Channels Tool with more than 6 colors

Hi all,
I have a stack of fluorescent images with more than 6 colors, up to 50 colors. While trying to use the channels tool in ImageJ I found that you can only use the composite option for up to 6 colors but above than only the color option work. I don’t expect to look at all the colors simultaneously but I was hopping to be able to overlay few colors at a time, is there another way to do that in ImageJ?

With the latest QuPath milestone* you could… see the ‘Channel viewer’ section here.

*-Still a work-in-progress. Use with caution… but potentially still handy for visualization at least.

Hi @petebankhead , Thank you very much, it’s exactly what we need for our Multiplex system. I did have some small “issue” with the adjustment of the brightness where I had to readjust the “set display range maximum” has it was to low and the auto adjustment of the contrast didn’t work properly.
Thank you for your hard work on this software it looks great!

Good! Under Edit → Preferences (or the little cog icon on the top right of the toolbar) you can adjust the Auto Brightness/Contrast saturation % to change how severe this is if the default does not work well for you.

You can keep this window and alongside the Brightness/Contrast pane and select one or more channels, trying different combinations of ‘Auto’ and ‘Reset’. You can also double-click on the ‘Min display’ or ‘Max display’ values for a channel to specify exact numbers for a single channel.

There is some further information at

It can also be done in ImageJ. Have a look at this guide which explains how to merge 8 or more color channels with ImageJ (see p. 53):


In additon I think this forum has a good history of related questions:

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