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HistomicsTK: A Python toolkit for pathology image analysis algorithms
Fattaneh Pourakpour1, Ákos Szölgyén2,3, Ramin Nateghi4
1Department of Electrical Engineering, McCormick School of Engineering, Northwestern University, USA.
Softwarex
|October 6, 2025
Summary
HistomicsTK is an open-source Python package addressing the underutilization of digital pathology data. It enables histology image analysis, facilitating biomedical research through accessible software tools.
Area of Science:
- Digital pathology and computational biology.
- Biomedical image analysis and bioinformatics.
Background:
- Digital imaging of glass tissue slides generates vast amounts of data.
- This valuable data remains underutilized in biomedical research due to a lack of accessible open-source software.
Purpose of the Study:
- To introduce HistomicsTK, an open-source Python package for histology image analysis.
- To demonstrate its capabilities in preprocessing, segmentation, and feature extraction for building image processing pipelines.
Main Methods:
- HistomicsTK offers preprocessing, segmentation, and feature extraction functionalities.
- It can be used as a standalone Python package or integrated into containerized pipelines via a web interface with the Digital Slide Archive.
Main Results:
- HistomicsTK provides a robust framework for developing histology image analysis workflows.
- Illustrative use cases demonstrate its practical application in biomedical research.
Conclusions:
- HistomicsTK enhances the utility of digital pathology data by providing open-source tools.
- The project fosters community engagement in software development and maintenance for broader impact.
