Virtual cell imaging: A review on simulation methods employed
in image cytometry

J 2016

Virtual cell imaging: A review on simulation methods employed in image cytometry

ULMAN, Vladimír, David SVOBODA, Matti NYKTER, Michal KOZUBEK, Pekka RUUSUVUORI et. al.

Basic information

Original name

Virtual cell imaging: A review on simulation methods employed in image cytometry

Authors

ULMAN, Vladimír (203 Czech Republic, belonging to the institution), David SVOBODA (203 Czech Republic, belonging to the institution), Matti NYKTER (246 Finland), Michal KOZUBEK (203 Czech Republic, guarantor, belonging to the institution) and Pekka RUUSUVUORI (246 Finland)

Edition

Cytometry Part A, John Wiley & Sons, 2016, 1552-4922

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10200 1.2 Computer and information sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.222

RIV identification code

RIV/00216224:14330/16:00088328

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1002/cyto.a.23031

UT WoS

000392724500004

Keywords in English

cell imaging; virtual imaging; simulation; digital cell; cell model; digital phantom; ground truth; validation; image cytometry

Abstract

V originále

The simulations of cells and microscope images thereof have been used to facilitate the development, selection, and validation of image analysis algorithms employed in cytometry as well as for modeling and understanding cell structure and dynamics beyond what is visible in the eyepiece. The simulation approaches vary from simple parametric models of specific cell components—especially shapes of cells and cell nuclei—to learning-based synthesis and multi-stage simulation models for complex scenes that simultaneously visualize multiple object types and incorporate various properties of the imaged objects and laws of image formation. This review covers advances in artificial digital cell generation at scales ranging from particles up to tissue synthesis and microscope image simulation methods, provides examples of the use of simulated images for various purposes ranging from subcellular object detection to cell tracking, and discusses how such simulators have been validated. Finally, the future possibilities and limitations of simulation-based validation are considered.

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

ULMAN, Vladimír, David SVOBODA, Matti NYKTER, Michal KOZUBEK and Pekka RUUSUVUORI. Virtual cell imaging: A review on simulation methods employed in image cytometry. Cytometry Part A. John Wiley & Sons, 2016, 89A, No 12, p. 1057-1072. ISSN 1552-4922. Available from: https://dx.doi.org/10.1002/cyto.a.23031.

@article{1360376,
   author = {Ulman, Vladimír and Svoboda, David and Nykter, Matti and Kozubek, Michal and Ruusuvuori, Pekka},
   article_number = {12},
   doi = {http://dx.doi.org/10.1002/cyto.a.23031},
   keywords = {cell imaging; virtual imaging; simulation; digital cell; cell model; digital phantom; ground truth; validation; image cytometry},
   language = {eng},
   issn = {1552-4922},
   journal = {Cytometry Part A},
   title = {Virtual cell imaging: A review on simulation methods employed in image cytometry},
   url = {http://dx.doi.org/10.1002/cyto.a.23031},
   volume = {89A},
   year = {2016}
}

TY  - JOUR
ID  - 1360376
AU  - Ulman, Vladimír - Svoboda, David - Nykter, Matti - Kozubek, Michal - Ruusuvuori, Pekka
PY  - 2016
TI  - Virtual cell imaging: A review on simulation methods employed in image cytometry
JF  - Cytometry Part A
VL  - 89A
IS  - 12
SP  - 1057-1072
EP  - 1057-1072
PB  - John Wiley & Sons
SN  - 15524922
KW  - cell imaging
KW  - virtual imaging
KW  - simulation
KW  - digital cell
KW  - cell model
KW  - digital phantom
KW  - ground truth
KW  - validation
KW  - image cytometry
UR  - http://dx.doi.org/10.1002/cyto.a.23031
L2  - http://dx.doi.org/10.1002/cyto.a.23031
N2  - The simulations of cells and microscope images thereof have been used to facilitate the development, selection, and validation of image analysis algorithms employed in cytometry as well as for modeling and understanding cell structure and dynamics beyond what is visible in the eyepiece. The simulation approaches vary from simple parametric models of specific cell components—especially shapes of cells and cell nuclei—to learning-based synthesis and multi-stage simulation models for complex scenes that simultaneously visualize multiple object types and incorporate various properties of the imaged objects and laws of image formation. This review covers advances in artificial digital cell generation at scales ranging from particles up to tissue synthesis and microscope image simulation methods, provides examples of the use of simulated images for various purposes ranging from subcellular object detection to cell tracking, and discusses how such simulators have been validated. Finally, the future possibilities and limitations of simulation-based validation are considered.
ER  -

ULMAN, Vladimír, David SVOBODA, Matti NYKTER, Michal KOZUBEK and Pekka RUUSUVUORI. Virtual cell imaging: A review on simulation methods employed in image cytometry. \textit{Cytometry Part A}. John Wiley \&{} Sons, 2016, 89A, No~12, p.~1057-1072. ISSN~1552-4922. Available from: https://dx.doi.org/10.1002/cyto.a.23031.

Detailed Information on Publication Record