Walkthrough for model-aware template matching - Revision history

Raffaele Coray: /* Getting the data */

2024-12-03T12:37:34Z

Getting the data

Raffaele Coray: /* Getting the data */

2024-12-03T12:37:29Z

Getting the data

Raffaele Coray: /* Getting the data */

2024-11-29T16:02:06Z

Getting the data

Raffaele Coray: /* Creating an oblique chunk */

2024-11-29T15:33:30Z

Creating an oblique chunk

Raffaele Coray: /* Running the project */

2024-11-29T15:31:24Z

Running the project

Raffaele Coray: /* Manual tesselation */

2024-11-29T15:29:55Z

Manual tesselation

Raffaele Coray: /* Non-model-aware template matching */

2024-11-29T15:28:33Z

Non-model-aware template matching

Raffaele Coray: /* Non-model-aware template matching */

2024-11-29T15:28:00Z

Non-model-aware template matching

Raffaele Coray: /* Getting the data */

2024-11-29T15:12:59Z

Getting the data

Raffaele Coray: /* Getting the data */

2024-11-29T15:12:30Z

Getting the data

@@ Line 25: / Line 25: @@
 <!--SORRY, THE TOMOGRAM AND TEMPLATE ARE CURRENLTY STILL UNDER EMBARGO. PLEASE CONTACT US TO ACCESS THE DATA.-->
-{{Template:Template:DownloadLinkTemplateRetromer}}
+{{Template:DownloadLinkTemplateRetromer}}
 It consists in: a tomogram tomogram100_sm.mrc, a template retromer_template.mrc, a mask retromer_mask.mrc, a model mfilamentWithTorsion.omd and a function file volume2cylindercoordinates.m

@@ Line 24: / Line 24: @@
 Currently the data necessary to tun this walkthrough can be downloaded using the link:
-SORRY, THE TOMOGRAM AND TEMPLATE ARE CURRENLTY STILL UNDER EMBARGO. PLEASE CONTACT US TO ACCESS THE DATA.
+<!--SORRY, THE TOMOGRAM AND TEMPLATE ARE CURRENLTY STILL UNDER EMBARGO. PLEASE CONTACT US TO ACCESS THE DATA.-->
+{{Template:Template:DownloadLinkTemplateRetromer}}
 It consists in: a tomogram tomogram100_sm.mrc, a template retromer_template.mrc, a mask retromer_mask.mrc, a model mfilamentWithTorsion.omd and a function file volume2cylindercoordinates.m

← Older revision		Revision as of 16:02, 29 November 2024
Line 24:		Line 24:
	Currently the data necessary to tun this walkthrough can be downloaded using the link:		Currently the data necessary to tun this walkthrough can be downloaded using the link:

−	SORRY, THE TOMOGRAM AND TEMPLATE ARE CURRENLTY STILL UNDER EMBARGO. ~~FEEL FREE TO~~ CONTACT US TO ACCESS THE DATA.	+	SORRY, THE TOMOGRAM AND TEMPLATE ARE CURRENLTY STILL UNDER EMBARGO. PLEASE CONTACT US TO ACCESS THE DATA.

@@ Line 421: / Line 421: @@
   <tt>dtmslice('tomogram100_sm.mrc');</tt>
-The goal is to create an oblique chunk in the GUI that contains most of the tubulation. An optimal chunk should follow the direction of the tubulation while being wide enough to contains the full coat and extra margins of at least the half-size of the template. To do this the basic functionalities of chunk manipulations are needed. These are: creating a chunk, resizing a chunk, moving a chunk and rotating a chunk.<br><br>
+The goal is to create an oblique chunk in the GUI that contains most of the tubulation. An optimal chunk should follow the direction of the tubulation while being wide enough to contains the full coat and extra margins of at least the half-size of the template. To do this the basic functionalities of chunk manipulations are needed. These are: creating a chunk, resizing a chunk, moving a chunk and rotating a chunk. These utilities are described in more depth in their [[Walkthrough for GUI-based template matching | own specific tutorial]].<br><br>
 Create a chunk by pointing the cursor on the tomogram and pressing the "B" key.

