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Whole Slide Imaging Python Packages

Python packages with the GitHub topic whole-slide-imaging. Sorted by relevance, with stars and monthly downloads.
cgohlke
tifffile

Read and write TIFF files.

26M 655 163
TissueImageAnalytics
tiatoolbox

Computational Pathology Toolbox developed by TIA Centre, University of Warwick.

35K 527 107
aignostics
aignostics

🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library.

17K 14 5
slideflow
slideflow

Powerful, open-source AI tools for digital pathology.

2K 361 64
nadeemlab
deepliif

DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification

1K 250 90
cytomine
cytomine-python-client

A web platform for collaborative analysis of very large bio-medical images

757 18 6
DIAGNijmegen
wholeslidedata

A package for working with whole-slide data including a fast batch iterator that can be used to train deep learning models.

567 114 31
SBU-BMI
wsinfer

🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images

544 85 14
tand826
wsiprocess

Whole Slide Image (WSI) Processing Library

410 25 3
PingjunChen
pyslide

Digital Pathology Whole Slide Image Analysis Toolbox

335 53 8
herrmannlab
dicomslide

Library for reading whole slide images and derived information in DICOM format.

229 9 3
jgamper
compay-syntax

:microscope: Syntax - the arrangement of whole-slide-images and their image tiles to create well-formed computational pathology pipelines.

170 55 1
luisvalesilva
wsipre

Handling whole-slide images with region-level annotations.

145 10 5
WonderLandxD
sdpc-for-python

Python library for processing whole slide images (WSIs) in sdpc format

132 71 14
PingjunChen
tissueloc

Whole Slide Digital Pathology Image Tissue Localization

121 45 12
WonderLandxD
sdpc-linux

a library for sdpcPY (linux version)

89 71 14
cgohlke
napari-tifffile

A napari plugin for reading files via tifffile

84 655 163
SBU-BMI
wsinfer-mil

CLI tool to run specimen-level inference on whole slide images

83 7 1
btcrabb
slideseg

A Python module that produces image patches and annotation masks from whole slide images for deep learning in digital pathology.

81 80 24
SBU-BMI
spinpath

CLI tool to run specimen-level inference on whole slide images

80 7 1
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