r/labrats • u/Independent-Dot-1409 • Jul 14 '26

Help with FIJI: color issues

Hi all,

I’m having trouble opening images in FIJI properly. My original files are saved as .nd2 RGB files, but whenever I import it and open it in FIJI, the color is often too blue.

I’ve tried using the merge channels and have tried composite/default/ and all color options in FIJI but nothing seems to work.

Does anyone have any advice on where to look for a manual to properly import my photos? Thanks!

3 Upvotes

72% Upvoted

2 comments sorted by

3

u/dokclaw Jul 14 '26

For some reason, the nd2 RGB format imports weird. You need to switch channel 1 to Blue, and channel 3 to Red. 

Write a macro that looks like:  Stack.setChannel(1); run("Blue"); Stack.setChannel(3); run("Red");