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@article{1530976, author = {Wiesner, David and Svoboda, David and Maška, Martin and Kozubek, Michal}, article_number = {21}, doi = {http://dx.doi.org/10.1093/bioinformatics/btz417}, keywords = {Simulation; Mathematical modeling; Benchmarking; Cell imaging; Web services}, language = {eng}, issn = {1367-4803}, journal = {Bioinformatics}, title = {CytoPacq: A web-interface for simulating multi-dimensional cell imaging}, url = {http://dx.doi.org/10.1093/bioinformatics/btz417}, volume = {35}, year = {2019} }
TY - JOUR ID - 1530976 AU - Wiesner, David - Svoboda, David - Maška, Martin - Kozubek, Michal PY - 2019 TI - CytoPacq: A web-interface for simulating multi-dimensional cell imaging JF - Bioinformatics VL - 35 IS - 21 SP - 4531-4533 EP - 4531-4533 PB - Oxford University Press SN - 13674803 KW - Simulation KW - Mathematical modeling KW - Benchmarking KW - Cell imaging KW - Web services UR - http://dx.doi.org/10.1093/bioinformatics/btz417 L2 - http://dx.doi.org/10.1093/bioinformatics/btz417 N2 - Objective assessment of bioimage analysis methods is an essential step towards understanding their robustness and parameter sensitivity, calling for the availability of heterogeneous bioimage datasets accompanied by their reference annotations. Because manual annotations are known to be arduous, highly subjective, and barely reproducible, numerous simulators have emerged over past decades, generating synthetic bioimage datasets complemented with inherent reference annotations. However, the installation and configuration of these tools generally constitutes a barrier to their widespread use. We present a modern, modular web-interface, CytoPacq, to facilitate the generation of synthetic benchmark datasets relevant for multi-dimensional cell imaging. CytoPacq poses a user-friendly graphical interface with contextual tooltips and currently allows a comfortable access to various cell simulation systems of fluorescence microscopy, which have already been recognized and used by the scientific community, in a straightforward and self-contained form. CytoPacq is a publicly available online service running at https://cbia.fi.muni.cz/simulator. More information about it as well as examples of generated bioimage datasets are available directly through the web-interface. ER -
WIESNER, David, David SVOBODA, Martin MAŠKA and Michal KOZUBEK. CytoPacq: A web-interface for simulating multi-dimensional cell imaging. \textit{Bioinformatics}. Oxford University Press, 2019, vol.~35, No~21, p.~4531-4533. ISSN~1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btz417.
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