On Benchmarking Cell Nuclei Segmentation Algorithms for Fluorescence Microscopy

Frederike Wirth, Eva-Maria Brinkmann, Klaus Brinker

2020

Abstract

Cell nuclei detection is an essential step in the context of many image analysis tasks related to microscopy images and therefore also plays a role in highly topical fields of research like the development of personalised immunotherapy approaches against several types of cancer. Motivated by this observation, a whole zoo of advanced methods to accomplish cell nuclei segmentation has been proposed in recent years. This development in turn stresses the need to set up a well-justified and reproducible standard of comparison for the evaluation of these sophisticated approaches. In this paper, we describe how such a reference framework based on standard seeded watershed segmentation for fully automatic cell nuclei detection can be obtained. In particular, we provide a detailed review of a publicly available dataset, give a detailed account of the methods and evaluation measures we consider to enable the highest possible reproducibility of our results and discuss the suitability of different variants of seeded watershed segmentation for the mentioned purposes.

Paper Citation

in Harvard Style

Wirth F., Brinkmann E. and Brinker K. (2020). On Benchmarking Cell Nuclei Segmentation Algorithms for Fluorescence Microscopy. In Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - Volume 2: BIOIMAGING; ISBN 978-989-758-398-8, SciTePress, pages 164-171. DOI: 10.5220/0008967901640171

in Bibtex Style

@conference{bioimaging20,
author={Frederike Wirth and Eva-Maria Brinkmann and Klaus Brinker},
title={On Benchmarking Cell Nuclei Segmentation Algorithms for Fluorescence Microscopy},
booktitle={Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - Volume 2: BIOIMAGING},
year={2020},
pages={164-171},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0008967901640171},
isbn={978-989-758-398-8},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - Volume 2: BIOIMAGING
TI - On Benchmarking Cell Nuclei Segmentation Algorithms for Fluorescence Microscopy
SN - 978-989-758-398-8
AU - Wirth F.
AU - Brinkmann E.
AU - Brinker K.
PY - 2020
SP - 164
EP - 171
DO - 10.5220/0008967901640171
PB - SciTePress