HoverFast: an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images
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| Main Authors: | , , , , , , , , , |
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| Format: | Preprint |
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2024
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| _version_ | 1866917673593470976 |
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| author | Liakopoulos, Petros Massonnet, Julien Bonjour, Jonatan Mizrakli, Medya Tekes Graham, Simon Cuendet, Michel A. Seipel, Amanda H. Michielin, Olivier Merkler, Doron Janowczyk, Andrew |
| author_facet | Liakopoulos, Petros Massonnet, Julien Bonjour, Jonatan Mizrakli, Medya Tekes Graham, Simon Cuendet, Michel A. Seipel, Amanda H. Michielin, Olivier Merkler, Doron Janowczyk, Andrew |
| contents | 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, HoverNet, 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 handling, 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. HoverFast has been made open-source and is available at andrewjanowczyk.com/open-source-tools/hoverfast. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2405_14028 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | HoverFast: an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images Liakopoulos, Petros Massonnet, Julien Bonjour, Jonatan Mizrakli, Medya Tekes Graham, Simon Cuendet, Michel A. Seipel, Amanda H. Michielin, Olivier Merkler, Doron Janowczyk, Andrew Quantitative Methods 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, HoverNet, 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 handling, 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. HoverFast has been made open-source and is available at andrewjanowczyk.com/open-source-tools/hoverfast. |
| title | HoverFast: an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images |
| topic | Quantitative Methods |
| url | https://arxiv.org/abs/2405.14028 |