Posted by
Thomas Boudier on
Aug 08, 2013; 2:20pm
URL: http://imagej.273.s1.nabble.com/Analyzing-particles-in-batch-proximity-ligation-assay-tp5004353p5004354.html
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.
>
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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
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