Changing a single channel's LUTs

I have a large number of clips (TIFF) which are 2 color (channel 1 = GFP, channel 2 = RFP). Fiji has autoassigned red to the GFP channel, and green to the RFP channel. I have found multiple examples of people doing similar LUT changes in RGB images or for merging images into composites, but nothing on how to change the color in an individual channel (they are going to be analyzed on their own). Is this possible?

Yes, there are a couple of ways to do it.

To change the color of a channel in a composite image, you can select the channel on the “C” slider at the bottom. Then do Image > Color > Channels Tool, then click More >> and choose a different color for that channel. Or do Image > Lookup Tables and select from a wider range of LUTs.

Or, even better, if you use the Bio-Formats importer (File > Import > Bio-Formats), you can specify Color Mode: Custom when you open the image. Then you can adjust the RGB sliders (see window below) so Channel 0 is pseudocolored green and Channel 1 red. Those color choices are “sticky,” so you just have to click OK for subsequent images.

All of this should also be doable in a macro or Process > Batch command.



I am attempting to open a stack with 19 channels and I would like to have a distinct color for each channel. Because the Bio-Formats importer does not allow you to open multiple images at one time, I created a stack and save it as a tiff. Now, I open the stack tif image in the Bio-Formats importer, it only gives me the option to color one channel, not multiple as you have demonstrated above.

Do you have any advice as to how I could open my images in order to be able to make each of 19 channels a different color?

Thank you,

When you go to Image-> Properties… (not through BioFormats), do you see 19 channels? I sometimes get odd effects when I create a stack and don’t force a channel/time/zstack format. So you might think you have 19 channels because that is what you know you put in, but you might have created a 19 layer Z stack. Also it might matter if your channels are monochromatic originally, or already false colored RGBs. Not sure.

Basically, I think more information on what you are doing is necessary :slight_smile:

You were right! The properties for the image was set to 1 channel, I changed it and the Bio-Format importer allowed me to pick different colors for all the channels. However, it didn’t process correctly. This popped up:


Any thoughts? 19 channels may just be too many for the system to handle.

Thank you!

It could be. You could try opening it in QuPath (using the BioFormats extension). I have used images iwth over 40 channels with false coloring there on MIBI images. It is always a bit awkward with that many colors anyway, there is only so much variation we can process visually.

It also depends on whether you want to just look at the images (which should be easy enough) or perform quantification on them. QuPath has a different set of quantification tools, and only access to some ImageJ1 plugins, so might not be as useful for you.

I will check that out. Thank you for all your help!


Yes, ImageJ’s standard (legacy) user interface supports a maximum of 7 channels with individual channel color tables.