Publication details

CytoPacq: A web-interface for simulating multi-dimensional cell imaging

Authors

WIESNER David SVOBODA David MAŠKA Martin KOZUBEK Michal

Type Article in Periodical
Magazine / Source Bioinformatics
MU Faculty or unit

Faculty of Informatics

Citation
Doi http://dx.doi.org/10.1093/bioinformatics/btz417
Keywords Simulation; Mathematical modeling; Benchmarking; Cell imaging; Web services
Description 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.
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