Whole Slide Imaging Python Packages

tifffile

Read and write TIFF files.

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.

tiatoolbox

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

cytomine-python-client

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

wholeslidedata

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

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]

kfbslide

纯 Python KFB（KFBio）数字病理切片读取库，提供与 OpenSlide 完全兼容的 API

slideflow

Powerful, open-source AI tools for digital pathology.

raw2features

OME-Zarr whole-slide images to patch- and slide-level foundation-model embeddings - cloud-native, FAIR, model- and backend-agnostic.

wsinfer

Run patch-based classification on pathology whole slide images.

pyslide

Python whole slide image analysis toolkit

wsiprocess

Whole Slide Image (WSI) Processing Library

dicomslide

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

sdpc-for-python

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

compay-syntax

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

wsipre

Handling whole-slide images with region-level annotations.

sdpc-linux

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

tissueloc

Localize the tissue regions in whole slide pathology images.

wsinfer-mil

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

napari-tifffile

Read and write TIFF files.

spinpath

Run specimen-level inference on whole slide images.

slideseg

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