CytoPacq: a web-interface for simulating multi-dimensional cell imaging
Autor: | Michal Kozubek, David Wiesner, David Svoboda, Martin Maška |
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Rok vydání: | 2019 |
Předmět: |
Statistics and Probability
0303 health sciences Computer science business.industry Machine learning computer.software_genre Applications Notes Biochemistry 030218 nuclear medicine & medical imaging Computer Science Applications 03 medical and health sciences Computational Mathematics 0302 clinical medicine Computational Theory and Mathematics Multi dimensional Fluorescence microscope Computer Simulation Artificial intelligence User interface Bioimage Informatics business Molecular Biology computer Software 030304 developmental biology |
Zdroj: | Bioinformatics |
ISSN: | 1460-2059 1367-4803 |
Popis: | Motivation 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. Results 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. Availability and implementation 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. Supplementary information Supplementary data are available at Bioinformatics online. |
Databáze: | OpenAIRE |
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