Hybridization Particle Analysis

Hi everyone!

This may be a very simple question, and it might have been answered already, but I’m very new to ImageJ/computer analysis software in general and would appreciate any pointers. I have samples of rat brain tissue that have been prepared through fluorescent in-situ hybridization to tag mRNA. My goal is to create a macro that automatically counts how many particles of tagged mRNA are in each cell of the sample. However, due to staining artifacts and background fuzziness, I am having issues isolating the particles, as well as developing a good way of segmenting the cells from background/each other.


Again, any help is appreciated!

Hey @lbmcp!!

Welcome to the Forum!

I’m going to point you to this other Forum post to help you get started with some helpful links for beginners to ImageJ/Fiji.

You should definitely look into the Trainable Weka Segmentation plugin. That would be the first tool for you to use to segment your cells.

Have a look at those links to get a start… if you have more specific questions - just post again. We are all here to help!

eta :slight_smile:

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