Sub-region selection
Hello, I am analyzing some tomography data. I am working with multiple maps - one which defines several cells and another that defines their inner organelles. I want to be able to select and save the map for individual cells and their corresponding map for the organelles. In addition to using the sub-region selection in Volume-viewer is there another way to select the cells? Thanks Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh@lbl.gov
Hello Soumya, There are several tools for dividing up a map or creating new maps with subsets of the original. I’m not an expert on this topic but can list some general approaches available in Chimera: (1) segmentation (2) adding point markers (or using atoms docked in) and then dividing up the map by zones around the points or atoms (3) masking by surfaces to get only the values within or outside of the surface (4) “erase” (zero out) parts of the map by hand to get a new map with just the part you want The “volume” command “save” option also lets you specify output region directly rather than having to draw a box with the mouse. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> The tool graphical interfaces are generally available from the Tools menu of Volume Viewer and the main menu, under Tools… Volume Data, and often there are commands to do the same things. A few things are commands only. See links below for details. (1) Segmentation, which tries to find the natural divisions in the data and draw surface blobs around them. There is a Segment Maps tool, and then in results dialog, a File menu to save the blob-delineated segmentation regions However, with noisy data, automatic segmentation may not be successful. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html> (2) You can add marker points with the mouse via the Volume Tracer tool, and then split the map into new maps by zones around these points with the Color Zone tool. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html> (3) There is a “mask” command that works with surfaces in general. Although I haven’t tested all these possibilities myself, I think you could use surfaces from IMOD segmentation, or molecular surfaces, or even surfaces made by placing points in individual data planes with Volume Tracer and then using its surface-creation feature. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#surfaces> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/imod.html> (4) The Volume Eraser tool is essentially a sphere you can move around interactively to “erase” (zero) the values within. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 4, 2017, at 1:58 PM, Soumya Govinda Remesh <sgremesh@lbl.gov> wrote: Hello, I am analyzing some tomography data. I am working with multiple maps - one which defines several cells and another that defines their inner organelles. I want to be able to select and save the map for individual cells and their corresponding map for the organelles. In addition to using the sub-region selection in Volume-viewer is there another way to select the cells? Thanks Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source Lawrence Berkeley National Laboratory
Thanks Elaine. I found an earlier post http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-April/010934.html It said to use sop split then use mask to generate the maps for individual cells. That seemed to work as well. Best, Soumya On Fri, May 5, 2017 at 9:19 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Soumya, There are several tools for dividing up a map or creating new maps with subsets of the original. I’m not an expert on this topic but can list some general approaches available in Chimera:
(1) segmentation (2) adding point markers (or using atoms docked in) and then dividing up the map by zones around the points or atoms (3) masking by surfaces to get only the values within or outside of the surface (4) “erase” (zero out) parts of the map by hand to get a new map with just the part you want
The “volume” command “save” option also lets you specify output region directly rather than having to draw a box with the mouse. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output
The tool graphical interfaces are generally available from the Tools menu of Volume Viewer and the main menu, under Tools… Volume Data, and often there are commands to do the same things. A few things are commands only. See links below for details.
(1) Segmentation, which tries to find the natural divisions in the data and draw surface blobs around them. There is a Segment Maps tool, and then in results dialog, a File menu to save the blob-delineated segmentation regions However, with noisy data, automatic segmentation may not be successful. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/ segment.html>
(2) You can add marker points with the mouse via the Volume Tracer tool, and then split the map into new maps by zones around these points with the Color Zone tool. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ volumepathtracer/framevolpath.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/ colorzone.html>
(3) There is a “mask” command that works with surfaces in general. Although I haven’t tested all these possibilities myself, I think you could use surfaces from IMOD segmentation, or molecular surfaces, or even surfaces made by placing points in individual data planes with Volume Tracer and then using its surface-creation feature. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ volumepathtracer/volumepathtracer.html#surfaces> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ volumeviewer/imod.html>
(4) The Volume Eraser tool is essentially a sphere you can move around interactively to “erase” (zero) the values within. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/ voleraser.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 4, 2017, at 1:58 PM, Soumya Govinda Remesh <sgremesh@lbl.gov> wrote: Hello, I am analyzing some tomography data. I am working with multiple maps - one which defines several cells and another that defines their inner organelles. I want to be able to select and save the map for individual cells and their corresponding map for the organelles. In addition to using the sub-region selection in Volume-viewer is there another way to select the cells? Thanks Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source Lawrence Berkeley National Laboratory
-- Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh@lbl.gov
participants (2)
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Elaine Meng -
Soumya Govinda Remesh