A problem of opening lsm files because of discrepancy between channel number and color

I am trying to open lsm files which have 4 channel, however the order of color is messed up. For example, a file has a green colored image in channel 1st channel, but a different file has red.

It seems ImageJ uses channel number to assign color, so sometimes color assignment go wrong.

The problem is when I want to retrieve an image with red, but it fails all the time.

Does anyone help me?


How exactly are you opening your files in Fiji? File > Open?

I’m asking this ‘silly’ question because there are in fact multiple ways to open image files. If working with .lsm files, I’d recommend opening your images via Bio-Formats (File > Import > Bio-Formats). This would be one thing to quickly test if you haven’t used it yet.

In any case - the color is relatively un-important (or at least it can be changed as you want/need), as it is only a pseudocolor image and a new LUT can be applied at any time (the Visualization page has some helpful stuff in there). The most important thing is that your channel order is consistent - so selecting the correct channel is not affected.

What are you next steps for processing? You can write a script too to be sure to set the channel colors as you’d like for each image, etc.


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Thank you so much for your kind message.

I have also tried to open images via Bio-Formats, but It did not solve the problem.

I could not explain well in my previous post, the problem this time happened because a student who acquired images randomly set the order of images and save them as lsm file. So the clue to identify which kind of image is only colors (i.g. hoechst is blue) .

So now I would like to know which color is used in each channel. Do you know any function that returns a color when I put the channel number of image.

Thank you so much.


You can check the functionality in the Colors menu - see if there is a particular function or combination there-in that will do what you need. Perhaps Show LUT ??

Are you scripting a workflow for this? This seems the only way I think it can be done… and it’s still not particularly straightforward I’m afraid. After checking the Built In Macro Functions list - I could not find anything that would do exactly what you need. So you’d need a work-around…


Thank you so much for your kind response.
Yes, I’ve tried everything I came up but as you mentioned I also failed.
I think I will give up scripting this even though it seems it’s not complicated process.

Thank you again.