PyPI Stats

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.

112K 49 10
Bayer-Group
tiffslide

TiffSlide - cloud native openslide-python replacement based on tifffile

46K 106 12
TissueImageAnalytics
tiatoolbox

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

33K 526 109
EIDOSlab
torchstain

Stain normalization tools for histological analysis and computational pathology

29K 179 30
rapidsai
cucim

cuCIM - RAPIDS GPU-accelerated image processing library

26K 456 81
rapidsai
cucim-cu12

cuCIM - RAPIDS GPU-accelerated image processing library

19K 456 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.

16K 14 5
histolab
histolab

Library for Digital Pathology Image Processing

13K 456 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

2K 100 5
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
TIO-IKIM
pathopatch

PathoPatcher is a Python project designed for accelerating Whole Slide Image Preprocessing, employing AI-based preprocessing techniques with features like annotation handling, color normalization, and configurable parameters

2K 11 8
rapidsai
cucim-cu13

cuCIM - RAPIDS GPU-accelerated image processing library

1K 456 81
rapidsai
cucim-cu11

cuCIM - RAPIDS GPU-accelerated image processing library

1K 456 81
CostaLab
pilotpy

Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)

1K 26 8
Dana-Farber-AIOS
pathml

Tools for computational pathology

1K 451 89
bayer-science-for-a-better-life
paquo

PAthological QUpath Obsession - QuPath and Python conversations

1K 134 19
sumanthratna
viewmask

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

949 4 1
hutaobo
histoseg

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

871 0 0
cytomine
cytomine-python-client

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

840 15 5
CielAl
torch-staintools

GPU-accelerated Stain Normalization and Augmentation in PyTorch

826 43 5
CamiloSinningUN
glasscut

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

511 0 0
HautaniemiLab
histolytics

Interpretable Analysis of Histological WSIs

415 17 0
okunator
cellseg-gsontools

Toolbelt for merging and extracting features from geojson masks.

371 19 0