Hello, currently it is possible to select only box-shaped subregions in Volume Viewer. I would be especially interested in segmenting electron density maps or their isosurfaces to different subregions with any shape interactively. Is anyone planning to add a feature like this? Regards, Juha Huiskonen
Hi Juha, We don't currently have a plan to add volume data segmentation tools to Chimera. Some electron microscopy people have expressed interest in segmentation tools in Chimera. But this is a big complex problem. A first step would be to make Chimera volume display able to use mask files that are produced by segmentation done with programs. I'd be the programmer to work on this. It would help me to have precise descriptions of exactly how segmentation tools would work. Then I could better judge how big a programming task it is. Tom
Hi Tom,
A first step would be to make Chimera volume display able to use mask files that are produced by segmentation done with programs.
A segment file would be another grid with integer values specifying the segment of the particular voxel. Density would be then divided into subsets that could be treated as separate grids. Of course, one can also do this outside chimera, and just read in multiple grids. More generally, a nice concept would be the possibility of mapping values from one grid to an isosurface calculated from another grid. The isosurface would be then colored based on the mapped values. The mapped value could represent a voxel belonging to some segment, or distance to some other voxel (e.g. center of the model) etc. Cheers, Juha
Hi Juha, There is a Chimera tool for coloring a volume isosurface using the values of another volume data set that was written by Steve Ludke at the National Center for Macromolecular Imaging. It is available as part of the EMAN (single particle EM reconstruction package) source code. http://ncmi.bcm.tmc.edu/~stevel/EMAN/doc/ The code is in eman/chimeraext/FilterKit/Colorizer.py and also requires a modified version of chimera/share/VolumeViewer/surface.py which is available for Chimera 1872 in eman/chimeraext/surface.py. Steve recently wrote this extension and there is no documentation that I am aware of. We will have better support for this capability in the coming year. Tom
participants (2)
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Juha Huiskonen -
Thomas Goddard