Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform - Inria - Institut national de recherche en sciences et technologies du numérique
Article Dans Une Revue Journal of the Royal Society Interface Année : 2017

Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform

Résumé

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 present CellStar, 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 seg-mentation, 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 compared CellStar with 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 the Evaluation Platform to gather this and additional information provided by others.
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Dates et versions

hal-01547623 , version 1 (27-06-2017)

Identifiants

Citer

Cristian Versari, Szymon Stoma, Kirill Batmanov, Artémis Llamosi, Filip Mroz, et al.. Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform. Journal of the Royal Society Interface, 2017, 14 (127), pp.32. ⟨10.1098/rsif.2016.0705⟩. ⟨hal-01547623⟩
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