MOTIVATION: Quantitative large-scale cell microscopy is widely used in biological and medical research. Such experiments produce huge amounts of image data and thus require automated analysis. However, automated detection of cell outlines (cell segmentation) is typically challenging due to, e.g. high cell densities, cell-to-cell variability and low signal-to-noise ratios. RESULTS: Here, we evaluate accuracy and speed of various state-of-the-art approaches for cell segmentation in light microscopy images using challenging real and synthetic image data. The results vary between datasets and show that the tested tools are either not robust enough or computationally expensive, thus limiting their application to large-scale experiments. We therefore developed fastER, a trainable tool that is orders of magnitude faster while producing state-of-the-art segmentation quality. It supports various cell types and image acquisition modalities, but is easy-to-use even for non-experts: it has no parameters and can be adapted to specific image sets by interactively labelling cells for training. As a proof of concept, we segment and count cells in over 200 000 brightfield images (1388 × 1040 pixels each) from a six day time-lapse microscopy experiment; identification of over 46 000 000 single cells requires only about two and a half hours on a desktop computer. AVAILABILITY AND IMPLEMENTATION: C ++ code, binaries and data at https://www.bsse.ethz.ch/csd/software/faster.html . CONTACT: [email protected] or [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Identifying cells in an image (cell segmentation) is essential for quantitative single-cell biology via optical microscopy. Although a plethora of segmentation methods exists, accurate segmentation is challenging and usually requires problem-specific tailoring of algorithms. In addition, most current segmentation algorithms rely on a few basic approaches that use the gradient field of the image to detect cell boundaries. However, many microscopy protocols can generate images with characteristic intensity profiles at the cell membrane. This has not yet been algorithmically exploited to establish more general segmentation methods. RESULTS: We present an automatic cell segmentation method that decodes the information across the cell membrane and guarantees optimal detection of the cell boundaries on a per-cell basis. Graph cuts account for the information of the cell boundaries through directional cross-correlations, and they automatically incorporate spatial constraints. The method accurately segments images of various cell types grown in dense cultures that are acquired with different microscopy techniques. In quantitative benchmarks and comparisons with established methods on synthetic and real images, we demonstrate significantly improved segmentation performance despite cell-shape irregularity, cell-to-cell variability and image noise. As a proof of concept, we monitor the internalization of green fluorescent protein-tagged plasma membrane transporters in single yeast cells. AVAILABILITY AND IMPLEMENTATION: Matlab code and examples are available at http://www.csb.ethz.ch/tools/cellSegmPackage.zip.

MOTIVATION: Biological systems are understood through iterations of modeling and experimentation. Not all experiments, however, are equally valuable for predictive modeling. This study introduces an efficient method for experimental design aimed at selecting dynamical models from data. Motivated by biological applications, the method enables the design of crucial experiments: it determines a highly informative selection of measurement readouts and time points. RESULTS: We demonstrate formal guarantees of design efficiency on the basis of previous results. By reducing our task to the setting of graphical models, we prove that the method finds a near-optimal design selection with a polynomial number of evaluations. Moreover, the method exhibits the best polynomial-complexity constant approximation factor, unless P = NP. We measure the performance of the method in comparison with established alternatives, such as ensemble non-centrality, on example models of different complexity. Efficient design accelerates the loop between modeling and experimentation: it enables the inference of complex mechanisms, such as those controlling central metabolic operation. AVAILABILITY: Toolbox 'NearOED' available with source code under GPL on the Machine Learning Open Source Software Web site (mloss.org).