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Cyclic ImmunoFluoresence (cycIF) Automatic Analysis Pipeline

Project description

# Cyclic ImmunoFluorescence Automatic Analysis Pipeline

This pipeline takes as input a set of cyclic immunofluorescence (cycIF) images and performs the following operations:
  • Registration

  • Nuclei segmentation (using CellPose or own trained Mask R-CNN model)

  • Background subtraction

  • Compute each marker exclusiveness to be used with Restore

  • Use Restore when possible for automatic gating (optionnal)

  • Features extraction

  • Cell type computation

  • Automatic visualization using Napari

  • Quality control (tissue loss and Restore based)

For installation, more information/details and full examples with code and data, visit: https://www.thibault.biz/Research/cycIFAAP/cycIFAAP.html

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