Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform.
With the continuous expansion of single cell biology, the observation of the behaviour of individual cells over extended durations and with high accuracy has become a problem of central importance. Surprisingly, even for yeast cells that have relatively regular shapes, no solution has been proposed that reaches the high quality required for long-term experiments for segmentation and tracking (S&T) based on brightfield images. Here, we presentCellStar, a tool chain designed to achieve good performance in long-term experiments. The key features are the use of a new variant of parametrized active rays for segmentation, a neighbourhood-preserving criterion for tracking, and the use of an iterative approach that incrementally improves S&T quality. A graphical user interface enables manual corrections of S&T errors and their use for the automated correction of other, related errors and for parameter learning. We created a benchmark dataset with manually analysed images and comparedCellStarwith six other tools, showing its high performance, notably in long-term tracking. As a community effort, we set up a website, the Yeast Image Toolkit, with the benchmark and theEvaluation Platformto gather this and additional information provided by others.
BioComputing, CRIStAL, Université Lille 1, Lille, France Cristian.Versari@univ-lille1.fr.
Cristian
C
Versari
Scientific Center for Optical and Electron Microscopy (ScopeM), ETH Zurich, Zurich, Switzerland.
Szymon
S
Stoma
BioComputing, CRIStAL, Université Lille 1, Lille, France.
Kirill
K
Batmanov
Laboratoire Matières et Systèmes Complexes, UMR7057, CNRS and Université Paris Diderot, Paris, France.|Inria and Université Paris-Saclay, Palaiseau, France.
Artémis
A
Llamosi
Institute of Computer Science, University of Wroclaw, Wroclaw, Poland.
Filip
F
Mroz
Institute of Computer Science, University of Wroclaw, Wroclaw, Poland.
Adam
A
Kaczmarek
Laboratoire Matières et Systèmes Complexes, UMR7057, CNRS and Université Paris Diderot, Paris, France.
Matt
M
Deyell
BioComputing, CRIStAL, Université Lille 1, Lille, France.
Cédric
0000-0002-3970-3761
C
Lhoussaine
Laboratoire Matières et Systèmes Complexes, UMR7057, CNRS and Université Paris Diderot, Paris, France.
Pascal
0000-0003-2379-4280
P
Hersen
Inria and Université Paris-Saclay, Palaiseau, France.
Gregory
0000-0003-1697-139X
G
Batt
D058948:Cell Tracking / Q000295:instrumentation* / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D012568:Schizosaccharomyces / Q000166:cytology*
image analysis; imaging benchmark; parameter learning; segmentation and tracking