More Stellaris FISH and GPU Deconvolution, 20140313Thur - part 2 of 4

Please see other content in the FISH Imaging section of

http://works.bepress.com/gmcnamara/subject_areas.html

for details on the microscope. Briefly: Leica DMI6000 inverted microscope, SOLA lamp, Hamamatsu FLASH4.0 sCMOS camera, 100 nm XY, 200 nm Z pixels, 32 planes (16 um Z), MetaMorph 7.8 acquisition software.

Four zip files:

http://works.bepress.com/gmcnamara/43

http://works.bepress.com/gmcnamara/44

http://works.bepress.com/gmcnamara/45

http://works.bepress.com/gmcnamara/46

with two dataset (001, 002), raw and deconvolved using Bruce & Butte GPU deconvolution in Fiji ImageJ,

http://www.ncbi.nlm.nih.gov/pubmed/23482010

http://www.opticsinfobase.org/vjbo/fulltext.cfm?uri=oe-21-4-4766&id=249375 (free download, as are all Optics Express papers).

http://tcell.stanford.edu/software.html

http://lists.umn.edu/cgi-bin/wa?A2=ind1312&L=confocalmicroscopy&P=5534

Note: "001 raw" (bepress 43) contains my "imaging SOP" on doing this.

Data acquired in Prof. Laurence Cooper lab, M.D. Anderson Cancer Center, with Ash Prabala and Nikhil Prabala.

FISH reagents from Biosearch Technologies, see http://stellarisfish.smugmug.com My thanks to Marc Beal, Sally and Sheila for enabling FISHing here.

Images are from a 4 month old slide (acquired March 12, 2014), so the FISH signals are not as bright as in December 2013. Some cells have autofluorescent features that untrained viewers may mid-intrepret as FISH signals. THe FISH data was acquired with 500 ms exposure per plane, so 16 seconds to acquire. The GPU deconvolution took 18 seconds per channel ... about 60x faster than using the ImageJ single CPU based deconvolution (that is, the CPU based deconvolver that produces adequate results - ImageJ fas faster ones that produce poor results).