ROI marking in z, background correction, measuring intensities

I have a z-stack image in 4 channels. I want to achieve the following:

  1. to mark roi (to mark the cell)
  2. to background correct
  3. to measure intensities in all four channels from this roi.

Ideally, I would like to mark the cell out in z.

Can this process be automated?

It would be a great help if anyone can suggest any plugin/ any other way to do this!

I would suggest you to have a look at the scripting system of Fiji (in Python here) :

You should find all the informations you need to achieve what you want.

Feel free to ask questions here if you need help.

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See the Segmentation page of the ImageJ wiki for an overview of how to do everything you seek.

Yes, see the Batch page for an introduction.