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On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model

By Brian C. Lee (6157757), Daniel J. Tward (6157760), Partha P. Mitra (35515) and Michael I. Miller (251507)

Abstract

<div><p>This paper presents a variational framework for dense diffeomorphic atlas-mapping onto high-throughput histology stacks at the 20 μm meso-scale. The observed sections are modelled as Gaussian random fields conditioned on a sequence of unknown section by section rigid motions and unknown diffeomorphic transformation of a three-dimensional atlas. To regularize over the high-dimensionality of our parameter space (which is a product space of the rigid motion dimensions and the diffeomorphism dimensions), the histology stacks are modelled as arising from a first order Sobolev space smoothness prior. We show that the joint maximum a-posteriori, penalized-likelihood estimator of our high dimensional parameter space emerges as a joint optimization interleaving rigid motion estimation for histology restacking and large deformation diffeomorphic metric mapping to atlas coordinates. We show that joint optimization in this parameter space solves the classical curvature non-identifiability of the histology stacking problem. The algorithms are demonstrated on a collection of whole-brain histological image stacks from the Mouse Brain Architecture Project.</p></div

Topics: Biophysics, Biochemistry, Medicine, Cell Biology, Pharmacology, Biotechnology, Ecology, Cancer, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Information Systems not elsewhere classified, order Sobolev space smoothness, atla, Mouse Brain Architecture Project, high-throughput histology stacks, optimization, variational, parameter space, brain serial-section histology, diffeomorphic, modelled, whole-brain histological image stacks, dimension
Year: 2018
DOI identifier: 10.1371/journal.pcbi.1006610
OAI identifier: oai:figshare.com:article/7523012
Provided by: FigShare
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