EMBO workshop 2019 - Revision history

Raffaele Coray at 13:19, 2 December 2024

2024-12-02T13:19:57Z

Daniel Castaño: /* In the room */

2019-09-06T09:26:40Z

In the room

Daniel Castaño: /* Program */

2019-09-06T09:25:14Z

Program

Daniel Castaño: /* Program */

2019-09-06T09:24:04Z

Program

Daniel Castaño: /* Program */

2019-09-06T09:23:28Z

Program

Daniel Castaño at 18:05, 2 September 2019

2019-09-02T18:05:29Z

Daniel Castaño: /* Program */

2019-09-02T16:17:06Z

Program

Daniel Castaño: Created page with "This page describes the contents of the practical hands-on sessions for tomography through ''Dynamo'' at the Birkbeck College during the EMBO School for Image processing in C..."

2019-09-02T16:15:24Z

Created page with "This page describes the contents of the practical hands-on sessions for tomography through ''Dynamo'' at the Birkbeck College during the EMBO School for Image processing in C..."

New page

This page describes the contents of the practical hands-on sessions for tomography through ''Dynamo'' at the Birkbeck College during the EMBO School for Image processing in Cryo Electron Microscopy (September 2019).

== Installing Dynamo on your laptops==

Workstations are provided by the organization. These instructions are intended for those students that want to install their own ''Dynamo''version in their laptops.
=== Donwload ===
The Dynamo versions on the three platforms can be obtained in the [[Downloads]] page. Please use the indications [[Installation|here]] to install it in your laptop.

=== Starting a ''Dynamo'' session ===

You need to run an activation shell (see below for information on how to do it on each platform) that can be used to run [[alignment project]]s or to initiate an interactive session using the ''Dynamo'' [[Dynamo console|console]]. For this, you can just type:

<tt>dynamo </tt>

on a ''Dynamo''-activated system shell and be patient: the first time a shell initiates a ''Dynamo'' process, it can takes several minutes. New invocations to the MCR libraries will be much faster, and commands inside the opened ''Dynamo'' session will run immediately.

==== Linux ====
On a Linux terminal, type:

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

==== Mac ====
On a Mac termina, type:

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

==== Windows ====
In a DOS terminal write:

<tt>C:\ <path to the Dynamo installation>\dynamo_activate_windows.bat </tt>

then open a ''Dynamo'' terminal by typing in the DOS

<tt>dynamo</tt>

If it doesn't work, type:

<nowiki> set PATH=%PATH%;%MCR_ROOT%\runtime\win64</nowiki>

and then '''again'''

<tt>C:\ <path to the Dynamo installation>\dynamo_activate_windows.bat </tt>

=== Running a ''Dynamo'' project in the standalone ===

When working with the standalone, it is '''not''' convenient to run projects directly pressing [Run] in the <tt>dcp</tt> GUI. It is a better approach to run the project in a different process.

* Open a new system shell (DOS shell in windows).
* Activate ''Dynamo'' in that shell. i.e.,
**Linux: <tt> source <DYNAMO_ROOT>/dynamo_activate_linux_with_shippedMRC.sh</tt>
* Do '''NOT''' start a ''Dynamo'' session, i.e., do not type <tt>dynamo</tt> in the shell.
* In the terminal, type the name of the execution script.
** Linux/Mac: <tt>./ptest.exe</tt>
** Windows: <tt>./ptest.bat</tt>

== Program ==

Before the hands-on session, we will go to [http://{{SERVERNAME}}/w/doc/presentations/oxford2017.pptx this presentation] for a general introduction of the ''Dynamo''software.

===General Introduction===

[[File:orthoPickMain.png|thumb|upright|250px| Clicking particles in the [[Starters guide ]] ]]

Guided presentation:

* [http://{{SERVERNAME}}/w/doc/misc/conceptsSheet.pdf Basic ''Dynamo'' jargon]

* [http://{{SERVERNAME}}/w/doc/misc/introductionTablesAndData.pdf tutorial on] basic elements: help, data and metadata formats.
* [http://{{SERVERNAME}}/w/doc/misc/introductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.

