HCRprocess

HCRprocess (GitHub) is an HCR-mFISH image processing pipeline written in MATLAB and Python 3 by Jack Vincent. It is composed of components developed by Jack Vincent, Michael Economo, and Will Cunningham.

Quickstart guide:

• Installation
• Input Files

Usage:

• Main
• Core Pipeline
  • Stitching
  • Spectral Unmixing
  • Registration
  • Finishing
• Post-processing
  • Allen CCF Registration
  • Cellpose-SAM Mask Segmentation and Quality Control
  • Final Cell Quality Control
• Core Manual GUIs
  • Spectral Unmixing GUI
  • Finding Fiducials GUI
• Post Processing Manual GUIs
  • Block Cut GUI
  • Finding Fiducials GUI
  • Lipofuscin Removal GUI
• Histology