Walkthrough on filament models

From Dynamo
Jump to navigation Jump to search

This walkthrough is a step-by-step guide that teaches how to extract subtomograms from filament-like structures using the Dynamo filament models.


We are going to demonstrate the basic ideas and tools on a synthetic dataset. This data is already available in the catalogue manager. It can be accessed by first opening the catalogue manager using the command:


After the catalogue manager opens, we create the synthetic tomogram that includes tubular looking objects (filaments) in the following way:

Filament step 1.png

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:

Filament step 2.png

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).

Filament step 3.png

Annotation using plane through filament

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.

Filament step 4.png

To mark the end of the filament, move to a low z-height. Place the mouse in the center of the same filament and press the key [2] on the keyboard to place the anchor in the end of the filament.

Filament step 5.png

Finally, a third anchor point (key [3]) is placed to define the width of the alternative view that we are creating:

Filament step 6.png

Click on set plane (orange box) to define a plane along the anchor points:

Filament step 7.png

Use the anchor for plane selection control (orange box) to activate and rotate the viewing plane around the filament:

Filament step 8.png

Annotations are done within a so called model. We open a new model as follows:

Filament step 9.png

Click and drag while holding the control key to rotate the view of the tomogram, if necessary:

Filament step 10.png
Filament step 11.png
Filament step 12.png
Filament step 13.png
Filament step 14.png
Filament step 15.png
Filament step 16.png
Filament step 17.png
Filament step 18.png
Filament step 19.png
Filament step 20.png
Filament step 21.png
Filament step 22.png
Filament step 23.png
Filament step 24.png
Filament step 25.png
Filament step 26.png