Working on your own:

* Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project.
* [[Advanced starters guide]] on a real tomogram. (~2 hours)
* Further work:
** {{pdftutorial|commandline|tutorial}} on the use command line operations for general purposes.
** {{pdftutorial|command_line_projects|tutorial}} on the use of the command line to manage projects.

===Geometric modeling===

[[File:membraneExampleCommandLineCroppingPositionsOnMesh.png|thumb|upright|200px| Geometric modeling for [http://{{SERVERNAME}}/w/doc/misc/modelMembrane.pdf surfaces] and [http://{{SERVERNAME}}/w/doc/misc/modelFilament.pdf filaments ]]]
Short guided presentation:

* [http://{{SERVERNAME}}/w/doc/misc/modelMembrane.pdf tutorial on] membrane modeling with <tt> dmslice </tt>
* Filament models with <tt>dtmslice</tt>
** [http://{{SERVERNAME}}/w/doc/misc/modelFilament.pdf tutorial ]
** [[Filament model | walkthrough]]
* Reusing model workflows ([[Walkthrough model worfklow reuse | walkthrough]])
* Further work: catalogue

Working on your own:
[[ File:FhvTmsliceUpdates.png |thumb|right|400px| [[Advanced starters guide | FHV tutorial on isolated membrane events (advanced starters guide)]] ]]
[[ File:HivBox.png|thumb|right|200px| [[Walkthrough for lattices on vesicles | HIV tutorial on densely packed slices]] ]]

* In the afternoon, after the research talks, we will focus on the extraction of particles [[Walkthrough for lattices on vesicles| from densely packed spherical geometry on HIV viral capsides]] (~1 hour)

===Template matching===

Working on your own:

* We will follow this [[Walkthrough for template matching | walkthrough]] for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)

[[ File:TemplateMatchingIntoCatalogueZoom.png |thumb|right|400px | [[Walkthrough for template matching | Template matching]] ]]

=== Adaptive bandpass filtering ===

Working on your own:
* We will follow this [[Walkthrough on adaptive bandpass filtering| walkthrough]] to create a small synthetic data set that illustrates the principles of [[adaptive bandpass filtering]], a way of conducting a ''golden standard'' alignment procedure . (~40 mins)

===Classification===

Short guided presentation:

* PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.] <br /> advanced subboxing tutorial: combining with PCA and MRA {{pdftutorial|subboxing_multireference_PCA|tutorial}}
* Multirefererence Analysis <br /> [http://{{SERVERNAME}}/w/doc/misc/workshopMRAintro.pptx Basic concepts.] <br />[[Walkthrough basic multireference|walkthrough]] (~10 min)
* Further work
** Commandline operations with PCA

=== Creation of 3D scenes ===

Working on your own:

* [[Walkthrough on creation of 3d scenes | Walkthrough on the FHV data set]] (~1hour)

[[ File:Fhv3dAntialiasing.png |thumb|right| 400px| [[Walkthrough on creation of 3d scenes | Scene creation]].]]

Further support material.

* [[Walkthrough on placement of averages on table positions | Walkthrough ]]on depiction and manipulation of triangulations (synthetic data).

===Additional tools===
Wednesday afternoon session.
* Subboxing
*: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx extraction of vertices from icosahedral viruses]
*: Basic subboxing ({{pdftutorial|subboxing_symmetry|tutorial}}l)
*: advanced subboxing tutorial: combining with MRA {{pdftutorial|subboxing_multireference_PCA|tutorial}}
*: suggested data set: prd1 Capsides (in the folder of isolated particles)
* Manual alignment.
* [[Workshop exercises| Exercises]]

== Data sets ==

The data sets will be updated here.

== Instructors ==

* Daniel Castaño-Díez, University of Basel.
* Giulia Zanetti, Birkbeck College.

← Older revision		Revision as of 13:19, 2 December 2024
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		+	[[Category:WalkthroughsSpecific]]
		+
	This page describes the contents of the practical hands-on sessions for tomography through ''Dynamo'' at the Birkbeck College during the EMBO School for Image processing in Cryo Electron Microscopy (September 2019).		This page describes the contents of the practical hands-on sessions for tomography through ''Dynamo'' at the Birkbeck College during the EMBO School for Image processing in Cryo Electron Microscopy (September 2019).

