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@lacan
Last active May 15, 2024 10:05
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Extract multi-series file and resave as TIFF stacks or slices #Fiji #ImageJ #Macro #BIOP
/*
* Complex Format EXPORT MACRO
* By Olivier Burri @ EPFL - SV - PTECH - BIOP
* Given a folder, extracts all series inside all multi-file files with given extension in new folders
* Last edit: 13.02.2017
*/
////////////////////// SET PARAMETERS //////////////////////
////////////////////////////////////////////////////////////
// Set the extension you would like this macro to work with.
// Do not add a . at the beggining
extension = "czi"; //eg "lif", "vsi", etc...
// Set to true if you want all planes of the image to be saved individually
// if set to false, it will save each series as a stack.
is_save_individual_planes = true; // set to either true or false
// Padding for the naming of the series if you want to save all
// Images individually
pad = 3; // 0 means no padding. 2 means '01', '02' etc...
//////////////////// END SET PARAMETERS ////////////////////
////////////////////////////////////////////////////////////
// Beggining of macro. You should now have anything to edit after this line.
dir = getDirectory("Select a directory containing one or several ."+extension+" files.");
files = getFileList(dir);
setBatchMode(true);
k=0;
n=0;
run("Bio-Formats Macro Extensions");
for(f=0; f<files.length; f++) {
if(endsWith(files[f], "."+extension)) {
k++;
id = dir+files[f];
Ext.setId(id);
Ext.getSeriesCount(seriesCount);
print(seriesCount+" series in "+id);
n+=seriesCount;
for (i=0; i<seriesCount; i++) {
run("Bio-Formats Importer", "open=["+id+"] color_mode=Default view=Hyperstack stack_order=XYCZT series_"+(i+1));
fullName = getTitle();
dirName = substring(fullName, 0,lastIndexOf(fullName, "."+extension));
fileName = substring(fullName, lastIndexOf(fullName, " - ")+3, lengthOf(fullName));
File.makeDirectory(dir+File.separator+dirName+File.separator);
print("Saving "+fileName+" under "+dir+File.separator+dirName);
getDimensions(x,y,c,z,t);
if(is_save_individual_planes) {
save_string = getSaveString(pad);
print(dir+File.separator+dirName+File.separator+fileName+"_"+save_string+".tif");
run("Image Sequence... ", "format=TIFF name=["+fileName+"] digits="+pad+" save=["+dir+File.separator+dirName+File.separator+"]");
} else {
saveAs("tiff", dir+File.separator+dirName+File.separator+fileName+"_"+(i+1)+".tif");
}
run("Close All");
}
}
}
Ext.close();
setBatchMode(false);
showMessage("Done with "+k+" files and "+n+" series!");
function getSaveString(pad) {
str ="";
getDimensions(x,y,c,z,t);
if(t > 1) str+="t_"+IJ.pad(1,pad);
if(z > 1) str+="z_"+IJ.pad(1,pad);
if(c > 1) str+="c_"+IJ.pad(1,pad);
return str;
}
@af21009
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af21009 commented Aug 9, 2023

Worked this time, thanks!

This was the output:

20 series in C:\Users\af21009\Downloads\MCF10A Starve baf stained 11th july 2023, imaged 18th july 2023.lif
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 2023.lif - MCF10A control DAPI, 488 LAMP2, 568 LC3B, 647 P62
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 2023.lif - MCF10A control DAPI, 488 LAMP2, 568 LC3B, 647 P62 2
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 2023.lif - MCF10A control DAPI, 488 LAMP2, 568 LC3B, 647 P62 3
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 2023.lif - MCF10A control DAPI, 488 LAMP2, 568 LC3B, 647 P62 4
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 2023.lif - MCF10A control DAPI, 488 LAMP2, 568 LC3B, 647 P62 5
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 2023.lif - MCF10A baf 50nm 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 2023.lif - MCF10A baf 50nm 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62 2
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 2023.lif - MCF10A baf 50nm 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62 3
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 2023.lif - MCF10A baf 50nm 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62 4
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 2023.lif - MCF10A baf 50nm 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62 5
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 2023.lif - MCF10A starve HBSS 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 202...- MCF10A starve HBSS 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62 2
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 202...- MCF10A starve HBSS 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62 3
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 202...- MCF10A starve HBSS 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62 4
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 202...- MCF10A starve HBSS 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62 5
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 202...arve HBSS AND BAF 50NM 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 202...ve HBSS AND BAF 50NM 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62 2
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 202...ve HBSS AND BAF 50NM 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62 3
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 202...ve HBSS AND BAF 50NM 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62 4
Name: MCF10A Starve baf stained 11th july 2023, imaged 18th july 202...ve HBSS AND BAF 50NM 2 hr DAPI, 488 LAMP2, 568 LC3B, 647 P62 5

@JennyLuong
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Is it possible to do split channels with this script? I tried added that option to the script but it messed up the file names.

@cfausto
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cfausto commented Feb 22, 2024

Hello!

Thank you so much for making this script! It has helped me tremendously in processing large datasets. I recently updated FIJI to the newest version, and am now getting an error. I was wondering if you can help me address this?

Specifically in line 54:
dirName = substring(fullName, 0,lastIndexOf(fullName, "."+extension));

I am now getting this error message attached below, with the following debug window. I am using ImageJ version 2.14.0/1.54f Build: c89e8500e4

Screenshot 2024-02-22 at 2 37 55 PM
Screenshot 2024-02-22 at 2 38 12 PM

@lacan
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lacan commented Feb 23, 2024

perhaps you put a dot when specifying the extension? or the image is the wrong extension?

@cfausto
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cfausto commented Feb 23, 2024

@lacan I appreciate that you are still active on this post!

I was just able to find the issue when manually saving at tifs last night, my .lif file name was too long and it created ellipsis! I guess FIJI does have a character limit for file naming. I was able to get it running after making the file name shorter. Good to know!

image

@lacan
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lacan commented Feb 24, 2024

good to know. the ellipsis might me talked to a Mac file path issue, as Fiji is just reading the filename in the macro. thanks for the report!

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