cycIFAAP

Name	cycIFAAP JSON
Version	5.7.7 JSON
	download
home_page	https://www.thibault.biz/Research/cycIFAAP/cycIFAAP.html
Summary	Cyclic ImmunoFluoresence (cycIF) Automatic Analysis Pipeline
upload_time	2023-07-05 17:38:31
maintainer	Guillaume THIBAULT
docs_url	None
author	Guillaume THIBAULT, Erik Burlingame, Young Hwan Chang
requires_python	>=3.8,<3.10
license	MIT
keywords	cyclic immunofluorescence cycif immunofluorescence registration segmentation features features extraction restore napari nuclei nucleus cells cell cell analysis cell type
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            # 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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