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Sun P, Parvathaneni P, Schilling KG, Gao Y, Janve V, Anderson A, Landman BA. Integrating histology and MRI in the first digital brain of common squirrel monkey, Saimiri sciureus. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2015; 9417:94171T. [PMID: 25914510 PMCID: PMC4405811 DOI: 10.1117/12.2081443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This effort is a continuation of development of a digital brain atlas of the common squirrel monkey, Saimiri sciureus, a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. Here, we present the integration of histology with multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. The central concept of this work is to use block face photography to establish an intermediate common space in coordinate system which preserves the high resolution in-plane resolution of histology while enabling 3-D correspondence with MRI. In vivo MRI acquisitions include high resolution T2 structural imaging (300 µm isotropic) and low resolution diffusion tensor imaging (600 um isotropic). Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging (both 300 µm isotropic). Cortical regions were manually annotated on the co-registered volumes based on published histological sections in-plane. We describe mapping of histology and MRI based data of the common squirrel monkey and construction of a viewing tool that enable online viewing of these datasets. The previously descried atlas MRI is used for its deformation to provide accurate conformation to the MRI, thus adding information at the histological level to the MRI volume. This paper presents the mapping of single 2D image slice in block face as a proof of concept and this can be extended to map the atlas space in 3D coordinate system as part of the future work and can be loaded to an XNAT system for further use.
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Affiliation(s)
- Peizhen Sun
- Electrical Engineering, Vanderbilt University, Nashville, TN USA
| | | | - Kurt G. Schilling
- Biomedical Engineering, Vanderbilt University, Nashville, TN USA
- Institute of Image Science, Vanderbilt University, Nashville, TN USA
| | - Yurui Gao
- Biomedical Engineering, Vanderbilt University, Nashville, TN USA
- Institute of Image Science, Vanderbilt University, Nashville, TN USA
| | - Vaibhav Janve
- Biomedical Engineering, Vanderbilt University, Nashville, TN USA
- Institute of Image Science, Vanderbilt University, Nashville, TN USA
| | - Adam Anderson
- Biomedical Engineering, Vanderbilt University, Nashville, TN USA
- Institute of Image Science, Vanderbilt University, Nashville, TN USA
| | - Bennett A. Landman
- Electrical Engineering, Vanderbilt University, Nashville, TN USA
- Biomedical Engineering, Vanderbilt University, Nashville, TN USA
- Institute of Image Science, Vanderbilt University, Nashville, TN USA
- Computer Science, Vanderbilt University, Nashville, TN USA
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Wang H, Lenglet C, Akkin T. Structure tensor analysis of serial optical coherence scanner images for mapping fiber orientations and tractography in the brain. JOURNAL OF BIOMEDICAL OPTICS 2015; 20:036003. [PMID: 25741662 PMCID: PMC4350401 DOI: 10.1117/1.jbo.20.3.036003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 02/19/2015] [Indexed: 05/05/2023]
Abstract
Quantitative investigations of fiber orientation and structural connectivity at microscopic resolution have led to great challenges for current neuroimaging techniques. Here, we present a structure tensor (ST) analysis of ex vivo rat brain images acquired by a multicontrast (MC) serial optical coherence scanner. The ST considers the gradients of images in local neighbors to generate a matrix whose eigen-decomposition can estimate the local features such as the edges, anisotropy, and orientation of tissue constituents. This computational analysis is applied on the conventional- and polarization-based contrasts of optical coherence tomography. The three-dimensional (3-D) fiber orientation maps are computed from the image stacks of sequential scans both at mesoresolution for a global view and at high-resolution for the details. The computational orientation maps demonstrate a good agreement with the optic axis orientation contrast which measures the in-plane fiber orientation. Moreover, tractography is implemented using the directional information extracted from the 3-D ST. The study provides a unique opportunity to leverage MC high-resolution information to map structural connectivity of the whole brain.
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Affiliation(s)
- Hui Wang
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota 55455, United States
- Address all correspondence to: Hui Wang, E-mail:
| | - Christophe Lenglet
- University of Minnesota, Center for Magnetic Resonance Research, Department of Radiology, Minneapolis, Minnesota 55455, United States
| | - Taner Akkin
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota 55455, United States
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Gao Y, Khare SP, Panda S, Choe AS, Stepniewska I, Li X, Ding Z, Anderson A, Landman BA. A brain MRI atlas of the common squirrel monkey, Saimiri sciureus.. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 9038:90380C. [PMID: 24817811 DOI: 10.1117/12.2043589] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The common squirrel monkey, Saimiri sciureus, is a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. It is one of the most commonly used South American primates in biomedical research. Unlike its Old World macaque cousins, no digital atlases have described the organization of the squirrel monkey brain. Here, we present a multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. In vivo MRI acquisitions include T2 structural imaging and diffusion tensor imaging. Ex vivo MRI acquisitions include T2 structural imaging and diffusion tensor imaging. Cortical regions were manually annotated on the co-registered volumes based on published histological sections.
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Affiliation(s)
- Yurui Gao
- Biomedical Engineering, Vanderbilt University, Nashville, TN USA ; Institute of Image Science, Vanderbilt University, Nashville, TN USA
| | - Shweta P Khare
- Computer Science, Vanderbilt University, Nashville, TN USA
| | - Swetasudha Panda
- Electrical Engineering, Vanderbilt University, Nashville, TN USA
| | - Ann S Choe
- Biomedical Engineering, Vanderbilt University, Nashville, TN USA ; Institute of Image Science, Vanderbilt University, Nashville, TN USA
| | | | - Xia Li
- Institute of Image Science, Vanderbilt University, Nashville, TN USA
| | - Zhoahua Ding
- Institute of Image Science, Vanderbilt University, Nashville, TN USA ; Electrical Engineering, Vanderbilt University, Nashville, TN USA
| | - Adam Anderson
- Biomedical Engineering, Vanderbilt University, Nashville, TN USA ; Institute of Image Science, Vanderbilt University, Nashville, TN USA
| | - Bennett A Landman
- Biomedical Engineering, Vanderbilt University, Nashville, TN USA ; Institute of Image Science, Vanderbilt University, Nashville, TN USA ; Computer Science, Vanderbilt University, Nashville, TN USA ; Electrical Engineering, Vanderbilt University, Nashville, TN USA
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