Challenges and Benchmarks in Bioimage Analysis

C 2016

Challenges and Benchmarks in Bioimage Analysis

KOZUBEK, Michal

Základní údaje

Originální název

Challenges and Benchmarks in Bioimage Analysis

Autoři

KOZUBEK, Michal (203 Česká republika, garant, domácí)

Vydání

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

Nakladatel

Springer

Další údaje

Jazyk

angličtina

Typ výsledku

Kapitola resp. kapitoly v odborné knize

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

elektronická verze "online"

Odkazy

URL

Kód RIV

RIV/00216224:14330/16:00087744

Organizační jednotka

Fakulta informatiky

ISBN

978-3-319-28547-4

DOI

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

UT WoS

000385738300010

Klíčová slova anglicky

bioimaging; image analysis; benchmark; challenge

Štítky

cbia-web

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 27. 4. 2017 13:24, RNDr. Pavel Šmerk, Ph.D.

Anotace

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.

Návaznosti

GBP302/12/G157, projekt VaV

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

Investor: Grantová agentura ČR, Dynamika a organizace chromosomů během buněčného cyklu a při diferenciaci v normě a patologii

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, s. 231-262. Advances in Anatomy, Embryology and Cell Biology 219. ISBN 978-3-319-28547-4. Dostupné z: 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}
}

TY  - CHAP
ID  - 1318626
AU  - Kozubek, Michal
PY  - 2016
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
KW  - benchmark
KW  - challenge
UR  - http://dx.doi.org/10.1007/978-3-319-28549-8_9
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, s.~231-262. Advances in Anatomy, Embryology and Cell Biology 219. ISBN~978-3-319-28547-4. Dostupné z: https://dx.doi.org/10.1007/978-3-319-28549-8\_{}9.

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