Macro for merging 2 channels of .nd2 files

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Macro for merging 2 channels of .nd2 files

litaiyuang
Hi,

I'm trying to write a macro where .nd2 images/file within a folder are
opened, split into 2 channels, and merged into a single image and saved as a
new merged file.

When I use Bio-Format Importer to split the channels, it generates 2
images/channels named:
"file_name" - C=0
"file_name" - C=1

Here's my macro code so far:

path = getDirectory('Choose Directory');
filelist = getFileList(path);
output = path+"MergedJPG"+File.separator;
File.makeDirectory(output);

setBatchMode(true);
for (i=0; i< filelist.length; i++) {
if (endsWith(filelist[i], ".nd2")) {

name = path + filelist[i];
run("Bio-Formats Importer", "open= ["+name+"] color_mode=Default
view=Hyperstack stack_order=XYCZT color_mode=Default split_channels");
        red = filelist[i]+" - C=1";
        green = filelist[i]+" - C=0";
run("Merge Channels...", "c1=["+red+"] c2=["+green+"] create");
saveAs("jpeg", output + filelist[i]);
run("Close");
setBatchMode(false);
}
}

It's almost there. When I run it,  I choose the directory (in this case the
folder "nd2" containing my .nd2 image files), it creates the MergedJPG
folder fine, but then this window pops up and I still have to click on each
.nd2 file with in my chosen folder, and in the right order, for each image
to get processed and saved as the merged .jpg files.
<http://imagej.1557.x6.nabble.com/file/t382408/Capturefuji.jpg>
I assume I'm just missing some simple thing in order for it to actually
automate and batch process all the .nd2 files in my chosen folder without me
having to select each.

Thanks for the help,
YL



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Re: Macro for merging 2 channels of .nd2 files

Krs5
try to use

Ext.openImagePlus(path+filelist[i]);
run("Split Channels");

instead of
name = path + filelist[i];
run("Bio-Formats Importer", "open= ["+name+"] color_mode=Default
view=Hyperstack stack_order=XYCZT color_mode=Default split_channels");

You have to check what the titles will be of the different channels after
splitting them and adjusting your code accordingly.

Hope this works

Best wishes

Kees

Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility

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Re: Macro for merging 2 channels of .nd2 files

Cammer, Michael-2
Perhaps this could serve as a model for one way to solve the problem.

http://microscopynotes.com/imagej/macros/simplefigure/index.html

Cheers-


Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016

[hidden email]<mailto:[hidden email]>  http://nyulmc.org/micros  http://microscopynotes.com/

Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567



________________________________
From: Krs5 <[hidden email]>
Sent: Tuesday, August 6, 2019 3:49:46 AM
To: [hidden email]
Subject: Re: Macro for merging 2 channels of .nd2 files

try to use

Ext.openImagePlus(path+filelist[i]);
run("Split Channels");

instead of
name = path + filelist[i];
run("Bio-Formats Importer", "open= ["+name+"] color_mode=Default
view=Hyperstack stack_order=XYCZT color_mode=Default split_channels");

You have to check what the titles will be of the different channels after
splitting them and adjusting your code accordingly.

Hope this works

Best wishes

Kees

Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.le.ac.uk_advanced-2Dimaging-2Dfacility&d=DwICAg&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=hUBj2D5n6oKThx2L01qn8IORZb5f-ruLVXPmQ1zQNnM&m=ivbeSXjq3_KWhZ8NKmF0R-LSI1Ex78fFwEHjXJNmpEU&s=pMb6EXqr9ndZI2_6XSYYI5xeiZ513Y0eetWIgCt_JbA&e=

________________________________________




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