Montage viewer for membrane picking

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This walkthorugh is an example of use of the montage viewer for membrane models initiated through the tomogram browser dtmslice. We use a tomogram that contains several liposomes. Liposomes can normally be modelled as vesicle models, if they are approximately spherical. If they depart too much from sphericity, you can use membrane models, as done in this walkthrough.


dtmslice view of a tomogram with several liposomes

Starting the Montage Viewer

From the full scene

The Montage viewer can be opened from the menu options in dtmslice. This is the path that we will follow in this walkthrough.

Opening the Montage viewer for the full scene

From a region

Remember that you can create a montage for a region in your tomogram. You just need to create a box in dtmslice (key [v]) and then secondary-clik on it. Among different options, you'll find an entry to open a montage viewer.

Options

With the default options, the montage shows at each z level the full projection of the intensity between a level and the next one.

Montage view of the full dtmslice scene

Once you open a Montage viewer, the distance between z-levels is fixed. If you want to vary it, you will need to change the options an then create a new montage.

Model system

The model pool currently accessed by dtmslice is also available through the Montage Viewer. Let us define a membrane model.

Creation of a membrane model (called Surface in this menu)

Local zoom and drag

We make certain that the clicking option is active. This connects the tools for entering points into the model and to change the viewed scene in the montage (zoom and drag options).

The clicking status must be active in order to proceed with the clicking

With the full view, can inspect the scene and locate areas of interest.

We select one liposome for track across levels

After selecting the region of interest we can zoom on it, possibly also dragging the scene. Make certain that you are working on the currently active z-level, which appears labelled in red.

  • Zoom in and out with the mouse wheel.
  • Drag the scene by moving the mouse while the secondary button is pressed
    • While the scene is being dragged, the cursor should appear as a hand.

Remember than the clicking tool must be activated in otder to have these controls operative:

Zoom in a region of interest.

Adding points

After activating the clicker, you can (main) click on a z-level of the montage. Each click creates a point.

Membrane points clicked on the selected z level

Other controls:

  • [d] : deletes the point in the same z-level that is closed to the current position of the cursor.
  • [m] : moves the closest point in the same-ze level to the current position of the cursor.
  • [backspace] : deletes the last added point.

The points created by clicking in the Montage Viewer will appear in dtmslice, and the other way round, as both viewers are connected to the same model pool.

The scene in dtmslice updates as we make annotations in the Montage Viewer

Remember that you need to indicate an interior point. This is available through [shift+c].

[Shift+C] creates a center point inside the membrane level

Automatic detection of points

Once you have clicked points on a level, you can try and check if the automatic tracker can locate them in the next one. To do so, activate the next slice (i.e., secondary click it, so that its frame becomes red), and press o. You can edit the points with d to delete the closest point, m to move the closest point to the position currently under the cursor, or l to delete all the points detected in the slice... in such a case, you probably want to check the tracking parameters before using o again!

Addition of further models

After visiting all the the zlevels where the membrane is defined, we can use the option for zooming out the view:

Icon in the toolbar for full zoom out
Full view

In this view, we can locate a new area of interest, create a new model and zoom again into the new area of interest. Once you repeat this operation for all your liposomes (one model for liposome), do not forget to save your work into the catalogue.

Full view

Once all the models are in the catalogue, you can process all of them in one shot from the command line using a loop on a model array, or by the creation of a model workflow thorugh the GUI.