Digital Pathology Python Packages

wsidicom

Python package for reading DICOM WSI file sets.

59K 51 10

cucim

cuCIM - RAPIDS GPU-accelerated image processing library

44K 463 84

tiffslide

TiffSlide - cloud native openslide-python replacement based on tifffile

39K 107 12

torchstain

Stain normalization tools for histological analysis and computational pathology

23K 185 30

opentile

Python library for reading tiles from wsi tiff-files.

16K 17 6

cucim-cu12

cuCIM - RAPIDS GPU-accelerated image processing library

15K 463 84

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.

13K 14 5

tiatoolbox

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

10K 537 106

cucim-cu13

cuCIM - RAPIDS GPU-accelerated image processing library

4K 463 84

cellseg-models-pytorch

Encoder-Decoder Cell and Nuclei segmentation models

4K 103 6

histolab

Library for Digital Pathology Image Processing

4K 460 66

paquo

PAthological QUpath Obsession - QuPath and Python conversations

3K 135 19

cytomine-python-client

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

2K 20 7

pilotpy

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

2K 26 8

cucim-cu11

cuCIM - RAPIDS GPU-accelerated image processing library

1K 463 84

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

1K 12 9

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]

1K 254 91