Moreover, microfluidics can be used to create time-varying environments. One can take advantage of microfluidic microchemostat that, unlike liquid bulk culture, enables long-term observations of cells growing as a monolayer. This is a decisive advantage to investigate a number of important biological problems, including chronological ageing, epigenetic heritability and dynamic features such as the cell cycle and circadian oscillations in non-synchronized cell populations. The former provides great statistical details on the diversity of the studied cell population, whereas the latter provides longitudinal information on single cells: individual cells can be tracked in time. Used in combination with fluorescence reporter techniques, flow cytometry and time-lapse microscopy are arguably the two most widely employed quantitative single-cell observation approaches. Observing cellular processes at the single cell level is often necessary to understand how cells respond to endogenous and environmental changes. 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. 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.
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. 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. Here, we present CellStar, a tool chain designed to achieve good performance in long-term experiments. 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. 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.