fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy.
BACKGROUND
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.


METHODS
C ++ code, binaries and data at https://www.bsse.ethz.ch/csd/software/faster.html .


BACKGROUND
oliver.hilsenbeck@bsse.ethz.ch or timm.schroeder@bsse.ethz.ch.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
Oliver
O
Hilsenbeck
Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.
Michael
M
Schwarzfischer
Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
Dirk
D
Loeffler
Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
Sotiris
S
Dimopoulos
Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
Simon
S
Hastreiter
Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.
Carsten
C
Marr
Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.|Department of Mathematics, Technische Universität München, Garching, Germany.
Fabian J
FJ
Theis
Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
Timm
T
Schroeder
D000465:Algorithms; D006367:HeLa Cells; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008853:Microscopy / Q000379:methods*