Changes between Version 5 and Version 6 of Optical

Timestamp:

May 1, 2014, 2:14:40 PM (11 years ago)

Author:

Tom Ferrin

Comment:

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Optical

@@ -17 +17 @@
 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.
 
-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.
+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 (now retired) and Bo Huang (Pharm Chem) 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 is being built by Max Krummel (with Eric Betzig's guidance) for UCSF's Biological Imaging Development Center [http://pathology.ucsf.edu/BIDC/resources.html BIDC].  Lastly, 3D confocal microscopy is quite common, but typically not as high resolution as Bessel Beam and has limited ability to capture dynamic data.  Currently Dyche Mullins and Enrico Gratton are our active optical microscopy collaborators, but Max Krummel will likely be very interested as well once his microscope comes on line and the flood of associated data starts flowing. Dyche Mullins thinks that the microscope technology is no longer the bottleneck in science, but rather it's the visualization of the data.  Here's a direct quote from him:
+{{{
+“We are in the early days of working out the mechanisms and molecules that drive 3D cell migration
+and we are still limited by technology. We are less limited now by the technology of the microscopes
+than by the technologies of visualization. How do we turn the terabytes of data generated by a
+Bessel Beam into something that a human can understand and begin to theorize about?”
+}}}
+   The work being done in Dyche's lab makes for a great Driving Biological Project!
 
-9. Measurement and segmentation would be the main analysis capabilities needed.  Good visualization would need to be developed before those.
+9. Measurement and segmentation would be the main analysis capabilities needed.  Good visualization would need to be developed before those.  To contrast Chimera's capabilites to other microscope software, take a look at Nico Stuurman's [https://micro-manager.org/ Micro-Manager] project.  Nico is a research associate in Ron Vale's lab.  He had an R01 grant to support his work, but I believe the grant ended and was not renewed.
 
-10. 5d optical microscopy data sets can be very large, for example Dyche Mullin's 3 minute cell motion data sets are about 50 Gbytes each (won't fit in memory), and often many data sets are acquired (I have about 1.5 Tbytes from Dyche).  Handling this fits with our Chimera 2 emphasis on handling large data.
+10. 5d optical microscopy data sets can be very large, for example Dyche Mullin's 3 minute cell motion data sets are about 50 Gbytes each (won't fit in memory), and often many data sets are acquired (I have about 1.5 Tbytes from Dyche).  Handling this fits with our Chimera 2 emphasis on handling large data and also falls within NIH's recent "Big Data to Knowledge" (BD2K) program.  Several RFAs have been released in 2014 under the BD2K umbrella.