Walkthrough on 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.
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:
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 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).
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  on the keyboard to place an anchor in the beginning of the filament.
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  on the keyboard to place the anchor in the end of the filament.
Finally, a third anchor point (key ) is placed to define the width of the alternative view that we are creating:
Click on set plane (orange box) to define a plane along the anchor points:
Use the anchor for plane selection control (orange box) to activate and rotate the viewing plane around the filament:
Annotations are done within a so called model. We open a new model as follows:
Click and drag while holding the control key to rotate the view of the tomogram, if necessary: