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Deep learning nuclei detection: A simple approach can deliver state-of-the-art results
Fraunhofer MEVIS, Germany.
Fraunhofer MEVIS, Germany.
Fraunhofer MEVIS, Germany.
Sectra AB, Teknikringen 20, S-58330 Linkoping, Sweden.
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2018 (English)In: Computerized Medical Imaging and Graphics, ISSN 0895-6111, E-ISSN 1879-0771, Vol. 70, p. 43-52Article in journal (Refereed) Published
Abstract [en]

Background: Deep convolutional neural networks have become a widespread tool for the detection of nuclei in histopathology images. Many implementations share a basic approach that includes generation of an intermediate map indicating the presence of a nucleus center, which we refer to as PMap. Nevertheless, these implementations often still differ in several parameters, resulting in different detection qualities. Methods: We identified several essential parameters and configured the basic PMap approach using combinations of them. We thoroughly evaluated and compared various configurations on multiple datasets with respect to detection quality, efficiency and training effort. Results: Post-processing of the PMap was found to have the largest impact on detection quality. Also, two different network architectures were identified that improve either detection quality or runtime performance. The best-performing configuration yields f1-measures of 0.816 on Hamp;E stained images of colorectal adenocarcinomas and 0.819 on Ki-67 stained images of breast tumor tissue. On average, it was fully trained in less than 15,000 iterations and processed 4.15 megapixels per second at prediction time. Conclusions: The basic PMap approach is greatly affected by certain parameters. Our evaluation provides guidance on their impact and best settings. When configured properly, this simple and efficient approach can yield equal detection quality as more complex and time-consuming state-of-the-art approaches. (C) 2018 The Authors. Published by Elsevier Ltd.

Place, publisher, year, edition, pages
PERGAMON-ELSEVIER SCIENCE LTD , 2018. Vol. 70, p. 43-52
Keywords [en]
Nuclei detection; Deep learning; PMap; Histology; Image analysis
National Category
Medical Image Processing
Identifiers
URN: urn:nbn:se:liu:diva-153683DOI: 10.1016/j.compmedimag.2018.08.010ISI: 000453497000005PubMedID: 30286333OAI: oai:DiVA.org:liu-153683DiVA, id: diva2:1276228
Note

Funding Agencies|Fraunhofer Society, Munich, Germany; Vinnova grant [2014-04257]

Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2019-01-07

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