[chimerax-users] Chimera for 4D imaging analysis

[Tom Goddard]

Hi John,

  Dyche made Chimera(X) look better than it is!  Here’s an example of things we did with some of Dyche’s data:

	http://www.rbvi.ucsf.edu/chimera/data/adcom16/chimerax.html <http://www.rbvi.ucsf.edu/chimera/data/adcom16/chimerax.html>

The Chimera vseries command and Volume Series window have a lot of rough edges.

	https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vseries.html <https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vseries.html>

	https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/volseries/volseries.html

We also show the volume time series with surface renderings in virtual reality headsets, the HTC Vive, using our next generation ChimeraX program.  We plan to develop much better 3d/4d/5d light microscopy tools — it was significant part of our NIH Chimera grant proposal with funding likely to start in July.  I’m working now with the Allen Institute of Cell Science and Dyche Mullins and Lil Fritz-Laylin and also Alex Ritter improving the ChimeraX capabilities for light microscopy.  All our tools will be aimed at 3 spatial dimensions (plus time / wavelengths), not 2D since our expertise is in 3D interactive graphics.

  To answer your question, I don’t know if Chimera/ChimeraX can help you with your 4D data — depends exactly what you want to do.  You can contact me directly by email if you want to discuss confidential details of your work, or you can tell me more about what you are looking for on this list.

	Tom


> On Apr 5, 2017, at 12:00 PM, John Daum wrote:
> 
> Ladies and Gents,
> 
> I recently heard a talk at Janelia Research Campus's "Frontiers in Imaging Science" given by Dyche Mullins, an investigator at USCF.  He heaped praise upon Chimera/ChimeraX and indicated that it had been adapted for working with 4D light microscopy images that might be quite useful for quantifying and or viewing objects in 3D space over time by surface rendering and other cool "tricks".
> 
> I'm writing to inquire if Chimera, ChimeraX, or another version (perhaps currently unavailble for download from the UCSF Chimera website) will help me with my problem (analyzing, viewing, 4D data)?
> 
> Thank you,
> 
> John Daum
> Laboratory Manager, Gorbsky Lab, Bell 216
> Cell Cycle and Cancer Biology
> Oklahoma Medical Research Foundation
> 825 N. E. 13th Street
> Oklahoma City, OK 73104
> daumj at omrf.org <mailto:daumj at omrf.org>
>  
> Voice: 405-271-2037
> Fax: 405-271-7312
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