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Selected Works of George McNamara
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Leica microscope GPU deconvolution Stellaris FISH dataset #1
(2013)
  • George McNamara, M.D. Anderson Cancer Center
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Abstract

McNamara 20131101Fri Leica widefield microscope CUDA Deconvolution Stellaris FISH probe cultured cells dataset #1.zip

A text file in the zip archive has experiment details. I am posting this online so that researchers - whether academic or commercial - can evaluate the acquired data, the Bruce and Butte 2013 Optics Express ( http://www.opticsinfobase.org/oe/fulltext.cfm?uri=oe-21-4-4766 ) deconvolution result (note: I may not have used optimal settings), and to compare these deconvolution results to other methods. If anyone generates alternative spatial deconvolution output, such as from: * SVI Huygens * Media Cy AutoQuant * Agard's ER-Decon (Arigovindan 2013 PNAS) * Vicidomini SGP GPU Deconv (Zanella 2013 Sci Rep) or other, please post the data online and let me know where to find it.

I am very interested in spectral unmixing. Especially: * autofluorescence (GFPcube channel) vs fluorescent dyes. * Quasar 570 vs Cal Fluor Red 610 (nominally Cy3cube vs TxRed cube). I plan to upgrade the microscope to get better optical separation of fluorophores, but have clear need for "spectral unmixing" and/or other methods of fluorophore channels separation.

My thanks to Sally and Marc at Biosearch Technologies for the slide.

Keywords
  • single molecules FISH,
  • mRNA FISH,
  • FISH,
  • fluorescence in situ hybridization,
  • CUDA GPU deconvolution,
  • oil immersion objective lens,
  • Stellaris FISH,
  • widefield microscope,
  • 5plex fluorescence
Disciplines
Publication Date
Fall November 4, 2013
Comments
Data are facts. Facts cannot be copyrighted (at least in the USA). Please feel free to reuse this data (would be nice to "give credit where credit is due" as to the data and specimen sources). If you find a better deconvolution or other image processing method to improve spatial resolution and/or contrast, please post your data online and email me where to find it.
Citation Information
George McNamara. "Leica microscope GPU deconvolution Stellaris FISH dataset #1" (2013)
Available at: http://works.bepress.com/gmcnamara/31/