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) : http://imagej.net/Jython_Scripting

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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4 posts were split to a new topic: Calculate size of nonspherical nanoparticles

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.