Walkthrough on filament models - Revision history

Raffaele Coray at 12:42, 2 December 2024

2024-12-02T12:42:35Z

Stefano Scaramuzza at 14:52, 12 August 2021

2021-08-12T14:52:18Z

Stefano Scaramuzza: /* Generate subtomogram coordinates */

2021-08-12T13:45:19Z

Generate subtomogram coordinates

Stefano Scaramuzza at 13:31, 12 August 2021

2021-08-12T13:31:23Z

Stefano Scaramuzza: /* Manual annotation */

2021-08-12T13:19:41Z

Manual annotation

Stefano Scaramuzza at 14:14, 11 August 2021

2021-08-11T14:14:52Z

Stefano Scaramuzza at 14:02, 11 August 2021

2021-08-11T14:02:27Z

Stefano Scaramuzza at 13:59, 11 August 2021

2021-08-11T13:59:53Z

Stefano Scaramuzza at 13:58, 11 August 2021

2021-08-11T13:58:04Z

Stefano Scaramuzza: /* Extracting tomograms */

2021-08-11T13:44:57Z

Extracting tomograms

← Older revision		Revision as of 12:42, 2 December 2024
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		+	[[Category:Walkthroughs]]
		+
	This walkthrough is a step-by-step guide that teaches how to extract subtomograms from filament-like structures using the ''Dynamo'' filament models.		This walkthrough is a step-by-step guide that teaches how to extract subtomograms from filament-like structures using the ''Dynamo'' filament models.

@@ Line 122: / Line 122: @@
 [[ File:filament_step_25.png |thumb|center| 500px|]]
-For the z and x axis you should see results similar to the following. These are 2D representations of the actually cropped 3D subtomograms:
+For the z and x axis you should see results similar to the following. These are 2D representations (projections) of the actually cropped 3D subtomograms:
 [[ File:filament_step_26.png |thumb|center| 700px|]]

@@ Line 80: / Line 80: @@
 [[ File:filament_step_17.png |thumb|center| 700px|]]
-You get a new window with the model workflow. It has three large buttons (and input parameters below) that are executed sequentially starting from top. Click on ''create a smooth backbone'':
+You get a new window with the model workflow. It has three large buttons (and corresponding input parameters below) that are executed sequentially starting from top. Click on ''create a smooth backbone'':
 [[ File:filament_step_18.png |thumb|center| 500px|]]

@@ Line 76: / Line 76: @@
 = Generate subtomogram coordinates =
-Using the clicked model we can now extract subvolumes. To do that, we first processes the clicked model points using the ''model workflow'' to generate a user specific cropping geometry. Open the workflow:
+Using the clicked model we can now define the coordinates where the subvolumes will be extracted. To do that, we first processes the clicked model points using the ''model workflow'' to generate a user specific cropping geometry. Open the workflow:
 [[ File:filament_step_17.png |thumb|center| 700px|]]

@@ Line 38: / Line 38: @@
 [[ File:filament_step_8.png |thumb|center| 700px|]]
-Annotations are done within a so called ''model''. We open a new model as follows:
+Annotations are done within a so called ''model''. We open a new model of type ''filament'' as follows:
 [[ File:filament_step_9.png |thumb|center| 700px|]]

