Cell and Developmental Biology Commons^™

Gadph Single Molecule Mrna Fish 20141104tue, George Mcnamara

George McNamara

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 …

More Fish (1 Of 4), George Mcnamara

George McNamara

More Stellaris FRISH and GPU Deconvolution, 20140313Thur - part 1 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" …

More Fish (2 Of 4), George Mcnamara

George McNamara

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" …

More Fish (3 Of 4), George Mcnamara

George McNamara

More Stellaris FISH and GPU Deconvolution, 20140313Thur - part 3 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" …

More Fish (4 Of 4), George Mcnamara

George McNamara

More Stellaris FISH and GPU Deconvolution, 20140313Thur - part 4 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" …

Stellaris Fishing 20131125mon Part 2 Of 2, George Mcnamara

George McNamara

Stellaris FISH dataset using three FISH probe sets.

Slides courtesy of Biosearch Technologies,

https://www.biosearchtech.com/store/product.aspx?catid=224,318,324

see http://stellarisfish.smugmug.com/ for online gallery by Biosearch.

This experiment was to evaluate the crosstalk between the Biosearch fluorophores:

Quasar 570

CAL Fluor Red 610 (CFR 610)

Quasar 670

DAPI (DNA counterstain)

Autofluorescence (green, but sometimes showing up in other channels).

and our lab's Leica DMI6000 fluorescence microscope with Leica filter sets:

DAPI

GFP (L5)

Cy3 (N3)

Texas Red (TxRed2)

Cy5 (Y5)

I also acquired green channel and red channel with exciter filters in our ASI excitation wheel:

GFP + 492 exciter

Texas Red (TxRed2) + 572 …

Leica Microscope Gpu Deconvolution Stellaris Fish Dataset #1, George Mcnamara

George McNamara

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 …