PyRank

Digital Pathology Python Packages

Python packages with the GitHub topic digital-pathology. Sorted by relevance, with stars and monthly downloads.
imi-bigpicture
wsidicom

Python package for reading DICOM WSI file sets.

94K 49 10
Bayer-Group
tiffslide

TiffSlide - cloud native openslide-python replacement based on tifffile

38K 107 12
TissueImageAnalytics
tiatoolbox

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

35K 527 107
EIDOSlab
torchstain

Stain normalization tools for histological analysis and computational pathology

33K 179 30
rapidsai
cucim

cuCIM - RAPIDS GPU-accelerated image processing library

27K 457 81
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
rapidsai
cucim-cu12

cuCIM - RAPIDS GPU-accelerated image processing library

15K 457 81
histolab
histolab

Library for Digital Pathology Image Processing

13K 457 66
imi-bigpicture
opentile

Python library for reading tiles from wsi tiff-files.

6K 16 5
okunator
cellseg-models-pytorch

Encoder-Decoder Cell and Nuclei segmentation models

3K 100 5
rapidsai
cucim-cu11

cuCIM - an extensible toolkit designed to provide GPU accelerated I/O, computer vision & image processing primitives for N-Dimensional images with a focus on biomedical imaging.

2K 457 81
nadeemlab
deepliif

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

1K 250 90
rapidsai
cucim-cu13

cuCIM - RAPIDS GPU-accelerated image processing library

1K 457 81
CostaLab
pilotpy

PatIent Level analysis with Optimal Transport (PILOT)

1K 26 8
CielAl
torch-staintools

GPU-accelerated Stain Normalization and Augmentation in PyTorch

998 43 5
TIO-IKIM
pathopatch

PathoPatch - Accelerating Artificial Intelligence Based Whole Slide Image Analysis with an Optimized Preprocessing Pipeline

996 11 8
hutaobo
histoseg

Python toolkit for H&E image analysis and spatial contour analysis.

859 0 0
sumanthratna
viewmask

A Python package and CLI to view XML annotations and NumPy masks.

775 4 1
cytomine
cytomine-python-client

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

757 18 6
Dana-Farber-AIOS
pathml

Tools for computational pathology

748 452 89
bayer-science-for-a-better-life
paquo

PAthological QUpath Obsession - QuPath and Python conversations

723 134 19
CamiloSinningUN
glasscut

A lightweight, extensible toolkit for preprocessing and analyzing whole slide images (WSI) in digital pathology.

582 0 0
okunator
cellseg-gsontools

Toolbelt for merging and extracting features from geojson masks.

458 19 0
HautaniemiLab
histolytics

Interpretable Analysis of Histological WSIs

379 17 0