Morphology Editing
In certain cases, in particular, when a morphology file is downloaded from an open database, this morphology could be broken, i.e. self-intersecting branches or overlapping samples on any of its arbors. For such reasons, we have added a little utility that allows the user to sketch the morphology skeleton and edit the skeleton samples by moving the samples from one point to another. Then, the user can either export this modified morphology skeleton or to use it for other toolboxes in NeuroMorphoVis.
When you toggle (or click on) the Morphology Editing tab highlighted above, the following panel, or a similar one depending on the version of NeuroMorphoVis, will appear.
After opening the Morphology Editing panel, the user can sketch the a tube representation of the morphology to visualizae and analyze its three-dimensional structure by clicking on Sketch Skeleton button. This will draw the entire morphology skeleton as a group of disconnected sections, where each section is drawn as an independent polyline.
The user can navigate in the scene and select a specific section to edit, given that the section has an obvious artifact.
After the selection of the arbor of interest, it is better to enlarge the view by zooming in the scene using the mouse.
The user can then modify the skeleton by clicking on the Edit Coordinates button on the Morphology Editing panel, which will convert the tubes representation into a skeleton with a series of points connected with poly-lines. Note that all the arbors of this morphology are all connected to the origin. When the outline of the morphology skeleton will appear, every sample in the skeleton will be clearly visible as a solid dot.
After identifying a broken sample from the sketched skeleton, the user can move it from one point to another. Select on the point (or sample) of interest using the right mouse click.
From the left side of Blender, switch from the select mode to the move mode by clicking on the arrows icon. Then the corrdinates will appear on the selected sample.
You can then move this sample to repair the morphology skeleton.
Once done and you are satisfied with the new position, you click on the Update Corrdinates button in the Morphology Editing panel.
The outline view of the morphology will disappear and the polylines will re-appear after editing the morphology skeleton.
A comparison between the section before and after the editing is shown in the following figure.
You can export this modified skeleton by clicking on the SWC(.swc) export button in the Morphology Editing panel.
From then you can use the updated skeleton to visualize the morphology from the Morphology Toolbox or create a mesh from the Mesh Toolbox.
- This toolbox is only valid to change the positions of the morphological samples only and cannot be used to scale their radii or remove any samples for the moment.
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