Dear all,
I am unfortunately unexperienced in macro programming, this is why I would ask for help for a probably easy problem. The goal is to count particles from microscope pictures with two stacks ('blue' and 'red') and summarize them into a .csv output file. The pictures were taken in .lif format, they're cells with a nucleus DAPI signal ('blue') and dotted signals ('red'). So far I am working manually with the LOCI plugin. First the red signal is thresholded and analyzed: -Plugins-LOCI-Bio-Formats importer choose file (split channels: on, autoscale: off) - open for red channel - Image-Adjust-threshold (Li, dark background) - analyze-analyze particles (0-Infinity, show outlines, display results, clear results) 'ok' here I note the number of particles and close the window. Then I count the number of nuclei: for blue channel - Image-Adjust-threshold (Li, dark background) - analyze-analyze particles (10-Infinity, show outlines, display results, clear results) 'ok' I recorded it with the macrorecorder ('file' and 'folder'are replacements); run("Bio-Formats Importer", "open='folder''file'.lif color_mode=Default split_channels view=Hyperstack stack_order=XYCZT series_1"); selectWindow("'file'_01 - C=1"); setAutoThreshold("Li dark"); //run("Threshold..."); run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Outlines display clear"); selectWindow("'file'_01 - C=0"); //run("Threshold..."); setAutoThreshold("Li dark"); run("Analyze Particles...", "size=10-Infinity circularity=0.00-1.00 show=Outlines display clear"); Is there a way to automate this process? I am handling hundreds of pictures what costs a tremendous amount of time. Thanks in advance! FloP |
Hi,
Use some loop over the directory where yout lif files are : dir=getDirectory("input"); save=getDirectory("Save results"); files=getFileList(dir); for(f=0;j<files.length;f++) { run("Bio-Formats Importer", "open="+dir+files[f]+" color_mode=Defaul split_channels view=Hyperstack stack_order=XYCZT series_1"); ... // saves your results saveAs("Results", save+files[f]+"_results.txt"); ... } that should be a good start best Thomas Le 08/08/2013 15:35, FloP a écrit : > Dear all, > > I am unfortunately unexperienced in macro programming, this is why I would > ask for help for a probably easy problem. > The goal is to count particles from microscope pictures with two stacks > ('blue' and 'red') and summarize them into a .csv output file. The pictures > were taken in .lif format, they're cells with a nucleus DAPI signal ('blue') > and dotted signals ('red'). So far I am working manually with the LOCI > plugin. First the red signal is thresholded and analyzed: > > > -Plugins-LOCI-Bio-Formats importer > choose file (split channels: on, autoscale: off) > - open > > for red channel > - Image-Adjust-threshold > (Li, dark background) > - analyze-analyze particles > (0-Infinity, show outlines, display results, clear results) 'ok' > > here I note the number of particles and close the window. Then I count the > number of nuclei: > > > for blue channel > - Image-Adjust-threshold > (Li, dark background) > - analyze-analyze particles > (10-Infinity, show outlines, display results, clear results) 'ok' > > > I recorded it with the macrorecorder ('file' and 'folder'are replacements); > > run("Bio-Formats Importer", "open='folder''file'.lif color_mode=Default > split_channels view=Hyperstack stack_order=XYCZT series_1"); > selectWindow("'file'_01 - C=1"); > setAutoThreshold("Li dark"); > //run("Threshold..."); > run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 > show=Outlines display clear"); > selectWindow("'file'_01 - C=0"); > //run("Threshold..."); > setAutoThreshold("Li dark"); > run("Analyze Particles...", "size=10-Infinity circularity=0.00-1.00 > show=Outlines display clear"); > > Is there a way to automate this process? I am handling hundreds of pictures > what costs a tremendous amount of time. > > Thanks in advance! > FloP > > > > -- > View this message in context: http://imagej.1557.x6.nabble.com/Analyzing-particles-in-batch-proximity-ligation-assay-tp5004353.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- /**********************************************************/ Thomas Boudier, MCU Université Pierre et Marie Curie, Modélisation Cellulaire et Imagerie Biologique (EE1), IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu. Tel : 01 44 27 46 92 Fax : 01 44 27 22 91 /*******************************************************/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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