Posted by
Krs5 on
Aug 06, 2010; 9:41am
URL: http://imagej.273.s1.nabble.com/Batch-split-channels-and-save-tp3687341p3687342.html
Dear Dan,
See if the macro below does what you want. At the moment it saves the results to a new directory called "analysed". If you want to save the result files in the same directory as your original files delete the line "dir2 = ....." and change in the first lane "dir1" into "dir2"
dir1 = getDirectory("Choose Source Directory ");
list = getFileList(dir1);
dir2 = dir1+"analysed"+File.separator;
File.makeDirectory(dir2);
for (i=0; i<list.length; i++)
{
if (File.isDirectory(dir1+list[i])){}
else{
path = dir1+list[i];
if (endsWith(path, ".db")){}
else{
open(path);
if (bitDepth!=24){}
else {
setBatchMode(true);
title = File.nameWithoutExtension ;
run("Split Channels");
close();
saveAs("Tiff", dir2+title+"d0.tif");
saveAs("Tiff", dir2+title+"d1.tif");
close();
saveAs("Tiff", dir2+title+"d2.tif");
close();
setBatchMode(false);
}
}
}
}
Best wishes
Kees
Dr K.R. Straatman
Senior Experimental Officer
Centre for Core Biotechnology Services
College of Medicine, Biological Sciences and Psychology
http://www.le.ac.uk/biochem/microscopy/home.html-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Dr D.J. Metcalf
Sent: 04 August 2010 17:14
To:
[hidden email]
Subject: Batch split channels and save
Hi,
I'd be grateful for some help on making my macro capable of batch
processing a folder of images. I'm not sure if it's possible to modify the
one I've written or if another approach is required.
The aim is to open RGB tif files and then save the individual channels but
with the added complication of discarding the blue image and saving the
green and red images. Ideally I'd like to save the green image twice with
different file names (see below).
My starting file names are A_A##f##.tif My result file names are
A_A##f##d0.tif, A_A##f##d1.tif, A_A##f##d2.tif (where d0 is the green
chanel, d1 is the green channel and d2 is the red channel)
Thanks,
Dan
open("V:\\Dan\\tif_files\\A_A06f12.tif"); run("Split Channels");
run("Save", "save=V:\\Dan\\tif_files\\discards\\C3-A_A06f12.tif"); close();
close(); run("Save",
"save=[V:\\Dan\\tif_files\\discards\\C1-A_A06f12.tif]"); close();
open("V:\\Dan\\tif_files\\discards\\C1-A_A06f12.tif");
open("V:\\Dan\\tif_files\\discards\\C3-A_A06f12.tif"); run("Merge
Channels...", "red=C3-A_A06f12.tif green=C1-A_A06f12.tif
blue=C1-A_A06f12.tif gray=*None* create"); run("Split Channels");
run("Save", "save=[V:\\Dan\\new files\\A_A06f12d0.tif]"); close();
run("Save", "save=[V:\\Dan\\new files\\A_A06f12d1.tif]"); close();
run("Save", "save=[V:\\Dan\\new files\\A_A06f12d2.tif]"); close();