone script called {{t|myProject.exe}}. Instead of running the project in the Console shell, the Console will be blocked until the project is finished (and wont show any results on screen).

=== On the computation shell===
To execute a project {{t|myProject}} in a shell, you don't need to open any [[Dynamo console]] first. Just type:

<tt>myProject.exe</tt>

or

<tt>./myProject.exe</tt>

depending on your system configuration. You might also need to adjust permissions through:

<tt>chmod u=rxw ./myProject.exe</tt>

Note, anyway, that you can run in the Linux shell any project that has been unfolded as standalone: you can thus create your projects in a Matlab shell, check and unfold them under Matlab, an then run them inside a Linux shell using the generated execution script.

[[File:Computing_environment_gui_standalone.png|thumb|center|400px|Computing environment GUI with the standalone option]]

===For independent commands===
You can use the standalone version to execute independent ''Dynamo'' commands from the linux shell (avoiding the ''Dynamo'' [[console]]). Use the sign <tt>"</tt> to encase the literal expression that you would write on a Matlab shell. Importantly do NOT use the short version of the commands, i.e., do not use {{t|dwrite}} instead of {{t|dynamo_write}}. For example, writing in your (''Dynamo''-activated) shell:

<tt> dynamo "x=rand(64,64,64);dynamo_write(x,'test.em');" </tt>

will create a cube containing random uniform noise in the temporary workspace and then write it into a file {{t|test.em}}. Note that the workspace is local to each call to ''Dynamo'' through the {{t|dynamo}} command, so that you can NOT divide the order in two:

<tt> dynamo "x=rand(64,64,64);"</tt>

<tt> dynamo "dynamo_write(x,'test.em');" </tt>

would throw an error on the second line.

In general, calling the command {{t|dynamo}} will require an initiation time of several seconds, so it is convenient to pile as many operations as possible inside a single call. Loops are allowed:

<tt>dynamo "for i=1:10;x=rand(64,64,64);dynamo_write(x,sprintf('test%d.em',i));end"</tt>

As an alternative, you can write Dynamo instructions in a text file and pass the name of the file to the {{t|dynamo}} command. For intance, if you have a text file called {{t|commnads.sh}} with this content:

<tt> x=rand(64,64,64);</tt>
<tt> dynamo_write(x,'test.em');</tt>

you can execute the script by writing:

<tt>dynamo commands.sh</tt>

Note that this imposes a maximum of 1024 characters for the full script.

With this technique, it is possible to [[ Scripted creation of a project in the Linux command line| fully design and run a project from the command line ]], or to integrate ''Dynamo'' operations in third party pipelines.

==Advantages over the Matlab version==
Besides the obvious advantage of not requiring the purchase of any Matlab license, there are some minor functionalities in ''Dynamo'' that would require an extra Toolbox on top of the basic Matlab license, as Statistics or Curve fitting. These functionalities are never used in the basic pipeline of ''Dynamo'', but are part of the extended tools offered by ''Dynamo'' through its command line.
When you use the standalone, all mathematical toolboxes are automatically available.

Additionally, the standalone version is automatically delivered with the newest Matlab version. If you are running ''Dynamo'' on Matlab versions previous to release R2014b, you can experiment visualization problems in some programs.

== Testing your standalone ==

You can quickly run a test project in order to check that your standalone is correctly installed:
# Open a system shell. Let's call it ''dynamo console shell''
# Activate Dynamo on this shell: <tt>source <Dynamo Root>/dynamo_activate_linux_shipped_MCR.sh</tt> or equivalently for your system (Mac or Windows).
#Start the ''Dynamo'' console on it by typing <tt> dynamo </tt> on it. Now this shell will work as a console when you can type ''Dynamo'' commands after the prompt <tt>Dynamo >> </tt>
#Under the <tt>Dynamo >></tt> prompt, we will create a tutorial project; <tt> dtutorial mytest -p ptest</tt> 
#Open a '''different''' system shell. Let's call it ''project execution shell''.
#On this shell, ''activate'' ''Dynamo'': <tt>source <Dynamo Root>/dynamo_activate_linux_shipped_MCR.sh</tt> 
#Go to same folder in which you created the project. Both shells should have the same <tt>pwd</tt>
#Execute the project in the ''project execution shell'': <tt>./ptest.exe </tt> Please note that this project has been unfolded during creation. For your own projects, you'll need to unfold them manually through the [[dcp GUI]] or with the command: <tt>dvunfold ptest</tt> invoked inside the ''Dynamo console''
# Check the result in the ''dynamo console shell'' by <tt>ddb ptest:a -v </tt> This should show a reconstructed thermosome.

