Can I merge 13 channels from multiplexed in one image. I used ImageJ for merging channels before analysis. It allowed only 7 colors

I used ImageJ for merging channels before analysis. It allowed only 7 colors. What software should I use? Any help?

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Can you describe a bit more what you want to do with “merging channels”- just make them into one file, make a pretty RGB image, etc?

In general, yes, in CellProfiler you can merge as many channels as you want in the GrayToColor module, but whether you should use “Stack” vs “Composite” mode will a depend on what kind of picture you want to make.

Taking a step back, in the bigger picture sense, what do you want to do with this merged image? You might not need to merge the channels at all, depending, so you might be able to skip this step.

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The idea is I wanna do single cell analysis from multiplexed image data. So I might need all channels intensity data in one time image analysis. I need the tiff file to analysis in Qupath not RGB.


I’m not enough of a QuPath expert to know if it will handle a 13 channel image ok (I’ll add their tag to this post too), but yes, in that case I would use the “Channels” “Stack” mode. Best of luck!

Edited to fix name of the mode.

You will be able to visualise all the multiplexed image channels in QuPath with the channel viewer (Show > Mini viewers… > Show channel viewer).

However, when it comes to the cell detection, you will need to choose a specific channel on which to apply the processing. I am not sure anyway what kind of concatenation you were thinking about? Could you please elaborate on that?

ImageJ allows you to concatenate far more than 7 channels, it sounds like you are trying to make a composite image instead of a stack though, which is probably not your best option.

I take it the original file format does not work in QuPath or there is no original file format for some reason? Most original file types should work.