Changes between Version 1 and Version 2 of Optical

Timestamp:

Apr 30, 2014, 6:46:09 PM (11 years ago)

Author:

Tom Goddard

Comment:

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Optical

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-Optical Microscopy in Chimera 2
+= Optical Microscopy in Chimera 2 =
 
 Should Chimera 2 support analysis of optical microscopy data?  Here are some of the considerations.
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 6. Optical microscopy, including the many super-resolution techniques is too low resolution to be compared directly to molecular structures -- the core capability of Chimera.  So adding optical microscopy capabilities would not benefit from the molecular analysis capabilities except to the extent that the same researchers also are interested in molecular structure and they could use the same software for both.  The same criticism applies to serial milling electron microscopy techniques (focused ion beam SEM, and serial block face SEM), data we do try to handle since the electron microscopy Chimera user base also uses those EM techniques.
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+7. An enticing reason for developing optical microscopy analysis software is that 3d optical imaging is producing exciting data (e.g. brain imaging), the emerging microscope technology is rapidly improving and software to support it seems not to have been developed.
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+8. A key requirement to develop optical microscopy software will be collaborators with compelling data and a need for such software.  At UCSF there are several researchers who might help.  Professors John Sedat and Bo Huang develop super-resolution 3d microscopes.  A fast (one 3d image per second) Bessel-beam microscope of the type used by Dyche Mullins at Janelia Farm built by Eric Betzig's lab will be available at UCSF within a year (not sure who has is getting it, Tom Ferrin knows).  3d confocal microscopy is quite common.  Currently Dyche Mullins and Enrico Gratton are our active optical microscopy collaborators.
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+9. Measurement and segmentation would be the main analysis capabilities needed.  Good visualization would need to be developed before those.