histolab: A Python library for reproducible Digital Pathology preprocessing with automated testing

Deep Learning (DL) is rapidly permeating the field of Digital Pathology with algorithms successfully applied to ease daily clinical practice and to discover novel associations. However, most DL workflows for Digital Pathology include custom code for data preprocessing, usually tailored to data and tasks of interest, resulting in software that is error-prone and hard to understand, peer-review, and test. In this work, we introduce histolab, a Python package designed to standardize the preprocessing of Whole Slide Images in a reproducible environment, supported by automated testing. In addition, the package provides functions for building datasets of WSI tiles, including augmentation and morpho-logical operators, a tile scoring framework, and stain normalization methods. histolab is modular, extensible, and easily integrable into DL pipelines, with support of the OpenSlide and large_image backends. To guarantee robustness, histolab embraces software engineering best practices such as multiplatform automated testing and Continuous Integration.(c) 2022 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Automated summary

This study introduces histolab, a Python package for standardizing the preprocessing of whole slide images in digital pathology. The package is supported by automated testing and provides functionalities such as building tile datasets, augmentation and morpho-logical operators, tile scoring framework, and stain normalization methods.