ArticleBioinformatics (Oxford, England)2019
CytoPacq: a web-interface for simulating multi-dimensional cell imaging.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- Halo-free quantitative phase imaging via physics-constrained self-supervised network.Journal of biomedical optics · 2026Article
- Robust Cell Segmentation for Size Distribution Estimation via Synthetic-Data Training.Biotechnology journal · 2026Article
- Comparison of Independent Analyses of Identical Image Sets Reveals Significant Analyst-to-Analyst Variability.Journal of biomolecular techniques : JBT · 2025Article
- Reducing Manual Annotation Costs for Cell Segmentation by Upgrading Low-Quality Annotations.Journal of imaging · 2024Article
- Structure preserving adversarial generation of labeled training samples for single-cell segmentation.Cell reports methods · 2023Article
- Synthesis of large scale 3D microscopic images of 3D cell cultures for training and benchmarking.PloS one · 2023Article
- Deep learning -- promises for 3D nuclear imaging: a guide for biologists.Journal of cell science · 2022Review
- BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows.Patterns (New York, N.Y.) · 2020Article
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4 authors.
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Abstract
motivationObjective 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.
resultsWe 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.
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