School of Medicine Publications and Presentations
Document Type
Article
Publication Date
4-16-2025
Abstract
The application of digital pathology tools has expanded in recent years, but non-neoplastic human brain tissue presents unique challenges due to its complexity. This study evaluated HALO and QuPath tau quantification performance in the hippocampus and mid-frontal gyrus across various tauopathies. Percent positivity emerged as the most reliable measure, showing strong correlations with Braak stages and CERAD scores, outperforming object and optical densities. QuPath demonstrated superior correlations with Braak stages, while HALO excelled in aligning with CERAD scoring. However, HALO’s optical density was less consistent. Paired t-tests revealed significant differences in object and optical densities between platforms, though percent positivity was consistent across both. QuPath’s threshold-based object density showed similar agreement with manual counts compared to HALO’s AI-dependent approach (all ρ > 0.70). Reanalysis of QuPath further improved its agreement with manual measurements and correlations with Braak and CERAD scores (all ρ > 0.70). HALO offers a user-friendly interface and excels in certain metrics but is hindered by frequent software malfunctions and more limited flexibility. In contrast, QuPath’s customizable workflows and superior performance in Braak staging make it more suitable for advanced and larger-scale analyses. Overall, our study highlights the strengths and limitations of these platforms, helping guide their application in neuropathology.
Recommended Citation
Gonzalez, A. D., Wadop, Y. N., Danner, B., Clarke, K. M., Dopler, M. B., Ghaseminejad-Bandpey, A., ... & Flanagan, M. E. (2025). Digital pathology in tau research: A comparison of QuPath and HALO. Journal of Neuropathology & Experimental Neurology, nlaf026. https://doi.org/10.1093/jnen/nlaf026
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License
Publication Title
Journal of Neuropathology & Experimental Neurology
DOI
10.1093/jnen/nlaf026
Academic Level
faculty
Mentor/PI Department
Neuroscience
Comments
© The Author(s) 2025. Published by Oxford University Press on behalf of American Association of Neuropathologists, Inc. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.