Getting the correct colors

Hey everyone,

I am new to imageJ. I have color images that were converted to RAW files and uploaded to the imageJ software. They appear as greyscale images. I am able to apply some colors by Image > Lookup Tables, but I want to change back to the colors that the images were before converting to RAW. Anyone know how to do this? Also, I have a time series of images and I want to get one average image of the series so I can say this was the average color intensity for each pixel over time. Is this possible?

I hope you all can enlighten me, and if so I greatly appreciate the help.

  • Shane
  1. Do you still have the non-converted images? Can they be opened in Fiji/ImageJ? If yes to both, you can open one of them and export the LUT. Then, you can import the LUT and apply it to your RAW images.
  2. Are you able to open the entire series as a stack (not a virtual one)? If so, you can use Image > Stacks > Z Project... > Average Intensity


Thank you so much for your response. I do have the images. They come from an obscure software. To export the non-converted image should I just save as jpg. and then bring into imageJ. From there exporting the LUT?

This list probably isn’t comprehensive. However, the general idea is to have the source of the images provide them in an indexed-color file format that is also recognized by Fiji. JPG is not on that list so I don’t think converting to JPG will work. If these are stacks/hyperstacks that you are dealing with, you likely will only need one slice since the color map should be recorded the same regardless of how large the stack is.