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

Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]

wholeslidedata

No description available

cytomine-python-client

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

wsinfer

Run patch-based classification on pathology whole slide images.

wsiprocess

Whole Slide Image (WSI) Processing Library for Histopathological / Cytopathological Machine Learning Tasks

pyslide

Digital Pathology Whole Slide Image Analysis Toolbox

wsipre

Handling whole-slide images with region-level annotations.

dicomslide

Python library for reading whole slide images 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.

tissueloc

Localize the tissue regions in whole slide pathology images.

wsinfer-mil

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

sdpc-linux

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

slideseg

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

napari-tifffile

Read and write TIFF files.

spinpath

Run specimen-level inference on whole slide images.