Cell detection with star-convex polygons

Research output: Contribution to book/Conference proceedings/Anthology/ReportConference contributionContributedpeer-review

Contributors

  • Uwe Schmidt - , Max Planck Institute of Molecular Cell Biology and Genetics, Center for Systems Biology Dresden (CSBD) (Author)
  • Martin Weigert - , Max Planck Institute of Molecular Cell Biology and Genetics, Center for Systems Biology Dresden (CSBD) (Author)
  • Coleman Broaddus - , Max Planck Institute of Molecular Cell Biology and Genetics, Center for Systems Biology Dresden (CSBD) (Author)
  • Gene Myers - , Max Planck Institute of Molecular Cell Biology and Genetics, Center for Systems Biology Dresden (CSBD), TUD Dresden University of Technology (Author)

Abstract

Automatic detection and segmentation of cells and nuclei in microscopy images is important for many biological applications. Recent successful learning-based approaches include per-pixel cell segmentation with subsequent pixel grouping, or localization of bounding boxes with subsequent shape refinement. In situations of crowded cells, these can be prone to segmentation errors, such as falsely merging bordering cells or suppressing valid cell instances due to the poor approximation with bounding boxes. To overcome these issues, we propose to localize cell nuclei via star-convex polygons, which are a much better shape representation as compared to bounding boxes and thus do not need shape refinement. To that end, we train a convolutional neural network that predicts for every pixel a polygon for the cell instance at that position. We demonstrate the merits of our approach on two synthetic datasets and one challenging dataset of diverse fluorescence microscopy images.

Details

Original languageEnglish
Title of host publicationMedical Image Computing and Computer Assisted Intervention – MICCAI 2018
Pages265-273
Number of pages9
ISBN (electronic)978-3-030-00934-2
Publication statusPublished - 2018
Peer-reviewedYes

Publication series

SeriesLecture Notes in Computer Science
Volume11071
ISSN0302-9743

External IDs

Scopus 85054101388
ORCID /0000-0002-7780-9057/work/176863466

Keywords