Dynamo - User contributions [en]

I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025

2025-12-12T14:28:14Z

Raffaele Coray: /* Time schedule */

[[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 do '''secondary click''' on the "View" botton:

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

In general, this corresponds to doing a ''right click'', but if you are working on a MAC laptop with no external mouse, just press with two fingers on the trackpad at the same time.

Note that sometimes the GUI does not refresh itself and in this case, doing right click on the "View" botton will not work. To manually refresh the GUI and load all of the previous results into it, you need to do a '''primary click''' on the "View" bottom first. After that, you can do '''right click''' and you should be able to access the "View" panel as usual.

=== Unzipping some of the data ===

In the amazon machines, the data for the walkthrough on Geometry aware template matching is in a zipped file, so in order to access it, we need to unzip it. To do so, open a terminal and write:

<tt> cd /home/student/data/TemplateMatchingGUI

unzip MCP_walkthrough_data.zip </tt>

== 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 - 10:30|| Hands-on tutorial. First steps and formats.
|-
| 2 || 10:30 - 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).
|-
| SBGrid || 12:30 - 13:00 || SBGrid Consortium presentation (Estrella Giménez)
|}

{| class="wikitable"
|+ Day 3 (Afternoon) 11th of December
|-
| 3 ||14:00 - 14:30 || General modelling
|-
| 3a ||14:30 - 15:00 || [[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 - 15:15 || [[Walkthrough_on_vesicle_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Vesicles ]]
|-
| 3c || 15:15 - 15:30 || [[Walkthrough_on_membrane_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Models: Surfaces ]]
|-
| coffee || 15:30 - 16:00 || Coffee Break
|-
| 4 || 16:00 - 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]]
|}

The presentation introducing the automatic tilt series alignment, template matching, and principal component analysis walkthroughs can be found [https://docs.google.com/presentation/d/1cf3Me75olaY_hQYKI9NjfpZHmHgr5Wad/edit?usp=drive_link&ouid=117959272098462742941&rtpof=true&sd=true here].

{| 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 - 15:30 || [[Walkthrough for GUI-based template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Geometry aware template Matching]]
|-
| coffee || 15:30 - 16:00 || Coffee Break
|-
| 8 || 16:00- 17:00 || [[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

2025-12-12T14:27:20Z

Raffaele Coray: /* Time schedule */

[[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 do '''secondary click''' on the "View" botton:

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

In general, this corresponds to doing a ''right click'', but if you are working on a MAC laptop with no external mouse, just press with two fingers on the trackpad at the same time.

Note that sometimes the GUI does not refresh itself and in this case, doing right click on the "View" botton will not work. To manually refresh the GUI and load all of the previous results into it, you need to do a '''primary click''' on the "View" bottom first. After that, you can do '''right click''' and you should be able to access the "View" panel as usual.

=== Unzipping some of the data ===

In the amazon machines, the data for the walkthrough on Geometry aware template matching is in a zipped file, so in order to access it, we need to unzip it. To do so, open a terminal and write:

<tt> cd /home/student/data/TemplateMatchingGUI

unzip MCP_walkthrough_data.zip </tt>

== 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 - 10:30|| Hands-on tutorial. First steps and formats.
|-
| 2 || 10:30 - 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).
|-
| SBGrid || 12:30 - 13:00 || SBGrid Consortium presentation (Estrella Giménez)
|}

{| class="wikitable"
|+ Day 3 (Afternoon) 11th of December
|-
| 3 ||14:00 - 14:30 || General modelling
|-
| 3a ||14:30 - 15:00 || [[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 - 15:15 || [[Walkthrough_on_vesicle_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Vesicles ]]
|-
| 3c || 15:15 - 15:30 || [[Walkthrough_on_membrane_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Models: Surfaces ]]
|-
| coffee || 15:30 - 16:00 || Coffee Break
|-
| 4 || 16:00 - 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]]
|}

The introducing presentation for the automatic tilt series alignment, template matching, and principal component analysis can be found [https://docs.google.com/presentation/d/1cf3Me75olaY_hQYKI9NjfpZHmHgr5Wad/edit?usp=drive_link&ouid=117959272098462742941&rtpof=true&sd=true here].