@@ Line 8: / Line 8: @@
 [[ File:filament_step_1.png |thumb|center| 700px|]]
-The catalogue manager will create a catalogue to archive the created tomogram and also the models that we will create around it. A new tomogram entry appears in the catalogue manager. Any further annotations (models) to the tomograms will be linked to this entry. Select the entry and open it:
+A new tomogram entry appears in the catalogue manager. Any further annotations (models) to the tomogram will be linked to this entry. Select the entry and open it:
 [[ File:filament_step_2.png |thumb|center| 700px|]]
-A tomogram viewer opens. 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).
+A tomogram viewer opens. 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:filament_step_3.png |thumb|center| 700px|]]
@@ Line 18: / Line 18: @@
 = Manual annotation =
-To be able to annotate a filament of interest, we first create an alternative view by using ''anchor points''. We start by marking the beginning of a filament. Move the slice up to a high z height. Place the mouse in the center of a filament and press the key [1] on the keyboard to place an anchor in the beginning of the filament.
+To be able to later annotate a filament of interest, we first create an alternative view by using the ''anchor points''. We start by marking the beginning of a filament. Move the slice up to a high z height. Place the mouse in the center of a filament and press the key [1] on the keyboard to place an anchor in the beginning of the filament. Note: to correct the anchor point just click the [1] key again.
 [[ File:filament_step_4.png |thumb|center| 700px|]]
@@ Line 46: / Line 46: @@
 [[ File:filament_step_10.png |thumb|center| 700px|]]
-To add annotation points to the model, place the mouse on the filament and press the key [c]. Use the right-click to delete points if needed. Note: A known bug may cause the clicked points to be generated slightly displaced from the mouse cursor. Maximize the window of the viewer to get rid of this effect. Generate about 10 points:
+To add annotation points to the model, place the mouse on the filament and press the key [c]. Use the right-click to delete points if needed. Note: A known bug may cause the clicked points to be generated slightly displaced from the mouse cursor. Maximize the window of the tomogram viewer to get rid of this effect. Generate about 10 points:
 [[ File:filament_step_11.png |thumb|center| 700px|]]
-We show you an alternative way to click the points on the filament. To demonstrate this, we first delete the current points as shown below):
+We show you an alternative way to click the points on the filament. To demonstrate this, we first delete the current points as shown below:
 [[ File:filament_step_12.png |thumb|center| 700px|]]
@@ Line 92: / Line 92: @@
 [[ File:filament_step_20.png |thumb|center| 700px|]]
-This looks good. We now create coordinates along this interpolation (backbone) which will be used as centers for the subtomogram extraction (cropping). Click on ''create final positions and angles for particle cropping''. Ignore the angles, as they are not part of this model. Visualize the crop positions.
+This looks good. We now create coordinates along this interpolation (backbone) which will be used as centers for the subtomogram extraction (cropping). Click on ''create final positions and angles for particle cropping''. Ignore the angles, as they are not part of this model. Visualize the crop positions:
 [[ File:filament_step_21.png |thumb|center| 700px|]]
-You can see that these are too many crop points. Adjust the spacing between the cropping points by changing the parameter ''subunits dz'' from 2 to 20. Click again ''create final positions and angles for particle cropping'' to update the information and visualize the new crop points:
+You can see that these are too many crop points. Adjust the spacing between the cropping points by changing the parameter ''subunits dz'' from 2 to 20 (see orange box). Click again ''create final positions and angles for particle cropping'' to update the information and visualize the new crop points:
 [[ File:filament_step_22.png |thumb|center| 700px|]]
-This looks much better and we can move to the subtomogram extraction.
+This looks much better. Save the model by clicking on '' save resulting model into catalogue'' and we can move to the subtomogram extraction.
-= Extract subtomograms (cropping) =
+= Extract subtomograms =
 In this final step we extract subvolumes at the coordinates defined before. First, open the partcile extraction GUI:
@@ Line 108: / Line 108: @@
 [[ File:filament_step_23.png |thumb|center| 700px|]]
-Set the sidelength to 64 and click on ''start cropping'':
+Set the sidelength to 64 and click on ''start cropping'' (orange box):
 [[ File:filament_step_24.png |thumb|center| 500px|]]
-To see the results, click on ''ddbrowse'':
+To see the results, click on ''ddbrowse'' (orange box):
@@ Line 118: / Line 118: @@
-In the new window activate the table, select the axis and click on show:
+In the new window activate the table, select the axis and click on show (orange boxes):
 [[ File:filament_step_25.png |thumb|center| 500px|]]
-For the z and x axis you should see results similar to the following. These are 2D representations of the actually cropped 3D subtomograms.
+For the z and x axis you should see results similar to the following. These are 2D representations of the actually cropped 3D subtomograms:
 [[ File:filament_step_26.png |thumb|center| 700px|]]

@@ Line 64: / Line 64: @@
 You get a new window with the view of the orthogonal slices through the filament:
-[[ File:filament_step_14.png |thumb|center| 700px|]]
+[[ File:filament_step_14.png |thumb|center| 500px|]]
 Same as before, using the [c] key, add model points at the center of the tube filament:
-[[ File:filament_step_15.png |thumb|center| 700px|]]
+[[ File:filament_step_15.png |thumb|center| 500px|]]
 When done, close the window and you should see your clicked points in the main view:
@@ Line 82: / Line 82: @@
 You get a new window with the model workflow. It has three large buttons (and input parameters below) that are executed sequentially starting from top. Click on ''create a smooth backbone'':
-[[ File:filament_step_18.png |thumb|center| 700px|]]
+[[ File:filament_step_18.png |thumb|center| 500px|]]
 This creates an interpolation through the points in the model. Visualize it by left-clicking on ''view'':
@@ Line 110: / Line 110: @@
 Set the sidelength to 64 and click on ''start cropping'':
-[[ File:filament_step_24.png |thumb|center| 700px|]]
+[[ File:filament_step_24.png |thumb|center| 500px|]]
 To see the results, click on ''ddbrowse'':
-[[ File:filament_step_245.png |thumb|center| 700px|]]
+[[ File:filament_step_245.png |thumb|center| 500px|]]
 In the new window activate the table, select the axis and click on show:
-[[ File:filament_step_25.png |thumb|center| 700px|]]
+[[ File:filament_step_25.png |thumb|center| 500px|]]
 For the z and x axis you should see results similar to the following. These are 2D representations of the actually cropped 3D subtomograms.
 [[ File:filament_step_26.png |thumb|center| 700px|]]

@@ Line 74: / Line 74: @@
 [[ File:filament_step_16.png |thumb|center| 700px|]]
-= Extracting tomograms =
+= Process model =
 Using the clicked model we can now extract subvolumes. To do that, we first processes the clicked model points using the ''model workflow'' to generate a user specific cropping geometry. Open the workflow: