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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
PubMed
Summary
This summary is machine-generated.

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.

Keywords:
Digital pathologyImage analysisMedical imagingMicroscopyPathology

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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.