Software suggestions for monochrome to color


I have exported monochrome images that were captured through a high throughput microscope of co-culture nuclei marked with two different dyes.
Though the nuclei have been marked with two different green dyes there is a difference in their wavelengths.

I have used cell profiler for my previous work with monochrome images however now I would like to convert the monochrome images into color images (for the different dyes) to get the counts.

Cell profiler does not have support for that. Please suggest which softwares can be used and preferably be integrated with a cell profiler pipeline for further analysis to get counts .

Dear Swati,
the images from a fluorescent experiment are always monochrome (gray scale)
You can change the color in ImageJ / fiji with a LUT (Look Up table) red , green, blue , fire etc…
or use Merge Channels and define the color

You can probably achieve this by adding a GreyToColor module to your pipeline. If you want to display a color image later then you might want to use SaveImages to output the overlaid image file somewhere. For obtaining counts this is not strictly necessary - MeasureObjectIntensity can consider multiple greyscale channels without needing an overlay.

Thank you @Alex.h and @DStirling for your help

@Alex.h I saw the options available in ImageJ, however it has just one option for green (and other colors) from the LUT . However, I have two dyes that are different shades of green. I can’t seem to figure out how to identify them differently.

@DStirling, in cell profiler too, it has support for one shade of green. I have dyes with two different shades of green and then I want to detect the number of objects for each of the two different green dyes.

Please let me know if I have not understood properly and there is a possibility of detecting and counting objects marked with two different green dyes in the same image

What do you mean by ‘one shade of green’? Do you mean that you have two greyscale images which are both in green channels, or one image with two shades of green on it? For the former you should be fine to just run measureobjectintensity with both channels. With the latter you could split them using ColorToGrey with one of the color deconvolution settings. If it’s the overlay you’re concerned about, overlaying in ‘Composite’ mode will let you overlay as many channels as you like and choose a colour for each.