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

WIESNER, David, David SVOBODA, Martin MAŠKA and Michal KOZUBEK. CytoPacq: A web-interface for simulating multi-dimensional cell imaging. 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.

Basic information

• Original name: CytoPacq: A web-interface for simulating multi-dimensional cell imaging
• Authors: WIESNER, David (203 Czech Republic, belonging to the institution), David SVOBODA (203 Czech Republic, belonging to the institution), Martin MAŠKA (203 Czech Republic, belonging to the institution) and Michal KOZUBEK (203 Czech Republic, guarantor, belonging to the institution).
• Edition: Bioinformatics, Oxford University Press, 2019, 1367-4803.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: United Kingdom of Great Britain and Northern Ireland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 5.610
• RIV identification code: RIV/00216224:14330/19:00107401
• Organization unit: Faculty of Informatics
• Doi: http://dx.doi.org/10.1093/bioinformatics/btz417
• UT WoS: 000499323900072
• Keywords in English: Simulation; Mathematical modeling; Benchmarking; Cell imaging; Web services
• Tags: cbia-web
• Tags: International impact, Reviewed

Abstract

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.

Links

• EF16_013/0001775, research and development project: Name: Modernizace a podpora výzkumných aktivit národní infrastruktury pro biologické a medicínské zobrazování Czech-BioImaging
• GA17-05048S, research and development project: Name: Segmentace a trekování živých buněk v multimodálních obrazech

Investor: Czech Science Foundation

• LM2015062, research and development project: Name: Národní infrastruktura pro biologické a medicínské zobrazování

Investor: Ministry of Education, Youth and Sports of the CR

• LTC17016, research and development project: Name: Benchmarking algoritmů segmentace a sledování buněk

Investor: Ministry of Education, Youth and Sports of the CR, Benchmarking of algorithms for cell segmentation and tracking, INTER-COST

• MUNI/A/1018/2018, interní kód MU: Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace VIII.

Investor: Masaryk University, Category A