{| 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 - 15:30 || [[Walkthrough for GUI-based template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Geometry aware template Matching]]
|-
| coffee || 15:30 - 16:00 || Coffee Break
|-
| 8 || 16:00- 17:00 || [[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

2025-12-12T14:27:01Z

Raffaele Coray: /* Time schedule */

[[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 do '''secondary click''' on the "View" botton:

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

In general, this corresponds to doing a ''right click'', but if you are working on a MAC laptop with no external mouse, just press with two fingers on the trackpad at the same time.

Note that sometimes the GUI does not refresh itself and in this case, doing right click on the "View" botton will not work. To manually refresh the GUI and load all of the previous results into it, you need to do a '''primary click''' on the "View" bottom first. After that, you can do '''right click''' and you should be able to access the "View" panel as usual.

=== Unzipping some of the data ===

In the amazon machines, the data for the walkthrough on Geometry aware template matching is in a zipped file, so in order to access it, we need to unzip it. To do so, open a terminal and write:

<tt> cd /home/student/data/TemplateMatchingGUI

unzip MCP_walkthrough_data.zip </tt>

== 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 - 10:30|| Hands-on tutorial. First steps and formats.
|-
| 2 || 10:30 - 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).
|-
| SBGrid || 12:30 - 13:00 || SBGrid Consortium presentation (Estrella Giménez)
|}

{| class="wikitable"
|+ Day 3 (Afternoon) 11th of December
|-
| 3 ||14:00 - 14:30 || General modelling
|-
| 3a ||14:30 - 15:00 || [[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 - 15:15 || [[Walkthrough_on_vesicle_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Vesicles ]]
|-
| 3c || 15:15 - 15:30 || [[Walkthrough_on_membrane_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Models: Surfaces ]]
|-
| coffee || 15:30 - 16:00 || Coffee Break
|-
| 4 || 16:00 - 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]]
|}

The introducing presentation for the automatic tilt series alignment, template matching, and principal component analysis can be found [[https://docs.google.com/presentation/d/1cf3Me75olaY_hQYKI9NjfpZHmHgr5Wad/edit?usp=drive_link&ouid=117959272098462742941&rtpof=true&sd=true here]].

{| 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 - 15:30 || [[Walkthrough for GUI-based template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Geometry aware template Matching]]
|-
| coffee || 15:30 - 16:00 || Coffee Break
|-
| 8 || 16:00- 17:00 || [[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

2025-12-05T10:46:15Z

Raffaele Coray: /* Workshop data */

I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025

2025-12-05T10:45:40Z

Raffaele Coray: /* Workshop data */

I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025

2025-12-05T10:44:42Z

Raffaele Coray: /* Workshop data */

Raffaele Coray: /* Basic concepts */

Template consist in using an object of interest by systematically comparing it against a tomogram to identify the positions and orientations of copies of that object in the tomogram. This procedure can be seen either as an approach for particle picking or even segmentation. In ''Dynamo'' this is done either with the <tt>dynamo_match</tt> function or directly through the <tt>dtmslice</tt> GUI.

== Basic concepts==

In this technique, a template representing an object of interest is systematically cross-correlated against a tomogram, producing a ''cross-correlation map'' of the tomogram. Each pixel in this map represents a score assigned the corresponding pixel in the tomogram map. This score measures the similarity of the neighbourhood of the tomogram pixel to the used template.
This similarity is measured exclusively inside a mask.

Once this cross-correlation map has been computed, local maxima can be identified to select the positions and orientations of the found particles in the tomogram.

In summary, ''Dynamo'' allows users to compute these cross-correlation map in multiple ways:
* '''Basic template matching''': this is the simplest way to use template matching in ''Dynamo''
* '''Template matching by GUI''': ''Dynamo'' provides a GUI to use template matching in a interactive way.
* '''Model-aware template matching''': this mode allows users to improve the speed and quality of the procedure by including additional prior informations on the geometry (i.e. model) of the sample to guide template matching.
* '''On-the-fly modus''': in this modus, a tilt series is given as input instead of a tomogram and sections are reconstructed on-the-fly.
* '''Single chunk modus''': this modus allow for the parallel inspection of single specific region of the tomogram (the so-called single chunk). Ideal for fine and exhaustive angular searches in a restricted region of the sample.

== Basic template matching==

Basic (non-model-aware) template matching is the simplest way to use template match in ''Dynamo''. In this mode, the template will be cross-correlated against a tomogram with the same set of rotation everywhere. The tomogram may be split into chunks, but this is done only so as not to crowd the memory during computation.

A full walkthrough of [[Walkthrough for template matching | template matching in this mode]] is available.

