histolab: A Python library for reproducible Digital Pathology preprocessing with automated testing
Alessia Marcolini, Nicole Bussola, Ernesto Arbitrio, Mohamed Amgad, Giuseppe Jurman, Cesare Furlanello
Abstract
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 morphological 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.