== Typical problems with the standalone ==

Some of the software installed in your system may enter in conflict with the [[MCR libraries]] supplied by ''Dynamo''. Is it also possible that some system libraries enter in conflict with the [[MCR libraries]]. In most cases, [[Library conflicts | preloading a valid library]] solves the problem.

Standalone

2025-12-05T13:32:11Z

Miguel Sanchez: /* Testing your standalone */

{{DISPLAYTITLE:''Dynamo'' standalone}}

The ''Dynamo standalone'' is the version of ''Dynamo'' that runs without any Matlab installation. A ''standalone'' package carries its own "Matlab" version in the form of [[MCR libraries]].

==Activating the standalone==
To use ''Dynamo'' is standalone modus in a shell, you need to activate first that shell, typically with:

<tt>source <DYNAMO_ROOT>/dynamo_activate_linux_shipped_MCR.sh</tt>

==Using the standalone==

Our advice to work with the ''Dynamo'' standalone is to use at least two linux shells. You would use one shell (let's call it ''console shell'') to run an interactive [[Dynamo console]], where you can create projects, view tomograms or analyse results. In a second linux shell (let's call it ''computing shell''), you can launch the projects edited on the first shell.

''Dynamo'' must be active in both shells!

=== On the Console shell===
A console shell can be launched through typing <tt>dynamo</tt> or <tt>dynamo x</tt>.

*Using the Wizard GUI
*:Make certain that when you create a project, you use the <tt>standalone</tt> option in the [[Computing environment GUI]]. Each "core" will be handled by a different openMP process. You can also run alignment projects in the GPU, in which case you also have to mark the set of [[GPU identifiers]].
*Using the command line
*: In case that you are designing your project from the command line, the parameter that controls the environment is called {{t|destination}}. To use the standalone, it should be tuned to {{t|system_omp}} for multicore projects, or to {{t|system_gpu}} for GPU projects.

In both cases you can check and unfold the project in the GUI handled by the [[Dynamo console]] to produce an [[execution script]]. A project called {{t|myProject}} will generate an standalone script called {{t|myProject.exe}}. Instead of running the project in the Console shell, the Console will be blocked until the project is finished (and wont show any results on screen).

=== On the computation shell===
To execute a project {{t|myProject}} in a shell, you don't need to open any [[Dynamo console]] first. Just type:

<tt>myProject.exe</tt>

or

<tt>./myProject.exe</tt>

depending on your system configuration. You might also need to adjust permissions through:

<tt>chmod u=rxw ./myProject.exe</tt>

Note, anyway, that you can run in the Linux shell any project that has been unfolded as standalone: you can thus create your projects in a Matlab shell, check and unfold them under Matlab, an then run them inside a Linux shell using the generated execution script.

[[File:Computing_environment_gui_standalone.png|thumb|center|400px|Computing environment GUI with the standalone option]]

===For independent commands===
You can use the standalone version to execute independent ''Dynamo'' commands from the linux shell (avoiding the ''Dynamo'' [[console]]). Use the sign <tt>"</tt> to encase the literal expression that you would write on a Matlab shell. Importantly do NOT use the short version of the commands, i.e., do not use {{t|dwrite}} instead of {{t|dynamo_write}}. For example, writing in your (''Dynamo''-activated) shell:

<tt> dynamo "x=rand(64,64,64);dynamo_write(x,'test.em');" </tt>

will create a cube containing random uniform noise in the temporary workspace and then write it into a file {{t|test.em}}. Note that the workspace is local to each call to ''Dynamo'' through the {{t|dynamo}} command, so that you can NOT divide the order in two:

<tt> dynamo "x=rand(64,64,64);"</tt>

<tt> dynamo "dynamo_write(x,'test.em');" </tt>

would throw an error on the second line.

In general, calling the command {{t|dynamo}} will require an initiation time of several seconds, so it is convenient to pile as many operations as possible inside a single call. Loops are allowed:

<tt>dynamo "for i=1:10;x=rand(64,64,64);dynamo_write(x,sprintf('test%d.em',i));end"</tt>

As an alternative, you can write Dynamo instructions in a text file and pass the name of the file to the {{t|dynamo}} command. For intance, if you have a text file called {{t|commnads.sh}} with this content:

<tt> x=rand(64,64,64);</tt>
<tt> dynamo_write(x,'test.em');</tt>

you can execute the script by writing:

<tt>dynamo commands.sh</tt>

Note that this imposes a maximum of 1024 characters for the full script.

