Statistical inference of biological structure and point spread functions in 3D microscopy

Joseph Schlecht, Kobus Barnard, Barry Pryor

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

2 Scopus citations

Abstract

We present a novel method for detecting and quantifying 3D structure in stacks of microscopic images captured at incremental focal lengths. We express the image data as stochastically generated by an underlying model for biological specimen and the effects of the imaging system. The method simultaneously fits a model for proposed structure and the imaging system's parameters, which include a model of the point spread function. We demonstrate our approach by detecting spores in image stacks of Alternaria, a microscopic genus of fungus. The spores are modeled as opaque ellipsoids and fit to the data using statistical inference. Since the number of spores in the data is not known, model selection is incorporated into the fitting process. Thus, we develop a reversible jump Markov chain Monte Carlo sampler to explore the parameter space. Our results show that simultaneous statistical inference of specimen and imaging models is useful for quantifying biological structures in 3D microscopic images. In addition, we show that inferring a model of the imaging system improves the overall fit of the specimen model to the data.

Original languageEnglish (US)
Title of host publicationProceedings - 3rd International Symposium on 3D Data Processing, Visualization, and Transmission, 3DPVT 2006
PublisherIEEE Computer Society
Pages373-380
Number of pages8
ISBN (Print)0769528252, 9780769528250
DOIs
StatePublished - Jan 1 2006
Event3rd International Symposium on 3D Data Processing, Visualization, and Transmission, 3DPVT 2006 - Chapel Hill, NC, United States
Duration: Jun 14 2006Jun 16 2006

Publication series

NameProceedings - Third International Symposium on 3D Data Processing, Visualization, and Transmission, 3DPVT 2006

Other

Other3rd International Symposium on 3D Data Processing, Visualization, and Transmission, 3DPVT 2006
CountryUnited States
CityChapel Hill, NC
Period6/14/066/16/06

ASJC Scopus subject areas

  • Computer Graphics and Computer-Aided Design
  • Computer Networks and Communications

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  • Cite this

    Schlecht, J., Barnard, K., & Pryor, B. (2006). Statistical inference of biological structure and point spread functions in 3D microscopy. In Proceedings - 3rd International Symposium on 3D Data Processing, Visualization, and Transmission, 3DPVT 2006 (pp. 373-380). [4155750] (Proceedings - Third International Symposium on 3D Data Processing, Visualization, and Transmission, 3DPVT 2006). IEEE Computer Society. https://doi.org/10.1109/3DPVT.2006.131