Scientific article
OA Policy
English

HoverFast : an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images

Published inJournal of open source software, vol. 9, no. 101, 7022
Publication date2024-09-26
Abstract

In computational digital pathology, accurate nuclear segmentation of Hematoxylin and Eosin (H&E) stained whole slide images (WSIs) is a critical step for many analyses and tissue characterizations. One popular deep learning-based nuclear segmentation approach, Hover- Net (Graham et al., 2019), offers remarkably accurate results but lacks the high-throughput performance needed for clinical deployment in resource-constrained settings. Our approach, HoverFast, aims to provide fast and accurate nuclear segmentation in H&E images using knowledge distillation from HoverNet. By redesigning the tool with software engineering best practices, HoverFast introduces advanced parallel processing capabilities, efficient data han- dling, and optimized postprocessing. These improvements facilitate scalable high-throughput performance, making HoverFast more suitable for real-time analysis and application in resource- limited environments. Using a consumer grade Nvidia A5000 GPU, HoverFast showed a 21x speed improvement as compared to HoverNet; reducing mean analysis time for 40x WSIs from ~2 hours to 6 minutes while retaining a concordant mean Dice score of 0.91 against the original HoverNet output. Peak memory usage was also reduced 71% from 44.4GB, to 12.8GB, without requiring SSD-based caching. To ease adoption in research and clinical contexts, HoverFast aligns with best-practices in terms of (a) installation, and (b) containerization, while (c) providing outputs compatible with existing popular open-source image viewing tools such as QuPath (Bankhead et al., 2017). HoverFast has been made open-source and is available at andrewjanowczyk.com/open-source-tools/hoverfast.

Citation (ISO format)
LIAKOPOULOS, Petros et al. HoverFast : an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images. In: Journal of open source software, 2024, vol. 9, n° 101, p. 7022. doi: 10.21105/joss.07022
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Additional URL for this publicationhttps://joss.theoj.org/papers/10.21105/joss.07022
Journal ISSN2475-9066
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