Whole Slide Imaging Python Packages

tifffile

Read and write TIFF files.

tiatoolbox

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

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.

slideflow

Powerful, open-source AI tools for digital pathology.

deepliif

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

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.

wsinfer

🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images

wsiprocess

Whole Slide Image (WSI) Processing Library

pyslide

Digital Pathology Whole Slide Image Analysis Toolbox

dicomslide

Library for reading whole slide images and derived information in DICOM 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-for-python

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

tissueloc

Whole Slide Digital Pathology Image Tissue Localization

sdpc-linux

a library for sdpcPY (linux version)

napari-tifffile

A napari plugin for reading files via tifffile

wsinfer-mil

CLI tool to 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.

spinpath

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