A statistical approach for intensity loss compensation of confocal microscopy images

S. Gopinath, Q. Wen, N. Thakoor, K. Luby-Phelps, J. X. Gao

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

In this paper, a probabilistic technique for compensation of intensity loss in confocal microscopy images is presented. For single-colour-labelled specimen, confocal microscopy images are modelled as a mixture of two Gaussian probability distribution functions, one representing the background and another corresponding to the foreground. Images are segmented into foreground and background by applying Expectation Maximization algorithm to the mixture. Final intensity compensation is carried out by scaling and shifting the original intensities with the help of parameters estimated for the foreground. Since foreground is separated to calculate the compensation parameters, the method is effective even when image structure changes from frame to frame. As intensity decay function is not used, complexity associated with estimation of the intensity decay function parameters is eliminated. In addition, images can be compensated out of order, as only information from the reference image is required for the compensation of any image. These properties make our method an ideal tool for intensity compensation of confocal microscopy images that suffer intensity loss due to absorption/scattering of light as well as photobleaching and the image can change structure from optical/temporal section-to-section due to changes in the depth of specimen or due to a live specimen. The proposed method was tested with a number of confocal microscopy image stacks and results are presented to demonstrate the effectiveness of the method.

Original languageEnglish (US)
Pages (from-to)143-159
Number of pages17
JournalJournal of Microscopy
Volume230
Issue number1
DOIs
StatePublished - Apr 2008

Fingerprint

Confocal microscopy
Confocal Microscopy
microscopy
Photobleaching
Normal Distribution
Color
Probability distributions
Distribution functions
Light
Compensation and Redress
Scattering
probability distribution functions
decay
color
scaling

Keywords

  • Compensation
  • Confocal microscopy
  • Expectation maximization
  • Intensity loss
  • Photobleaching

ASJC Scopus subject areas

  • Instrumentation

Cite this

A statistical approach for intensity loss compensation of confocal microscopy images. / Gopinath, S.; Wen, Q.; Thakoor, N.; Luby-Phelps, K.; Gao, J. X.

In: Journal of Microscopy, Vol. 230, No. 1, 04.2008, p. 143-159.

Research output: Contribution to journalArticle

Gopinath, S. ; Wen, Q. ; Thakoor, N. ; Luby-Phelps, K. ; Gao, J. X. / A statistical approach for intensity loss compensation of confocal microscopy images. In: Journal of Microscopy. 2008 ; Vol. 230, No. 1. pp. 143-159.
@article{b08fcd79ff0741a78f9f5b1148a78fcb,
title = "A statistical approach for intensity loss compensation of confocal microscopy images",
abstract = "In this paper, a probabilistic technique for compensation of intensity loss in confocal microscopy images is presented. For single-colour-labelled specimen, confocal microscopy images are modelled as a mixture of two Gaussian probability distribution functions, one representing the background and another corresponding to the foreground. Images are segmented into foreground and background by applying Expectation Maximization algorithm to the mixture. Final intensity compensation is carried out by scaling and shifting the original intensities with the help of parameters estimated for the foreground. Since foreground is separated to calculate the compensation parameters, the method is effective even when image structure changes from frame to frame. As intensity decay function is not used, complexity associated with estimation of the intensity decay function parameters is eliminated. In addition, images can be compensated out of order, as only information from the reference image is required for the compensation of any image. These properties make our method an ideal tool for intensity compensation of confocal microscopy images that suffer intensity loss due to absorption/scattering of light as well as photobleaching and the image can change structure from optical/temporal section-to-section due to changes in the depth of specimen or due to a live specimen. The proposed method was tested with a number of confocal microscopy image stacks and results are presented to demonstrate the effectiveness of the method.",
keywords = "Compensation, Confocal microscopy, Expectation maximization, Intensity loss, Photobleaching",
author = "S. Gopinath and Q. Wen and N. Thakoor and K. Luby-Phelps and Gao, {J. X.}",
year = "2008",
month = "4",
doi = "10.1111/j.1365-2818.2008.01964.x",
language = "English (US)",
volume = "230",
pages = "143--159",
journal = "Journal of Microscopy",
issn = "0022-2720",
publisher = "Wiley-Blackwell",
number = "1",

}

TY - JOUR

T1 - A statistical approach for intensity loss compensation of confocal microscopy images

AU - Gopinath, S.

AU - Wen, Q.

AU - Thakoor, N.

AU - Luby-Phelps, K.

AU - Gao, J. X.

PY - 2008/4

Y1 - 2008/4

N2 - In this paper, a probabilistic technique for compensation of intensity loss in confocal microscopy images is presented. For single-colour-labelled specimen, confocal microscopy images are modelled as a mixture of two Gaussian probability distribution functions, one representing the background and another corresponding to the foreground. Images are segmented into foreground and background by applying Expectation Maximization algorithm to the mixture. Final intensity compensation is carried out by scaling and shifting the original intensities with the help of parameters estimated for the foreground. Since foreground is separated to calculate the compensation parameters, the method is effective even when image structure changes from frame to frame. As intensity decay function is not used, complexity associated with estimation of the intensity decay function parameters is eliminated. In addition, images can be compensated out of order, as only information from the reference image is required for the compensation of any image. These properties make our method an ideal tool for intensity compensation of confocal microscopy images that suffer intensity loss due to absorption/scattering of light as well as photobleaching and the image can change structure from optical/temporal section-to-section due to changes in the depth of specimen or due to a live specimen. The proposed method was tested with a number of confocal microscopy image stacks and results are presented to demonstrate the effectiveness of the method.

AB - In this paper, a probabilistic technique for compensation of intensity loss in confocal microscopy images is presented. For single-colour-labelled specimen, confocal microscopy images are modelled as a mixture of two Gaussian probability distribution functions, one representing the background and another corresponding to the foreground. Images are segmented into foreground and background by applying Expectation Maximization algorithm to the mixture. Final intensity compensation is carried out by scaling and shifting the original intensities with the help of parameters estimated for the foreground. Since foreground is separated to calculate the compensation parameters, the method is effective even when image structure changes from frame to frame. As intensity decay function is not used, complexity associated with estimation of the intensity decay function parameters is eliminated. In addition, images can be compensated out of order, as only information from the reference image is required for the compensation of any image. These properties make our method an ideal tool for intensity compensation of confocal microscopy images that suffer intensity loss due to absorption/scattering of light as well as photobleaching and the image can change structure from optical/temporal section-to-section due to changes in the depth of specimen or due to a live specimen. The proposed method was tested with a number of confocal microscopy image stacks and results are presented to demonstrate the effectiveness of the method.

KW - Compensation

KW - Confocal microscopy

KW - Expectation maximization

KW - Intensity loss

KW - Photobleaching

UR - http://www.scopus.com/inward/record.url?scp=41749106912&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=41749106912&partnerID=8YFLogxK

U2 - 10.1111/j.1365-2818.2008.01964.x

DO - 10.1111/j.1365-2818.2008.01964.x

M3 - Article

C2 - 18387049

AN - SCOPUS:41749106912

VL - 230

SP - 143

EP - 159

JO - Journal of Microscopy

JF - Journal of Microscopy

SN - 0022-2720

IS - 1

ER -