Random-walk Segmentation of Nuclei in Fluorescence Microscopic Images with Automatic Seed Detection

Tabea Margareta Grace Pakull, Frederike Wirth, Klaus Brinker

2022

Abstract

In personalized immunotherapy against cancer analysis of cell nuclei in tissue samples can provide helpful information to predict whether the benefits of the therapy outweigh the usually severe side effects. Since segmentation of nuclei is the basis for all further analyses of cell images, research into suitable methods is of particular relevance. In this paper we present and evaluate two versions of a segmentation pipeline based on the established random-walk method. These versions contain automatic seed detection, using a distance transformation in one of them. In addition, we present a method to select the required hyper-parameter of the random-walk algorithm. The evaluation using a benchmark dataset shows that promising results can be achieved with respect to common evaluation metrics. Furthermore, the segmentation accuracy can compete with a reference CellProfiler segmentation pipeline, based on the watershed transformation. Based on the presented pipeline, the random-walk method can also be integrated into more advanced pipelines to further improve segmentation results.

Paper Citation

in Harvard Style

Pakull T., Wirth F. and Brinker K. (2022). Random-walk Segmentation of Nuclei in Fluorescence Microscopic Images with Automatic Seed Detection. In Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2022) - Volume 2: BIOIMAGING; ISBN 978-989-758-552-4, SciTePress, pages 103-110. DOI: 10.5220/0010780400003123

in Bibtex Style

@conference{bioimaging22,
author={Tabea Margareta Grace Pakull and Frederike Wirth and Klaus Brinker},
title={Random-walk Segmentation of Nuclei in Fluorescence Microscopic Images with Automatic Seed Detection},
booktitle={Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2022) - Volume 2: BIOIMAGING},
year={2022},
pages={103-110},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0010780400003123},
isbn={978-989-758-552-4},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2022) - Volume 2: BIOIMAGING
TI - Random-walk Segmentation of Nuclei in Fluorescence Microscopic Images with Automatic Seed Detection
SN - 978-989-758-552-4
AU - Pakull T.
AU - Wirth F.
AU - Brinker K.
PY - 2022
SP - 103
EP - 110
DO - 10.5220/0010780400003123
PB - SciTePress