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GADPH single molecule mRNA FISH 20141104Tue
(2014)
  • George McNamara, M.D. Anderson Cancer Center
Abstract

GADPH single molecule mRNA FISH 20141104Tue

Raw data on NVidia TITAN GPU card deconvolution using original Bruce and Butte 2013 Optics Express software running inside Fiji ImageJ.

B&B GPU Deconvolution Reference:

http://www.opticsinfobase.org/oe/fulltext.cfm?uri=oe-21-4-4766&id=249375

Acquired at 63x1x using leica plan apo 1.4 NA objective lens on Cooper lab Leica DMI6000 microscope, SOLA (initial release) LED lamp using only "green" LED, 554x Semrock exciter filter (in ASI ex wheel), Leica N3 (Cy3) filter cube, center 600 nm emission wavelength.

Hamamatsu FLASH4.0 sCMOS, 100 ms exposure time so 6.4 seconds acquisition time (64 planes X 4 seconds). Acquired with MetaMorph 7.8.8.

XY 100 nm

Z 300 nm.

100 iterations.

The B&B 2013 deconvolution may suffer from some NVidia CUDA FFT library issues (see previous posts here and on confocal listserv). While we await the (improved in many ways) commercial release from http://www.microvolution.com

we are posting the data her to see if:

1. Bruce&Butte can improve on the deconvolved results in this dataset's zip file.

2. Other deconvolvers, whether corporate or academic, can do better with respect to image quality and deconvolution speed.

Data set 1 - 2048x2048 pixels, 64 planes, 87 seconds to deconvolve (Dell Precision Workstation T7500, TITAN card).

Data set 2 - 1024x1024 pixels, 64 planes, 9 seconds.

Data set 2 = Gorgeous cell at top!

Keywords
  • gPU deconvolution,
  • single molecule FISH,
  • Stellaris FISH
Disciplines
Publication Date
Fall November 4, 2014
Comments
Data are facts. Facts cannot be copyrighted. Please acknowledge the data source if you use this data.
Citation Information
George McNamara. "GADPH single molecule mRNA FISH 20141104Tue" (2014)
Available at: http://works.bepress.com/gmcnamara/64/