Difference between revisions of "Montage viewer for membrane picking"
Line 31: | Line 31: | ||
[[File:MontageMembranesLocateFirstGlobal.png|thumb|center|500px| We select one liposome for track across levels ]] | [[File:MontageMembranesLocateFirstGlobal.png|thumb|center|500px| We select one liposome for track across levels ]] | ||
− | After selecting the region of interest we can zoom on it, possibly also dragging the scene. | + | 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. | * Zoom in and out with the mouse wheel. | ||
* Drag the scene by moving the mouse while the secondary button is pressed | * 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. | ** 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: | |
[[File:MontageMembranesLocateFirstLocal.png|thumb|center|500px| Zoom in a region of interest. ]] | [[File:MontageMembranesLocateFirstLocal.png|thumb|center|500px| Zoom in a region of interest. ]] | ||
− | |||
==Adding points== | ==Adding points== | ||
Line 43: | Line 42: | ||
[[File:MontageMembranesZoomedFirstSelection.png|thumb|center|500px| Membrane points clicked on the selected ''z'' level ]] | [[File:MontageMembranesZoomedFirstSelection.png|thumb|center|500px| 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 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]]. | ||
Line 49: | Line 53: | ||
[[File:MontageMembranesCenter.png|thumb|center|500px| [Shift+C] creates a center point inside the membrane level ]] | [[File:MontageMembranesCenter.png|thumb|center|500px| [Shift+C] creates a center point inside the membrane level ]] | ||
+ | |||
+ | ==Automatic detection of points== | ||
After visiting all the the ''z''levels where the membrane is defined, we can use the option for zooming out the view: | After visiting all the the ''z''levels where the membrane is defined, we can use the option for zooming out the view: |
Revision as of 09:53, 28 February 2017
Here an example of use of the montage viewer for membrane models through the tomogram browser dtmslice is presented.
Contents
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.
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.
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.
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).
With the full view, can inspect the scene and locate areas of interest.
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:
Adding points
After activating the clicker, you can (main) click on a z-level of the montage. Each click creates a point.
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.
Automatic detection of points
After visiting all the the zlevels where the membrane is defined, we can use the option for zooming out the 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