3 Jul 2020

Segmentation of Pathological Osteocytes in an Undecalcified Piece of Mouse Bone using Amira-Avizo2D

This is a workflow to segment out osteocytes in mouse bone sample using Amira-Avizo2D.


This Amira-Avizo2D workflow segments out osteocytes present in mouse bone sample. The sample was acquired using a transmission electron microscope at 200kV and a magnification of 13.500x.

The image processing challenge was to isolate the osteocytes from the multitude of other cellular structures present in the sample. Simple thresholding would not suffice as all the cellular structures are at similar grayscale intensities.

To overcome the challenge, the image was first denoised and then a structure enhancing module was applied to isolate the elongated osteocytes. Then a thresholding was applied and the unwanted noise was removed. Finally the osteocytes were labelled as separate structures and can be used for further analysis.