Performance and Sensitivity Evaluation of 3-D Spot Detection
Methods in Confocal Microscopy

J 2015

Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy

ŠTĚPKA, Karel, Pavel MATULA, Petr MATULA, Stefan WOERZ, Karl ROHR et. al.

Základní údaje

Originální název

Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy

Autoři

ŠTĚPKA, Karel (203 Česká republika, garant, domácí), Pavel MATULA (203 Česká republika, domácí), Petr MATULA (203 Česká republika, domácí), Stefan WOERZ (276 Německo), Karl ROHR (276 Německo) a Michal KOZUBEK (203 Česká republika, domácí)

Vydání

Cytometry Part A, John Wiley & Sons, 2015, 1552-4922

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.181

Kód RIV

RIV/00216224:14330/15:00080577

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1002/cyto.a.22692

UT WoS

000358643200011

Klíčová slova anglicky

fluorescence microscopy; 3D imaging; diffraction-limited spot detection; parameter sensitivity

Štítky

cbia-web

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 9. 2. 2022 09:19, doc. RNDr. Pavel Matula, Ph.D.

Anotace

V originále

Reliable 3D detection of diffraction-limited spots in fluorescence microscopy images is an important task in subcellular observation. Generally, fluorescence microscopy images are heavily degraded by noise and non-specifically stained background, making reliable detection a challenging task. In this work, we have studied the performance and parameter sensitivity of eight recent methods for 3D spot detection. The study is based on both 3D synthetic image data and 3D real confocal microscopy images. The synthetic images were generated using a simulator modeling the complete imaging setup, including the optical path as well as the image acquisition process. We studied the detection performance and parameter sensitivity under different noise levels and under the influence of uneven background signal. To evaluate the parameter sensitivity, we propose a novel measure based on the gradient magnitude of the F1 score. We measured the success rate of the individual methods for different types of the image data and found that the type of image degradation is an important factor. Using the F1 score and the newly proposed sensitivity measure, we found that the parameter sensitivity is not necessarily proportional to the success rate of a method. This also provided an explanation why the best performing method for synthetic data was outperformed by other methods when applied to the real microscopy images. On the basis of the results obtained, we conclude with the recommendation of the HDome method for data with relatively low variations in quality, or the Sorokin method for image sets in which the quality varies more. We also provide alternative recommendations for high-quality images, and for situations in which detailed parameter tuning might be deemed expensive.

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

MUNI/A/1159/2014, interní kód MU

Název: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace IV.

Investor: Masarykova univerzita, Rozsáhlé výpočetní systémy: modely, aplikace a verifikace IV., DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

ŠTĚPKA, Karel, Pavel MATULA, Petr MATULA, Stefan WOERZ, Karl ROHR a Michal KOZUBEK. Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy. Cytometry Part A. John Wiley & Sons, 2015, roč. 87A, č. 8, s. 759-772. ISSN 1552-4922. Dostupné z: https://dx.doi.org/10.1002/cyto.a.22692.

@article{1139067,
   author = {Štěpka, Karel and Matula, Pavel and Matula, Petr and Woerz, Stefan and Rohr, Karl and Kozubek, Michal},
   article_number = {8},
   doi = {http://dx.doi.org/10.1002/cyto.a.22692},
   keywords = {fluorescence microscopy; 3D imaging; diffraction-limited spot detection; parameter sensitivity},
   language = {eng},
   issn = {1552-4922},
   journal = {Cytometry Part A},
   title = {Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy},
   url = {http://dx.doi.org/10.1002/cyto.a.22692},
   volume = {87A},
   year = {2015}
}

TY  - JOUR
ID  - 1139067
AU  - Štěpka, Karel - Matula, Pavel - Matula, Petr - Woerz, Stefan - Rohr, Karl - Kozubek, Michal
PY  - 2015
TI  - Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy
JF  - Cytometry Part A
VL  - 87A
IS  - 8
SP  - 759-772
EP  - 759-772
PB  - John Wiley & Sons
SN  - 15524922
KW  - fluorescence microscopy
KW  - 3D imaging
KW  - diffraction-limited spot detection
KW  - parameter sensitivity
UR  - http://dx.doi.org/10.1002/cyto.a.22692
N2  - Reliable 3D detection of diffraction-limited spots in fluorescence microscopy images is an important task in subcellular observation. Generally, fluorescence microscopy images are heavily degraded by noise and non-specifically stained background, making reliable detection a challenging task. In this work, we have studied the performance and parameter sensitivity of eight recent methods for 3D spot detection. The study is based on both 3D synthetic image data and 3D real confocal microscopy images. The synthetic images were generated using a simulator modeling the complete imaging setup, including the optical path as well as the image acquisition process. We studied the detection performance and parameter sensitivity under different noise levels and under the influence of uneven background signal. To evaluate the parameter sensitivity, we propose a novel measure based on the gradient magnitude of the F1 score. We measured the success rate of the individual methods for different types of the image data and found that the type of image degradation is an important factor. Using the F1 score and the newly proposed sensitivity measure, we found that the parameter sensitivity is not necessarily proportional to the success rate of a method. This also provided an explanation why the best performing method for synthetic data was outperformed by other methods when applied to the real microscopy images. On the basis of the results obtained, we conclude with the recommendation of the HDome method for data with relatively low variations in quality, or the Sorokin method for image sets in which the quality varies more. We also provide alternative recommendations for high-quality images, and for situations in which detailed parameter tuning might be deemed expensive.
ER  -

ŠTĚPKA, Karel, Pavel MATULA, Petr MATULA, Stefan WOERZ, Karl ROHR a Michal KOZUBEK. Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy. \textit{Cytometry Part A}. John Wiley \&{} Sons, 2015, roč.~87A, č.~8, s.~759-772. ISSN~1552-4922. Dostupné z: https://dx.doi.org/10.1002/cyto.a.22692.

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