HistomicsTK: A Python toolkit for pathology image analysis algorithms

Growth in the digital imaging of glass tissue slides has produced petabytes of data, however, this data remains underutilized in biomedical research due in part to a lack of open-source software. HistomicsTK is an open-source Python package that provides preprocessing, segmentation, and feature extr...

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Published inSoftwareX Vol. 31; p. 102318
Main Authors Pourakpour, Fattaneh, Szölgyén, Ákos, Nateghi, Ramin, Gutman, David A, Manthey, David, Cooper, Lee AD
Format Journal Article
LanguageEnglish
Published Netherlands Elsevier B.V 01.09.2025
Elsevier
Subjects
Digital pathology
Image analysis
Medical imaging
Microscopy
Pathology
Digital pathology
Pathology
Image analysis
Medical imaging
Microscopy
Online AccessGet full text
ISSN2352-7110
2352-7110
DOI10.1016/j.softx.2025.102318

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Summary:Growth in the digital imaging of glass tissue slides has produced petabytes of data, however, this data remains underutilized in biomedical research due in part to a lack of open-source software. HistomicsTK is an open-source Python package that provides preprocessing, segmentation, and feature extraction capabilities for building histology image processing pipelines. HistomicsTK can function as a standalone Python package or serve containerized pipelines through a web-based interface using the Digital Slide Archive platform. This paper provides an overview of HistomicsTK with illustrative use cases and describes how this project engages the community in software development and maintenance.
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ISSN:2352-7110
2352-7110
DOI:10.1016/j.softx.2025.102318