With this technique, it is possible to [[ Scripted creation of a project in the Linux command line| fully design and run a project from the command line ]], or to integrate ''Dynamo'' operations in third party pipelines.

==Advantages over the Matlab version==
Besides the obvious advantage of not requiring the purchase of any Matlab license, there are some minor functionalities in ''Dynamo'' that would require an extra Toolbox on top of the basic Matlab license, as Statistics or Curve fitting. These functionalities are never used in the basic pipeline of ''Dynamo'', but are part of the extended tools offered by ''Dynamo'' through its command line.
When you use the standalone, all mathematical toolboxes are automatically available.

Additionally, the standalone version is automatically delivered with the newest Matlab version. If you are running ''Dynamo'' on Matlab versions previous to release R2014b, you can experiment visualization problems in some programs.

== Testing your standalone ==

You can quickly run a test project in order to check that your standalone is correctly installed:
# Open a system shell. Let's call it ''dynamo console shell''
# Activate Dynamo on this shell: <tt>source <Dynamo Root>/dynamo_activate_linux_shipped_MCR.sh</tt> or equivalently for your system (Mac or Windows).
#Start the ''Dynamo'' console on it by typing <tt> dynamo </tt> on it. Now this shell will work as a console when you can type ''Dynamo'' commands after the prompt <tt>Dynamo >> </tt>
#Under the <tt>Dynamo >></tt> prompt, we will create a tutorial project; <tt> dtutorial mytest -p ptest</tt> 
#Open a '''different''' system shell. Let's call it ''project execution shell''.
#On this shell, ''activate'' ''Dynamo'': <tt>source <Dynamo Root>/dynamo_activate_linux_with_shippedMRC.sh</tt> 
#Go to same folder in which you created the project. Both shells should have the same <tt>pwd</tt>
#Execute the project in the ''project execution shell'': <tt>./ptest.exe </tt> Please note that this project has been unfolded during creation. For your own projects, you'll need to unfold them manually through the [[dcp GUI]] or with the command: <tt>dvunfold ptest</tt> invoked inside the ''Dynamo console''
# Check the result in the ''dynamo console shell'' by <tt>ddb ptest:a -v </tt> This should show a reconstructed thermosome.

== Typical problems with the standalone ==

Some of the software installed in your system may enter in conflict with the [[MCR libraries]] supplied by ''Dynamo''. Is it also possible that some system libraries enter in conflict with the [[MCR libraries]]. In most cases, [[Library conflicts | preloading a valid library]] solves the problem.

Standalone

2025-12-05T13:31:27Z

Miguel Sanchez: /* Activating the standalone */

{{DISPLAYTITLE:''Dynamo'' standalone}}

The ''Dynamo standalone'' is the version of ''Dynamo'' that runs without any Matlab installation. A ''standalone'' package carries its own "Matlab" version in the form of [[MCR libraries]].

==Activating the standalone==
To use ''Dynamo'' is standalone modus in a shell, you need to activate first that shell, typically with:

<tt>source <DYNAMO_ROOT>/dynamo_activate_linux_shipped_MCR.sh</tt>

==Using the standalone==

Our advice to work with the ''Dynamo'' standalone is to use at least two linux shells. You would use one shell (let's call it ''console shell'') to run an interactive [[Dynamo console]], where you can create projects, view tomograms or analyse results. In a second linux shell (let's call it ''computing shell''), you can launch the projects edited on the first shell.

''Dynamo'' must be active in both shells!

=== On the Console shell===
A console shell can be launched through typing <tt>dynamo</tt> or <tt>dynamo x</tt>.

*Using the Wizard GUI
*:Make certain that when you create a project, you use the <tt>standalone</tt> option in the [[Computing environment GUI]]. Each "core" will be handled by a different openMP process. You can also run alignment projects in the GPU, in which case you also have to mark the set of [[GPU identifiers]].
*Using the command line
*: In case that you are designing your project from the command line, the parameter that controls the environment is called {{t|destination}}. To use the standalone, it should be tuned to {{t|system_omp}} for multicore projects, or to {{t|system_gpu}} for GPU projects.

In both cases you can check and unfold the project in the GUI handled by the [[Dynamo console]] to produce an [[execution script]]. A project called {{t|myProject}} will generate an standalone script called {{t|myProject.exe}}. Instead of running the project in the Console shell, the Console will be blocked until the project is finished (and wont show any results on screen).

