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

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

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

V originále

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