== GUI-based template matching==

Template matching can be done in ''Dynamo'' directly from the <tt>dtmslice</tt> GUI with a tomogram as input. It has a tab called Template Matching in the top bar of the GUI. It is through this tab that general attributes, parameters and region of interest for template matching processes can be manipulated. More information on how to use the GUI can be found in [[Walkthrough for GUI-based template matching | the GUI walkthrough]]. It is also possible to add custom functionalities to the GUI as described in the [[Programmatic GUI customization for template matching | corresponding tutorial]].

== Model-aware template matching==

Model-aware template matching is meant as an extension of the normal template matching algorithm in ''Dynamo''. As such, all basic commands described in the previous sections are valid in this mode as well.

The main change introduced in model-aware template matching is that the partition of the tomogram in regions of interest (chunks) is meant to be meaningful from the point of view of the tomogram models. This allows for the reduction of needed computation by restricting the angular combinations of the template to be scanned. The description of which chunks are created and their corresponding restricted angular combinations will be called a tessellation policy.

A walkthrough on [[Walkthrough for model-aware template matching | model-aware template matching]] is available. Additionally, here template mathcing using on-the-fly reconstructions and single-chunk modus are also described.

Template matching

2025-07-30T13:14:27Z

Raffaele Coray:

Template consist in using an object of interest by systematically comparing it against a tomogram to identify the positions and orientations of copies of that object in the tomogram. This procedure can be seen either as an approach for particle picking or even segmentation. In ''Dynamo'' this is done either with the <tt>dynamo_match</tt> function or directly through the <tt>dtmslice</tt> GUI.

== Basic concepts==

In this technique, a template representing an object of interest is systematically cross-correlated against a tomogram, producing a ''cross-correlation map'' of the tomogram. Each pixel in this map represents a score assigned the corresponding pixel in the tomogram map. This score measures the similarity of the neighbourhood of the tomogram pixel to the used template.
This similarity is measured exclusively inside a mask.

Once this cross-correlation map has been computed, local maxima can be identified to select the positions and orientations of the found particles in the tomogram.

In summary, ''Dynamo'' allows users to compute these cross-correlation map in multiple ways:
* Basic template matching: this is the simplest way to use template matching in ''Dynamo''
* Template matching by GUI: ''Dynamo'' provides a GUI to use template matching in a interactive way.
* Model-aware template matching: this mode allows users to improve the speed and quality of the procedure by including additional prior informations on the geometry (i.e. model) of the sample to guide template matching.
* On-the-fly template matching: in this mode, a tilt series is given as input instead of a tomogram and sections are reconstructed on-the-fly.
* Single chunk modus template matching: this model allow for the parallel inspection of single specific region of the tomogram (the so-called single chunk). Ideal for fine and exhaustive angular searches in restricted regions of the sample.

== Basic template matching==

Basic (non-model-aware) template matching is the simplest way to use template match in ''Dynamo''. In this mode, the template will be cross-correlated against a tomogram with the same set of rotation everywhere. The tomogram may be split into chunks, but this is done only so as not to crowd the memory during computation.

A full walkthrough of [[Walkthrough for template matching | template matching in this mode]] is available.

== GUI-based template matching==

Template matching can be done in ''Dynamo'' directly from the <tt>dtmslice</tt> GUI with a tomogram as input. It has a tab called Template Matching in the top bar of the GUI. It is through this tab that general attributes, parameters and region of interest for template matching processes can be manipulated. More information on how to use the GUI can be found in [[Walkthrough for GUI-based template matching | the GUI walkthrough]]. It is also possible to add custom functionalities to the GUI as described in the [[Programmatic GUI customization for template matching | corresponding tutorial]].

== Model-aware template matching==

Model-aware template matching is meant as an extension of the normal template matching algorithm in ''Dynamo''. As such, all basic commands described in the previous sections are valid in this mode as well.

The main change introduced in model-aware template matching is that the partition of the tomogram in regions of interest (chunks) is meant to be meaningful from the point of view of the tomogram models. This allows for the reduction of needed computation by restricting the angular combinations of the template to be scanned. The description of which chunks are created and their corresponding restricted angular combinations will be called a tessellation policy.

A walkthrough on [[Walkthrough for model-aware template matching | model-aware template matching]] is available. Additionally, here template mathcing using on-the-fly reconstructions and single-chunk modus are also described.