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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.

25M 654 163
TissueImageAnalytics
tiatoolbox

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

33K 526 109
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.

16K 14 5
slideflow
slideflow

Powerful, open-source AI tools for digital pathology.

2K 360 64
nadeemlab
deepliif

Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]

2K 249 90
DIAGNijmegen
wholeslidedata

No description available

951 113 31
cytomine
cytomine-python-client

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

840 15 5
SBU-BMI
wsinfer

Run patch-based classification on pathology whole slide images.

658 86 14
tand826
wsiprocess

Whole Slide Image (WSI) Processing Library for Histopathological / Cytopathological Machine Learning Tasks

566 25 3
PingjunChen
pyslide

Digital Pathology Whole Slide Image Analysis Toolbox

462 53 8
luisvalesilva
wsipre

Handling whole-slide images with region-level annotations.

232 10 5
herrmannlab
dicomslide

Python library for reading whole slide images in DICOM format

221 9 3
WonderLandxD
sdpc-for-python

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

145 71 14
jgamper
compay-syntax

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

130 55 1
PingjunChen
tissueloc

Localize the tissue regions in whole slide pathology images.

129 45 12
SBU-BMI
wsinfer-mil

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

108 7 1
WonderLandxD
sdpc-linux

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

95 71 14
btcrabb
slideseg

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

72 80 24
cgohlke
napari-tifffile

Read and write TIFF files.

69 654 163
SBU-BMI
spinpath

Run specimen-level inference on whole slide images.

67 7 1
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