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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- Download URL: cycIFAAP-5.7.7-py3-none-any.whl
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- Uploaded via: twine/4.0.2 CPython/3.9.12
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