PySlyde: A Lightweight, Open-Source Toolkit for Pathology Preprocessing

TL;DR

PySlyde is an open-source Python toolkit that simplifies and standardizes the preprocessing of whole-slide images in pathology, improving reproducibility and accelerating AI dataset preparation.

Contribution

It introduces a unified, easy-to-use toolkit built on OpenSlide for comprehensive WSI preprocessing tasks, addressing fragmentation in existing workflows.

Findings

Streamlines WSI preprocessing workflows.

Enhances reproducibility of pathology data analysis.

Accelerates AI dataset generation from pathology images.

Abstract

The integration of artificial intelligence (AI) into pathology is advancing precision medicine by improving diagnosis, treatment planning, and patient outcomes. Digitised whole-slide images (WSIs) capture rich spatial and morphological information vital for understanding disease biology, yet their gigapixel scale and variability pose major challenges for standardisation and analysis. Robust preprocessing, covering tissue detection, tessellation, stain normalisation, and annotation parsing is critical but often limited by fragmented and inconsistent workflows. We present PySlyde, a lightweight, open-source Python toolkit built on OpenSlide to simplify and standardise WSI preprocessing. PySlyde provides an intuitive API for slide loading, annotation management, tissue detection, tiling, and feature extraction, compatible with modern pathology foundation models. By unifying these processes, it streamlines WSI preprocessing, enhances reproducibility, and accelerates the generation of AI-ready datasets, enabling researchers to focus on model development and downstream analysis.