NDLI: Statistical Inference of Biological Structure and Point Spread Functions in 3D Microscopy

Content Provider	IEEE Xplore Digital Library
Author	Schlecht, J. Barnard, K. Pryor, B.
Copyright Year	2006
Description	Author affiliation: Dept. of Comput. Sci., Arizona Univ., Tucson, AZ (Schlecht, J.; Barnard, K.)
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.
Starting Page	373
Ending Page	380
File Size	262935
Page Count	8
File Format	PDF
ISBN	0769528252
DOI	10.1109/3DPVT.2006.131
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2006-06-14
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Biological system modeling Fungi Optical microscopy Optical imaging Biomedical optical imaging Geometrical optics Solid modeling Monte Carlo methods Data analysis Biology
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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