@@ Line 204: / Line 204: @@
 Note the flag 'fineAssembly'. This flag is used to request that the assembly of the cross-correlation chunks be done taking into account chunk overlap. AS in this cases overlap is present, the flag should be set to true.<br>
-The general syntax of the <tt>dynamo_match</tt> command and its main inputs is described in TUTORILA BASIC. In summmary, TM will be run on a tesselation with four chunk with sizes [180,300,180] with pre-orientation along the tubulation and a restricted cone of 60 degrees but full azimuthal range, both sampled each 5 degrees. The computation is requested to run on a single GPU, cpp accelerated rotations and finally assembled taking into account overlap.<br>
+The general syntax of the <tt>dynamo_match</tt> command and its main inputs is described in the [[Walkthrough for template matching | basic TM tutorial]]. In summary, TM will be run on a tessellation with four chunk with sizes [180,300,180] with pre-orientation along the tubulation and a restricted cone of 60 degrees but full azimuthal range, both sampled each 5 degrees. The computation is requested to run on a single GPU, cpp accelerated rotations and finally assembled taking into account overlap.<br>
 This command required ~460 seconds of GPU computing time using a single NVIDIA GeForce RTX 4090.
@@ Line 212: / Line 212: @@
 [[ File:folder_structure_TM.png |thumb|center|500px| Folder structure of a completed model-aware TM project]]
-The project contain the assembled tomogram, cross-correlation map, the angular maps and a subfolder containing the specific results for each chunk in the tesselation.<br><br>
+The project contain the assembled tomogram, cross-correlation map, the angular maps and a subfolder containing the specific results for each chunk in the tessellation.<br><br>
 Some common functionalities are the loading of a existing TM project with:

@@ Line 165: / Line 165: @@
 [[ File:semi_automatic_tesselation_Fil.png |thumb|center|500px| Representation of the automatic tesselation with non-cubic chunks]]
-=== Manual tesselation ===
+=== Manual tessellation ===
-Tesselation can be created, loaded, modified and saved using the GUI functionalities.<br>
+Tessellations can be created, loaded, modified and saved using the GUI functionalities.<br>
-These utilities are described in their own specific tutorial.
+These utilities are described in their [[Walkthrough for GUI-based template matching | own specific tutorial]].
 == Running a model-aware TM ==

@@ Line 11: / Line 11: @@
 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 template matching in this mode [[Walkthrough for template matching | template matching in this mode]] is available.
+A full walkthrough of [[Walkthrough for template matching | template matching in this mode]] is available.
 == Model-aware template matching ==

← Older revision		Revision as of 15:12, 29 November 2024
Line 24:		Line 24:
	Currently the data necessary to tun this walkthrough can be downloaded using the link:		Currently the data necessary to tun this walkthrough can be downloaded using the link:

−	SORRY, THE TOMOGRAM AND TEMPLATE ARE CURRENLTY STILL UNDER EMBARGO. FEEL FREE TO CONTACT US.	+	SORRY, THE TOMOGRAM AND TEMPLATE ARE CURRENLTY STILL UNDER EMBARGO. FEEL FREE TO CONTACT US TO ACCESS THE DATA.

← Older revision		Revision as of 15:12, 29 November 2024
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	=== Getting the data ===		=== Getting the data ===

−	Currently the data necessary to tun this walkthrough can be ~~donwloaded~~ using the link:	+	Currently the data necessary to tun this walkthrough can be downloaded using the link:
−
−	~~SORRY, THE TOMOGRAM AND TEMPLATE ARE CURRENLTY STILL UNDER EMBARGO.~~

		+	SORRY, THE TOMOGRAM AND TEMPLATE ARE CURRENLTY STILL UNDER EMBARGO. FEEL FREE TO CONTACT US.