=== On the computation shell===
To execute a project {{t|myProject}} in a shell, you don't need to open any [[Dynamo console]] first. Just type:

<tt>myProject.exe</tt>

or

<tt>./myProject.exe</tt>

depending on your system configuration. You might also need to adjust permissions through:

<tt>chmod u=rxw ./myProject.exe</tt>

Note, anyway, that you can run in the Linux shell any project that has been unfolded as standalone: you can thus create your projects in a Matlab shell, check and unfold them under Matlab, an then run them inside a Linux shell using the generated execution script.

[[File:Computing_environment_gui_standalone.png|thumb|center|400px|Computing environment GUI with the standalone option]]

===For independent commands===
You can use the standalone version to execute independent ''Dynamo'' commands from the linux shell (avoiding the ''Dynamo'' [[console]]). Use the sign <tt>"</tt> to encase the literal expression that you would write on a Matlab shell. Importantly do NOT use the short version of the commands, i.e., do not use {{t|dwrite}} instead of {{t|dynamo_write}}. For example, writing in your (''Dynamo''-activated) shell:

<tt> dynamo "x=rand(64,64,64);dynamo_write(x,'test.em');" </tt>

will create a cube containing random uniform noise in the temporary workspace and then write it into a file {{t|test.em}}. Note that the workspace is local to each call to ''Dynamo'' through the {{t|dynamo}} command, so that you can NOT divide the order in two:

<tt> dynamo "x=rand(64,64,64);"</tt>

<tt> dynamo "dynamo_write(x,'test.em');" </tt>

would throw an error on the second line.

In general, calling the command {{t|dynamo}} will require an initiation time of several seconds, so it is convenient to pile as many operations as possible inside a single call. Loops are allowed:

<tt>dynamo "for i=1:10;x=rand(64,64,64);dynamo_write(x,sprintf('test%d.em',i));end"</tt>

As an alternative, you can write Dynamo instructions in a text file and pass the name of the file to the {{t|dynamo}} command. For intance, if you have a text file called {{t|commnads.sh}} with this content:

<tt> x=rand(64,64,64);</tt>
<tt> dynamo_write(x,'test.em');</tt>

you can execute the script by writing:

<tt>dynamo commands.sh</tt>

Note that this imposes a maximum of 1024 characters for the full script.

With this technique, it is possible to [[ Scripted creation of a project in the Linux command line| fully design and run a project from the command line ]], or to integrate ''Dynamo'' operations in third party pipelines.

==Advantages over the Matlab version==
Besides the obvious advantage of not requiring the purchase of any Matlab license, there are some minor functionalities in ''Dynamo'' that would require an extra Toolbox on top of the basic Matlab license, as Statistics or Curve fitting. These functionalities are never used in the basic pipeline of ''Dynamo'', but are part of the extended tools offered by ''Dynamo'' through its command line.
When you use the standalone, all mathematical toolboxes are automatically available.

Additionally, the standalone version is automatically delivered with the newest Matlab version. If you are running ''Dynamo'' on Matlab versions previous to release R2014b, you can experiment visualization problems in some programs.

== Testing your standalone ==

You can quickly run a test project in order to check that your standalone is correctly installed:
# Open a system shell. Let's call it ''dynamo console shell''
# Activate Dynamo on this shell: <tt>source <Dynamo Root>/dynamo_activate_linux_with_shippedMRC.sh</tt> or equivalently for your system (Mac or Windows).
#Start the ''Dynamo'' console on it by typing <tt> dynamo </tt> on it. Now this shell will work as a console when you can type ''Dynamo'' commands after the prompt <tt>Dynamo >> </tt>
#Under the <tt>Dynamo >></tt> prompt, we will create a tutorial project; <tt> dtutorial mytest -p ptest</tt> 
#Open a '''different''' system shell. Let's call it ''project execution shell''.
#On this shell, ''activate'' ''Dynamo'': <tt>source <Dynamo Root>/dynamo_activate_linux_with_shippedMRC.sh</tt> 
#Go to same folder in which you created the project. Both shells should have the same <tt>pwd</tt>
#Execute the project in the ''project execution shell'': <tt>./ptest.exe </tt> Please note that this project has been unfolded during creation. For your own projects, you'll need to unfold them manually through the [[dcp GUI]] or with the command: <tt>dvunfold ptest</tt> invoked inside the ''Dynamo console''
# Check the result in the ''dynamo console shell'' by <tt>ddb ptest:a -v </tt> This should show a reconstructed thermosome.

== Typical problems with the standalone ==

Some of the software installed in your system may enter in conflict with the [[MCR libraries]] supplied by ''Dynamo''. Is it also possible that some system libraries enter in conflict with the [[MCR libraries]]. In most cases, [[Library conflicts | preloading a valid library]] solves the problem.