How to open multi-colored image according to metadata from confocal microscope



When I open a multi-colored image in Fiji, it displays every channel as the same color, even though the metadata from Zeiss has each channel as a different color. A colleague of mine who has not updated Fiji in over 2 years does not have this problem. Is there a setting I can change so that the color of each channel reflects the color listed in the metadata?



How exactly are you opening your images? In general, we recommend using Bio-Formats to import your images - this way the metadata is read in correctly. Just go to File > Import > Bio-Formats

Give that try and let us know if that helps. In any case - you can always just change the LUTs manually as you need or write a little script to change the LUTs for these images upon opening them.




I was opening my images by going to File–>Open. I tried using Bio-Formats, but it did not help the situation. Ultimately, I copied my colleague’s old Fiji (from 3/16/2016), and this solved my problem. An update since that date must have inserted this “bug” into the program, as re-installing the latest version of Fiji did not solve my problem.


I sometimes get these situations from microscopic images.
Bio-formats can not perfectly read the metadata which is created from various microscopes.
So in that situation we need to change the LUTs ourselves as we wish.
Since LUT is a pseudo color, I think that it is not important for image analysis.
However, the LUT is useful for visually separating the display of each channel or the brightness on same channel.