Metadata-Version: 2.1
Name: cycIFAAP
Version: 5.6.2
Summary: Cyclic ImmunoFluoresence (cycIF) Automatic Analysis Pipeline
Home-page: https://www.thibault.biz/Research/cycIFAAP/cycIFAAP.html
Download-URL: https://www.thibault.biz/Doc/cycIFAAP/cycIFAAP-5.6.2.tar.gz
Author: Guillaume THIBAULT, Erik Burlingame, Young Hwan Chang
Author-email: thibaulg@ohsu.edu, chanyo@ohsu.edu
Maintainer: Guillaume THIBAULT
Maintainer-email: thibaulg@ohsu.edu
License: MIT
Keywords: cyclic Immunofluorescence,cycif,immunofluorescence,registration,segmentation,features,features extraction,restore,napari,nuclei,nucleus,cells,cell,cell analysis,cell type
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Environment :: GPU
Classifier: Environment :: GPU :: NVIDIA CUDA :: 10.2
Classifier: Environment :: Other Environment
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Java
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Image Processing
Classifier: Topic :: Scientific/Engineering :: Image Recognition
Requires-Python: >=3.8,<3.10

# 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


