Detect Specific Colors within Defined Areas


I am imaging multicellular fungal spores using live/dead dyes. Is there a way for ImageJ to

  1. define and count the outline of multiple spores
  2. count the number of red (dead) and green (live) pixels within each spore defined in part 1?



Welcome to the Forum!

So… to answer you quickly:

  1. Yes.
  2. Yes.

:slight_smile: So that’s the good news!!!

The best thing would be if you could post an image - the original format if possible. Then we can better assist you in getting started… If you want to get a head-start - take a look at some of these helpful links:

eta :slight_smile:


Thanks for answering so quickly! Attached are .png files of the .czi file, but I am unsure how to visualize it in ImageJ as overlapping (so that both green and red would appear on a single image). At the bottom of the image is my spore with both green (live) and red (dead) fluorescenceThank you also for the links.


Hey @JGolan

Ok. Let’s get you set up… I’d recommend opening your .czi files using Bio-Formats - just go to File > Import > Bio-Formats. Too - for visualizing - you can use the Channels Tool. That will let you look at both channels simultaneously or just single channels at a time.

A great place to get started with things is to look at these living workshops. They are a great introduction to using ImageJ/Fiji, as well as how to do Segmentation, which is the direction you are going in your work.

Hope this helps a bit to get you started. You can always post more questions as you go…

eta :slight_smile: