Re: Separating intracellular objects from extracellular objects

Posted by Krs5 on
URL: http://imagej.273.s1.nabble.com/Separating-intracellular-objects-from-extracellular-objects-tp5021479p5021489.html

Dear Maria,

Would the 3D watershed or the 3D Spot Segmentation be of use? For both see: http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:start and they are part of the 3D ImageJ suite.

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility

-----Original Message-----
From: María Victoria Pepe <[hidden email]>
Sent: 20 November 2018 15:12
To: [hidden email]
Subject: Separating intracellular objects from extracellular objects

Hi

I´m studying efferocytosis of apoptotic cells by epithelial cells, for which I´m using the *3D Objects Counter* tool. I make a map of the apoptotic cell channel and then, I merge this map with the reslice of the epithelial cells channel. Then I decide if the object in the map is inside or outside the cell.  This is a slow process but generally it works. But there are some problems when I have two objects close to each other, one outside and one inside, because sometimes they are consider like one only object.
How can I generate a solid mask using the reslice of the epithelial cells channel to use it to separate intracellular objects from extracellular objects?


I attached one image as an example.



Thanks for your time

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