Rapid semi-automated segmentation and analysis of neuronal morphology and function from confocal image data

David R. Holmes III, Michael J. Moore, Carlos Bernardo Mantilla, Gary C Sieck, Richard A. Robb

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

Confocal microscopy combined with cellular labeling techniques can be an effective method for imaging the morphology of a cell as well as various functional characteristics in vivo. Current analysis methods are manual, and therefore, time-consuming and prone to error. Through the development of custom algorithms and application design, the analysis process can be improved to decrease analysis time and increase reproducibility. Utilizing off-the-self PC hardware and software, a custom application was designed that would provide useful three-dimensional (3D) segmentation and analysis tools to analyze confocal image data of neurons. Techniques such as dynamic thresholding, adaptive filtering, and morphological processing were implemented to provide a robust and efficient analysis package. The automated method was compared with the standard manual method using two metrics - reproducibility and overall time necessary for analysis. The semi-automated method was more time efficient with very high reproducibility. Additional studies are necessary to further assess and improve upon the automated technique.

Original languageEnglish (US)
Title of host publicationProceedings - International Symposium on Biomedical Imaging
PublisherIEEE Computer Society
Pages233-236
Number of pages4
Volume2002-January
ISBN (Print)078037584X
DOIs
StatePublished - 2002
EventIEEE International Symposium on Biomedical Imaging, ISBI 2002 - Washington, United States
Duration: Jul 7 2002Jul 10 2002

Other

OtherIEEE International Symposium on Biomedical Imaging, ISBI 2002
CountryUnited States
CityWashington
Period7/7/027/10/02

Fingerprint

Adaptive filtering
Confocal microscopy
Labeling
Neurons
Hardware
Imaging techniques
Processing
Confocal Microscopy
Software

ASJC Scopus subject areas

  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging

Cite this

Holmes III, D. R., Moore, M. J., Mantilla, C. B., Sieck, G. C., & Robb, R. A. (2002). Rapid semi-automated segmentation and analysis of neuronal morphology and function from confocal image data. In Proceedings - International Symposium on Biomedical Imaging (Vol. 2002-January, pp. 233-236). [1029236] IEEE Computer Society. https://doi.org/10.1109/ISBI.2002.1029236

Rapid semi-automated segmentation and analysis of neuronal morphology and function from confocal image data. / Holmes III, David R.; Moore, Michael J.; Mantilla, Carlos Bernardo; Sieck, Gary C; Robb, Richard A.

