Boundary fitting based segmentation of fluorescence microscopy images

Soonam Lee, Paul Salama, Kenneth Dunn, Edward J. Delp

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

5 Citations (Scopus)

Abstract

Segmentation is a fundamental step in quantifying characteristics, such as volume, shape, and orientation of cells and/or tissue. However, quantification of these characteristics still poses a challenge due to the unique properties of microscopy volumes. This paper proposes a 2D segmentation method that utilizes a combination of adaptive and global thresholding, potentials, z direction refinement, branch pruning, end point matching, and boundary fitting methods to delineate tubular objects in microscopy volumes. Experimental results demonstrate that the proposed method achieves better performance than an active contours based scheme.

Original languageEnglish (US)
Title of host publicationProceedings of SPIE - The International Society for Optical Engineering
PublisherSPIE
Volume9408
ISBN (Print)9781628414981
DOIs
StatePublished - 2015
EventImaging and Multimedia Analytics in a Web and Mobile World 2015 - San Francisco, United States
Duration: Feb 11 2015Feb 12 2015

Other

OtherImaging and Multimedia Analytics in a Web and Mobile World 2015
CountryUnited States
CitySan Francisco
Period2/11/152/12/15

Fingerprint

Fluorescence Microscopy
Fluorescence microscopy
Microscopic examination
Segmentation
microscopy
Microscopy
fluorescence
z direction
Active Contours
Tissue
End point
Thresholding
Pruning
Quantification
Refinement
Branch
Cell
Experimental Results
cells
Demonstrate

Keywords

  • Adaptive thresholding
  • Biomedical imaging
  • Ellipse fitting
  • Image segmentation

ASJC Scopus subject areas

  • Applied Mathematics
  • Computer Science Applications
  • Electrical and Electronic Engineering
  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics

Cite this

Lee, S., Salama, P., Dunn, K., & Delp, E. J. (2015). Boundary fitting based segmentation of fluorescence microscopy images. In Proceedings of SPIE - The International Society for Optical Engineering (Vol. 9408). [940805] SPIE. https://doi.org/10.1117/12.2085417

Boundary fitting based segmentation of fluorescence microscopy images. / Lee, Soonam; Salama, Paul; Dunn, Kenneth; Delp, Edward J.

Proceedings of SPIE - The International Society for Optical Engineering. Vol. 9408 SPIE, 2015. 940805.

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

Lee, S, Salama, P, Dunn, K & Delp, EJ 2015, Boundary fitting based segmentation of fluorescence microscopy images. in Proceedings of SPIE - The International Society for Optical Engineering. vol. 9408, 940805, SPIE, Imaging and Multimedia Analytics in a Web and Mobile World 2015, San Francisco, United States, 2/11/15. https://doi.org/10.1117/12.2085417
Lee S, Salama P, Dunn K, Delp EJ. Boundary fitting based segmentation of fluorescence microscopy images. In Proceedings of SPIE - The International Society for Optical Engineering. Vol. 9408. SPIE. 2015. 940805 https://doi.org/10.1117/12.2085417
Lee, Soonam ; Salama, Paul ; Dunn, Kenneth ; Delp, Edward J. / Boundary fitting based segmentation of fluorescence microscopy images. Proceedings of SPIE - The International Society for Optical Engineering. Vol. 9408 SPIE, 2015.
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