alihashmiii / 3d-segmentation-of-cell-nuclei

segment cell nuclei in a 3-D cluster

3D-Segmentation-of-Cell-Nuclei-in-Aggregates

Authors: @Jan Liphardt (Stanford) and @Ali Hashmi with help from Anton-Antonov for Quantile-Envelopes

Date: 2015

The Mathematica Package QuantileNucleiSegmentation.m can be used to segment cell nuclei in spheroid bodies. The algorithm relies on an elaborate 3D watershed segmentation scheme coupled with Quantile Envelopes to bound nuclei.

Note: the package is not yet fully optimized for speed. Although I know of a few ways (SparseArray implementations at a few places etc..) to speed up the code, I do not have sufficient time at present to implement those schemes.

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