Proceedings - International Symposium on Biomedical Imaging. Vol. 2002-January IEEE Computer Society, 2002. p. 233-236 1029236.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Holmes III, DR, Moore, MJ, Mantilla, CB, Sieck, GC & Robb, RA 2002, Rapid semi-automated segmentation and analysis of neuronal morphology and function from confocal image data. in Proceedings - International Symposium on Biomedical Imaging. vol. 2002-January, 1029236, IEEE Computer Society, pp. 233-236, IEEE International Symposium on Biomedical Imaging, ISBI 2002, Washington, United States, 7/7/02. https://doi.org/10.1109/ISBI.2002.1029236
Holmes III DR, Moore MJ, Mantilla CB, Sieck GC, Robb RA. Rapid semi-automated segmentation and analysis of neuronal morphology and function from confocal image data. In Proceedings - International Symposium on Biomedical Imaging. Vol. 2002-January. IEEE Computer Society. 2002. p. 233-236. 1029236 https://doi.org/10.1109/ISBI.2002.1029236
Holmes III, David R. ; Moore, Michael J. ; Mantilla, Carlos Bernardo ; Sieck, Gary C ; Robb, Richard A. / Rapid semi-automated segmentation and analysis of neuronal morphology and function from confocal image data. Proceedings - International Symposium on Biomedical Imaging. Vol. 2002-January IEEE Computer Society, 2002. pp. 233-236
@inproceedings{c6017d9ea1ee4a28a892fc3dbfe4b206,
title = "Rapid semi-automated segmentation and analysis of neuronal morphology and function from confocal image data",
abstract = "Confocal microscopy combined with cellular labeling techniques can be an effective method for imaging the morphology of a cell as well as various functional characteristics in vivo. Current analysis methods are manual, and therefore, time-consuming and prone to error. Through the development of custom algorithms and application design, the analysis process can be improved to decrease analysis time and increase reproducibility. Utilizing off-the-self PC hardware and software, a custom application was designed that would provide useful three-dimensional (3D) segmentation and analysis tools to analyze confocal image data of neurons. Techniques such as dynamic thresholding, adaptive filtering, and morphological processing were implemented to provide a robust and efficient analysis package. The automated method was compared with the standard manual method using two metrics - reproducibility and overall time necessary for analysis. The semi-automated method was more time efficient with very high reproducibility. Additional studies are necessary to further assess and improve upon the automated technique.",
author = "{Holmes III}, {David R.} and Moore, {Michael J.} and Mantilla, {Carlos Bernardo} and Sieck, {Gary C} and Robb, {Richard A.}",
year = "2002",
doi = "10.1109/ISBI.2002.1029236",
language = "English (US)",
isbn = "078037584X",
volume = "2002-January",
pages = "233--236",
booktitle = "Proceedings - International Symposium on Biomedical Imaging",
publisher = "IEEE Computer Society",

}

TY - GEN

T1 - Rapid semi-automated segmentation and analysis of neuronal morphology and function from confocal image data

AU - Holmes III, David R.

AU - Moore, Michael J.

AU - Mantilla, Carlos Bernardo

AU - Sieck, Gary C

AU - Robb, Richard A.

PY - 2002

Y1 - 2002

N2 - Confocal microscopy combined with cellular labeling techniques can be an effective method for imaging the morphology of a cell as well as various functional characteristics in vivo. Current analysis methods are manual, and therefore, time-consuming and prone to error. Through the development of custom algorithms and application design, the analysis process can be improved to decrease analysis time and increase reproducibility. Utilizing off-the-self PC hardware and software, a custom application was designed that would provide useful three-dimensional (3D) segmentation and analysis tools to analyze confocal image data of neurons. Techniques such as dynamic thresholding, adaptive filtering, and morphological processing were implemented to provide a robust and efficient analysis package. The automated method was compared with the standard manual method using two metrics - reproducibility and overall time necessary for analysis. The semi-automated method was more time efficient with very high reproducibility. Additional studies are necessary to further assess and improve upon the automated technique.

AB - Confocal microscopy combined with cellular labeling techniques can be an effective method for imaging the morphology of a cell as well as various functional characteristics in vivo. Current analysis methods are manual, and therefore, time-consuming and prone to error. Through the development of custom algorithms and application design, the analysis process can be improved to decrease analysis time and increase reproducibility. Utilizing off-the-self PC hardware and software, a custom application was designed that would provide useful three-dimensional (3D) segmentation and analysis tools to analyze confocal image data of neurons. Techniques such as dynamic thresholding, adaptive filtering, and morphological processing were implemented to provide a robust and efficient analysis package. The automated method was compared with the standard manual method using two metrics - reproducibility and overall time necessary for analysis. The semi-automated method was more time efficient with very high reproducibility. Additional studies are necessary to further assess and improve upon the automated technique.

UR - http://www.scopus.com/inward/record.url?scp=12444341516&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=12444341516&partnerID=8YFLogxK

U2 - 10.1109/ISBI.2002.1029236

DO - 10.1109/ISBI.2002.1029236

M3 - Conference contribution

AN - SCOPUS:12444341516

SN - 078037584X

VL - 2002-January

SP - 233

EP - 236

BT - Proceedings - International Symposium on Biomedical Imaging

PB - IEEE Computer Society

ER -