Challenges and Benchmarks in Bioimage Analysis

C 2016

Challenges and Benchmarks in Bioimage Analysis

KOZUBEK, Michal

Basic information

Original name

Challenges and Benchmarks in Bioimage Analysis

Authors

KOZUBEK, Michal (203 Czech Republic, guarantor, belonging to the institution)

Edition

Berlin, Focus on Bio-Image Informatics, p. 231-262, 32 pp. Advances in Anatomy, Embryology and Cell Biology 219, 2016

Publisher

Springer

Other information

Language

English

Type of outcome

Kapitola resp. kapitoly v odborné knize

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

References:

URL

RIV identification code

RIV/00216224:14330/16:00087744

Organization unit

Faculty of Informatics

ISBN

978-3-319-28547-4

DOI

http://dx.doi.org/10.1007/978-3-319-28549-8_9

UT WoS

000385738300010

Keywords in English

bioimaging; image analysis; benchmark; challenge

Abstract

V originále

Similar to the medical imaging community, the bioimaging community has recently realized the need to benchmark various image analysis methods to compare their performance and assess their suitability for specific applications. Challenges sponsored by prestigious conferences have proven to be an effective means of encouraging benchmarking and new algorithm development for a particular type of image data. Bioimage analysis challenges have recently complemented medical image analysis challenges, especially in the case of the International Symposium on Biomedical Imaging (ISBI). This review summarizes recent progress in this respect and describes the general process of designing a bioimage analysis benchmark or challenge, including the proper selection of datasets and evaluation metrics. It also presents examples of specific target applications and biological research tasks that have benefited from these challenges with respect to the performance of automatic image analysis methods that are crucial for the given task. Finally, available benchmarks and challenges in terms of common features, possible classification and implications drawn from the results are analysed.

Links

GBP302/12/G157, research and development project

Name: Dynamika a organizace chromosomů během buněčného cyklu a při diferenciaci v normě a patologii

Investor: Czech Science Foundation

Citovat

KOZUBEK, Michal. Challenges and Benchmarks in Bioimage Analysis. Online. In DeVos WH, Munck S, Timmermans JP. Focus on Bio-Image Informatics. Berlin: Springer, 2016, p. 231-262. Advances in Anatomy, Embryology and Cell Biology 219. ISBN 978-3-319-28547-4. Available from: https://dx.doi.org/10.1007/978-3-319-28549-8_9.

@inbook{1318626,
   author = {Kozubek, Michal},
   address = {Berlin},
   booktitle = {Focus on Bio-Image Informatics},
   doi = {http://dx.doi.org/10.1007/978-3-319-28549-8_9},
   editor = {DeVos WH, Munck S, Timmermans JP},
   keywords = {bioimaging; image analysis; benchmark; challenge},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Berlin},
   isbn = {978-3-319-28547-4},
   pages = {231-262},
   publisher = {Springer},
   title = {Challenges and Benchmarks in Bioimage Analysis},
   url = {http://dx.doi.org/10.1007/978-3-319-28549-8_9},
   year = {2016}
}

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AU  - Kozubek, Michal
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TI  - Challenges and Benchmarks in Bioimage Analysis
VL  - Advances in Anatomy, Embryology and Cell Biology 219
PB  - Springer
CY  - Berlin
SN  - 9783319285474
KW  - bioimaging
KW  - image analysis
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L2  - http://dx.doi.org/10.1007/978-3-319-28549-8_9
N2  - Similar to the medical imaging community, the bioimaging community has recently realized the need to benchmark various image analysis methods to compare their performance and assess their suitability for specific applications. Challenges sponsored by prestigious conferences have proven to be an effective means of encouraging benchmarking and new algorithm development for a particular type of image data. Bioimage analysis challenges have recently complemented medical image analysis challenges, especially in the case of the International Symposium on Biomedical Imaging (ISBI). This review summarizes recent progress in this respect and describes the general process of designing a bioimage analysis benchmark or challenge, including the proper selection of datasets and evaluation metrics. It also presents examples of specific target applications and biological research tasks that have benefited from these challenges with respect to the performance of automatic image analysis methods that are crucial for the given task. Finally, available benchmarks and challenges in terms of common features, possible classification and implications drawn from the results are analysed.
ER  -

KOZUBEK, Michal. Challenges and Benchmarks in Bioimage Analysis. Online. In DeVos WH, Munck S, Timmermans JP. \textit{Focus on Bio-Image Informatics}. Berlin: Springer, 2016, p.~231-262. Advances in Anatomy, Embryology and Cell Biology 219. ISBN~978-3-319-28547-4. Available from: https://dx.doi.org/10.1007/978-3-319-28549-8\_{}9.

Detailed Information on Publication Record