Whole Slide Imaging Python Packages | PyRank

tifffile

Read and write TIFF files.

19.3M 670 164

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.

7K 14 4

tiatoolbox

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

3K 557 113

lazyslide

Accessible and interoperable whole slide image analysis for digital pathology in Python

2K 328 32

wholeslidedata

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

2K 119 31

kfbslide

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

1K 16 2

slideflow

Powerful, open-source AI tools for digital pathology.

768 376 66

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, MICCAI'26]

594 263 90

cytomine-python-client

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

355 26 11

pyslide

Digital Pathology Whole Slide Image Analysis Toolbox

296 55 10

wsinfer

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

290 87 14

wsiprocess

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

222 25 3

imzdesk

WSI-MSI Workbench

213 0 0

deepspotm

Multimodal foundation model predicting transcriptome-wide virtual spatial transcriptomics from histology.

186 59 10

dicomslide

Python library for reading whole slide images in DICOM format

170 9 3

sdpc-for-python

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

156 78 15

raw2features

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

152 4 2

pyisyntax-fastio

Unofficial pyisyntax fork with positional I/O and bounded codeblock prefetching

94 0 0

tissueloc

Whole Slide Digital Pathology Image Tissue Localization

91 45 12

compay-syntax

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

83 55 1

spinpath

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

78 7 1

histopia

Histology Spatial Topology for Omics Profiling and Inter-section Alignment

74 748 6

sdpc-linux

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

71 78 15

wsipre

Handling whole-slide images with region-level annotations.

71 10 5