A graph-based cell tracking algorithm with few manually tunable parameters and automated segmentation error correction

PLoS One. 2021 Sep 7;16(9):e0249257. doi: 10.1371/journal.pone.0249257. eCollection 2021.

Abstract

Automatic cell segmentation and tracking enables to gain quantitative insights into the processes driving cell migration. To investigate new data with minimal manual effort, cell tracking algorithms should be easy to apply and reduce manual curation time by providing automatic correction of segmentation errors. Current cell tracking algorithms, however, are either easy to apply to new data sets but lack automatic segmentation error correction, or have a vast set of parameters that needs either manual tuning or annotated data for parameter tuning. In this work, we propose a tracking algorithm with only few manually tunable parameters and automatic segmentation error correction. Moreover, no training data is needed. We compare the performance of our approach to three well-performing tracking algorithms from the Cell Tracking Challenge on data sets with simulated, degraded segmentation-including false negatives, over- and under-segmentation errors. Our tracking algorithm can correct false negatives, over- and under-segmentation errors as well as a mixture of the aforementioned segmentation errors. On data sets with under-segmentation errors or a mixture of segmentation errors our approach performs best. Moreover, without requiring additional manual tuning, our approach ranks several times in the top 3 on the 6th edition of the Cell Tracking Challenge.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Cell Tracking / methods*
  • Computer Graphics
  • Databases, Factual
  • Humans

Grants and funding

We are grateful for funding by the Helmholtz Association in the program Natural, Artificial and Cognitive Information Processing (TS, RM) and HIDSS4Health - the Helmholtz Information & Data Science School for Health (KL, RM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We acknowledge support by the KIT-Publication Fund of the Karlsruhe Institute of Technology.