@@ Line 68: / Line 68: @@
 * [http://{{SERVERNAME}}/w/doc/misc/introductionTablesAndData.pdf tutorial on] basic elements: help, data and metadata formats.
 * [http://{{SERVERNAME}}/w/doc/misc/introductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
-* [[ File:FhvTmsliceUpdates.png |thumb|right|400px|   [[Practicals Birkbeck 2019 | FHV tutorial on isolated membrane events  (Practicals Birkbeck 2019)]]  ]]
+* [[File:FhvTmsliceUpdates.png |thumb|right|400px|   [[Practicals Birkbeck 2019 | FHV tutorial on isolated membrane events  (Practicals Birkbeck 2019)]]  ]]
 ==== Working on your own ====

@@ Line 68: / Line 68: @@
 * [http://{{SERVERNAME}}/w/doc/misc/introductionTablesAndData.pdf tutorial on] basic elements: help, data and metadata formats.
 * [http://{{SERVERNAME}}/w/doc/misc/introductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
-−
+\
-* [[ File:FhvTmsliceUpdates.png |thumb|right|400px|   [[Advanced starters guide | FHV tutorial on isolated membrane events  (advanced starters guide)]]  ]]
+* [[ File:FhvTmsliceUpdates.png |thumb|right|400px|   [[Practicals Birkbeck 2019 | FHV tutorial on isolated membrane events  (Practicals Birkbeck 2019)]]  ]]
 ==== Working on your own ====:

@@ Line 88: / Line 88: @@
 * Reusing model workflows ([[Walkthrough model worfklow reuse | walkthrough]])
 * Further work: catalogue
 [[  File:HivBox.png|thumb|right|200px|   [[Walkthrough for lattices on vesicles | HIV tutorial  on densely packed slices]]  ]]
@@ Line 96: / Line 94: @@
 | [[File:FhvTmsliceUpdates.png|thumb|right|200px| lattice directions ]]
 |} -->
-* In the afternoon, after the research talks, we will focus on the extraction of particles  [[Walkthrough for lattices on vesicles| from densely packed spherical geometry  on HIV viral capsides]]  (~1 hour)
+*   [[Walkthrough for lattices on vesicles| from densely packed spherical geometry  on HIV viral capsides]]  (~1 hour)
 ===Template matching===

@@ Line 59: / Line 59: @@
 Before the hands-on session, we will go to  [http://{{SERVERNAME}}/w/doc/presentations/oxford2017.pptx this presentation] for a general introduction of the ''Dynamo''software.
-===General Introduction===
+===In the room===
 [[File:orthoPickMain.png|thumb|upright|250px|  Clicking particles in the [[Starters guide ]] ]]
@@ Line 66: / Line 66: @@
 * [http://{{SERVERNAME}}/w/doc/misc/conceptsSheet.pdf Basic ''Dynamo'' jargon]
 * [http://{{SERVERNAME}}/w/doc/misc/introductionTablesAndData.pdf tutorial on] basic elements: help, data and metadata formats.
 * [http://{{SERVERNAME}}/w/doc/misc/introductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
-Working on your own:
+* [[ File:FhvTmsliceUpdates.png |thumb|right|400px|   [[Advanced starters guide | FHV tutorial on isolated membrane events  (advanced starters guide)]]  ]]
 * Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project.
@@ Line 78: / Line 79: @@
 ** {{pdftutorial|command_line_projects|tutorial}} on the use of the command line to manage projects.
-===Geometric modeling===
+==== Geometric modeling ====
 [[File:membraneExampleCommandLineCroppingPositionsOnMesh.png|thumb|upright|200px| Geometric modeling for [http://{{SERVERNAME}}/w/doc/misc/modelMembrane.pdf surfaces] and [http://{{SERVERNAME}}/w/doc/misc/modelFilament.pdf filaments ]]]
@@ Line 90: / Line 91: @@
 * Further work: catalogue
-Working on your own:
-[[ File:FhvTmsliceUpdates.png |thumb|right|400px|   [[Advanced starters guide | FHV tutorial on isolated membrane events  (advanced starters guide)]]  ]]
 [[  File:HivBox.png|thumb|right|200px|   [[Walkthrough for lattices on vesicles | HIV tutorial  on densely packed slices]]  ]]
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