An imagej macro example to process a folder of images, split the channels and save them in an output directory

split_channels.ijm

// 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 @PatrickJS44 ,

Is it possible to modify the "save as" phase so that I can customize the renaming rule for each channel? Like adding prefix or suffix for splitted Blue channel output image.

you could modify the loop like this :

// let's assume you have 3 channels
prefix_array = { "ch1_prefix" ,  "ch2_prefix" ,  "ch3_prefix" }
for ( c = 1 ; c <= ch_nbr ; c++){
	selectImage(c);
	currentImage_name = getTitle();
	saveAs("tiff", output_dir+prefix_array [c-1]+currentImage_name); // -1 because array start at 0
}

Cheers,

R

Hi all, I am fairly new to imageJ and writing code in general, and I used this macro to split my channels. however, it converted all of my RGB images to 8-bit grayscale. I'd like the images to remain in color, is there an addition to this macro that will do this? Thanks.

Hi @castrojenna ,

it converted all of my RGB images to 8-bit grayscale
Great that the expected results 😄 !

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

// let's assume the images are RGB, we define an arrray with the colors
colors = newArray("Red","Green","Blue");
for ( c = 1 ; c <= ch_nbr ; c++){
	selectImage(c);
	currentImage_name = getTitle();
	run(colors[c-1]);
	//run("RGB Color"); // uncomment to convert to RGB so the images has this color when opened in another software (Photoshop...)
	saveAs("tiff", output_dir+currentImage_name);
}

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!