ROI selection in threshold images

Image 1 : Original Image

Image 2 : Result of “Create Selection”

Image 3 : Result of “Analyze Particles”

I want to select the interior boundaries of each cell as ROI and I want to individually process each cell boundaries. On using “Edit > Selection > Create Selection” option, the selection is a one whole selection. And the processing of such an ROI results in simultaneous processing of all the cells boundaries.

When using Analysis Particle, I get weird results.

I basically want to different roi selection of each cell.[And I want it to be automatic]


Welcome to the Forum!

So… I would threshold & create a mask instead of your create selection call. I did the following steps:

setAutoThreshold("Default dark");
run("Create Mask");
run("Analyze Particles...", "exclude add");

HOWEVER - this was just running it on the cropped ‘original’ image you posted here. But is this truly the original dataset? It would be better to have original dataset to start with…

You can read up more on Segmentation here. There is also a workshop walking through Segmentation. And if you want to automate this all - just check out Scripting and this scripting workshop.

Hope this helps get you started!

eta :slight_smile:

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Thanks for the reply! :smiley:

Can you please provide me an image of the result you got?

This is the original dataset:-

I’m trying to mark the cell memabrane(or the white lines). It can be called cell segmentation too.[This is one of the simplest images] My major aim is get a roi within each cell so that I could apply LevelSet(Active Contours) to get the exact edges of that cell.


I did not save that info - sorry. But you can just follow the code I posted there step-by-step: threshold, create mask, analyze particles… again, that was not done on the ‘real’ data anyway.

Given the image you just posted now - I would say you should really take a look at using the Morphological Segmentation plugin. That should do what you need! Just read up on that page and you can always do another post if you need more specific help.

eta :slight_smile: