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mahmoodlab / PathomicFusion

Fusing Histology and Genomics via Deep Learning - IEEE TMI
http://www.mahmoodlab.org
GNU General Public License v3.0
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KNN for Cell Graph Construction #5

Closed sgudaparthi closed 3 years ago

sgudaparthi commented 3 years ago

I could not find the part in the code where a cell graph is constructed from the histology image (segmented using cGAN). I have two questions in this regard:

  1. Could you point me to the code (maybe line numbers) where edge detection using top-K nearest neighbor is performed?
  2. Is cGAN part of this code? If not, where should I store the instance mask in the file system after performing nuclei segmentation?
Richarizardd commented 3 years ago

Hi @sgudaparthi, thank you for your interest in our repository.

  1. I just added a Jupyter Notebook w/ example data on how graph construction is done.
  2. cGAN is not part of the code, but can be found in our other code base at: https://github.com/mahmoodlab/NucleiSegmentation