I would like to analyze two channels of my primary cell images using Fiji: create a binary mask in one channel and then apply this to my second channel and read the fluorescence intensity in the second channel, normalized to the background. Is there a macro for this? Explicit instructions would be helpful! Thanks!
There is no macro that does exactly this… you’ll have to script one yourself. But that shouldn’t be a problem. Just take a look at the following links and you’ll be well on your way:
- Segmentation page of the ImageJ wiki
- **“Segmentation in Fiji” workshop and corresponding slides (more recently updated slides are here)
- Scripting overview page on the wiki
- **A helpful workshop on Scripting with Fiji - the corresponding slides are here (more recently updates slides are here)
- Introduction into Macro Programming page of the wiki
- Built-In Macro Functions list
The workshops are the best thing to work through… if you have more specific questions after doing that - just post here. We are here to help.
Have you considered using CellProfiler? That’s probably the toolkit that I would use to perform the analysis you describe. These tutorials may help you build your own CellProfiler pipeline:
But of course an ImageJ macro will work. Up to you!