Last active
April 26, 2024 00:18
-
-
Save romainGuiet/cf42f3b1d31222a76d602dfe2f028894 to your computer and use it in GitHub Desktop.
An imagej macro example to process a folder of images, split the channels and save them in an output directory
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
// ask user to select a folder | |
dir = getDirectory("Select A folder"); | |
// get the list of files (& folders) in it | |
fileList = getFileList(dir); | |
// prepare a folder to output the images | |
output_dir = dir + File.separator + "output" + File.separator ; | |
File.makeDirectory(output_dir); | |
//activate batch mode | |
setBatchMode(true); | |
// LOOP to process the list of files | |
for (i = 0; i < lengthOf(fileList); i++) { | |
// define the "path" | |
// by concatenation of dir and the i element of the array fileList | |
current_imagePath = dir+fileList[i]; | |
// check that the currentFile is not a directory | |
if (!File.isDirectory(current_imagePath)){ | |
// open the image and split | |
open(current_imagePath); | |
// get some info about the image | |
getDimensions(width, height, channels, slices, frames); | |
// if it's a multi channel image , or a RGB | |
if ((channels > 1)||( bitDepth() == 24 )) run("Split Channels"); | |
// now we save all the generated images as tif in the output_dir | |
ch_nbr = nImages ; | |
for ( c = 1 ; c <= ch_nbr ; c++){ | |
selectImage(c); | |
currentImage_name = getTitle(); | |
saveAs("tiff", output_dir+currentImage_name); | |
} | |
// make sure to close every images befores opening the next one | |
run("Close All"); | |
} | |
} | |
setBatchMode(false); |
Hi, thank you so much your macro, it is really helpful to.
I have tried to run it on the server with headless mode and it gave error below:
java.lang.VerifyError: Bad type on operand stack
I googled it, it is about the "this" statement missing, and I am really confuse about it.
Could you help me with that?
Thank you for the code!
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Hi @castrojenna ,
If you want to keep the Red, Green, Blue Lookup Tables , which make grey images look red, green or blue you could use the lines below