Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control
The rat has arguably the most widely studied brain among all animals, with numerous reference atlases for rat brain having been published since 1946. For example, many neuroscientists have used the atlases of Paxinos and Watson (PW, first published in 1982) or Swanson (S, first published in 1992) as...
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Frontiers Media S.A.
2018-05-01
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Series: | Frontiers in Systems Neuroscience |
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Online Access: | http://journal.frontiersin.org/article/10.3389/fnsys.2018.00007/full |
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language |
English |
format |
Article |
sources |
DOAJ |
author |
Arshad M. Khan Arshad M. Khan Arshad M. Khan Arshad M. Khan Jose G. Perez Jose G. Perez Claire E. Wells Claire E. Wells Claire E. Wells Olac Fuentes Olac Fuentes Olac Fuentes |
spellingShingle |
Arshad M. Khan Arshad M. Khan Arshad M. Khan Arshad M. Khan Jose G. Perez Jose G. Perez Claire E. Wells Claire E. Wells Claire E. Wells Olac Fuentes Olac Fuentes Olac Fuentes Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control Frontiers in Systems Neuroscience stereotaxic stereotactic atlas data migration registration computer vision |
author_facet |
Arshad M. Khan Arshad M. Khan Arshad M. Khan Arshad M. Khan Jose G. Perez Jose G. Perez Claire E. Wells Claire E. Wells Claire E. Wells Olac Fuentes Olac Fuentes Olac Fuentes |
author_sort |
Arshad M. Khan |
title |
Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control |
title_short |
Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control |
title_full |
Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control |
title_fullStr |
Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control |
title_full_unstemmed |
Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control |
title_sort |
computer vision evidence supporting craniometric alignment of rat brain atlases to streamline expert-guided, first-order migration of hypothalamic spatial datasets related to behavioral control |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Systems Neuroscience |
issn |
1662-5137 |
publishDate |
2018-05-01 |
description |
The rat has arguably the most widely studied brain among all animals, with numerous reference atlases for rat brain having been published since 1946. For example, many neuroscientists have used the atlases of Paxinos and Watson (PW, first published in 1982) or Swanson (S, first published in 1992) as guides to probe or map specific rat brain structures and their connections. Despite nearly three decades of contemporaneous publication, no independent attempt has been made to establish a basic framework that allows data mapped in PW to be placed in register with S, or vice versa. Such data migration would allow scientists to accurately contextualize neuroanatomical data mapped exclusively in only one atlas with data mapped in the other. Here, we provide a tool that allows levels from any of the seven published editions of atlases comprising three distinct PW reference spaces to be aligned to atlas levels from any of the four published editions representing S reference space. This alignment is based on registration of the anteroposterior stereotaxic coordinate (z) measured from the skull landmark, Bregma (β). Atlas level alignments performed along the z axis using one-dimensional Cleveland dot plots were in general agreement with alignments obtained independently using a custom-made computer vision application that utilized the scale-invariant feature transform (SIFT) and Random Sample Consensus (RANSAC) operation to compare regions of interest in photomicrographs of Nissl-stained tissue sections from the PW and S reference spaces. We show that z-aligned point source data (unpublished hypothalamic microinjection sites) can be migrated from PW to S space to a first-order approximation in the mediolateral and dorsoventral dimensions using anisotropic scaling of the vector-formatted atlas templates, together with expert-guided relocation of obvious outliers in the migrated datasets. The migrated data can be contextualized with other datasets mapped in S space, including neuronal cell bodies, axons, and chemoarchitecture; to generate data-constrained hypotheses difficult to formulate otherwise. The alignment strategies provided in this study constitute a basic starting point for first-order, user-guided data migration between PW and S reference spaces along three dimensions that is potentially extensible to other spatial reference systems for the rat brain. |
topic |
stereotaxic stereotactic atlas data migration registration computer vision |
url |
http://journal.frontiersin.org/article/10.3389/fnsys.2018.00007/full |
work_keys_str_mv |
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doaj-ac5922353e0a4430b75ba541e081e79c2020-11-24T23:02:10ZengFrontiers Media S.A.Frontiers in Systems Neuroscience1662-51372018-05-011210.3389/fnsys.2018.00007339238Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral ControlArshad M. Khan0Arshad M. Khan1Arshad M. Khan2Arshad M. Khan3Jose G. Perez4Jose G. Perez5Claire E. Wells6Claire E. Wells7Claire E. Wells8Olac Fuentes9Olac Fuentes10Olac Fuentes11UTEP Systems Neuroscience Laboratory, University of Texas at El PasoEl Paso, TX, United StatesDepartment of Biological Sciences, University of Texas at El PasoEl Paso, TX, United StatesBUILDing SCHOLARS Program, University of Texas at El PasoEl Paso, TX, United StatesBorder Biomedical Research Center, University of Texas at El PasoEl Paso, TX, United StatesBUILDing SCHOLARS Program, University of Texas at El PasoEl Paso, TX, United StatesDepartment of Computer Science, University of Texas at El PasoEl Paso, TX, United StatesUTEP Systems Neuroscience Laboratory, University of Texas at El PasoEl Paso, TX, United StatesDepartment of Biological Sciences, University of Texas at El PasoEl Paso, TX, United StatesGraduate Program in Pathobiology, University of Texas at El PasoEl Paso, TX, United StatesBUILDing SCHOLARS Program, University of Texas at El PasoEl Paso, TX, United StatesDepartment of Computer Science, University of Texas at El PasoEl Paso, TX, United StatesVision & Learning Lab, University of Texas at El PasoEl Paso, TX, United StatesThe rat has arguably the most widely studied brain among all animals, with numerous reference atlases for rat brain having been published since 1946. For example, many neuroscientists have used the atlases of Paxinos and Watson (PW, first published in 1982) or Swanson (S, first published in 1992) as guides to probe or map specific rat brain structures and their connections. Despite nearly three decades of contemporaneous publication, no independent attempt has been made to establish a basic framework that allows data mapped in PW to be placed in register with S, or vice versa. Such data migration would allow scientists to accurately contextualize neuroanatomical data mapped exclusively in only one atlas with data mapped in the other. Here, we provide a tool that allows levels from any of the seven published editions of atlases comprising three distinct PW reference spaces to be aligned to atlas levels from any of the four published editions representing S reference space. This alignment is based on registration of the anteroposterior stereotaxic coordinate (z) measured from the skull landmark, Bregma (β). Atlas level alignments performed along the z axis using one-dimensional Cleveland dot plots were in general agreement with alignments obtained independently using a custom-made computer vision application that utilized the scale-invariant feature transform (SIFT) and Random Sample Consensus (RANSAC) operation to compare regions of interest in photomicrographs of Nissl-stained tissue sections from the PW and S reference spaces. We show that z-aligned point source data (unpublished hypothalamic microinjection sites) can be migrated from PW to S space to a first-order approximation in the mediolateral and dorsoventral dimensions using anisotropic scaling of the vector-formatted atlas templates, together with expert-guided relocation of obvious outliers in the migrated datasets. The migrated data can be contextualized with other datasets mapped in S space, including neuronal cell bodies, axons, and chemoarchitecture; to generate data-constrained hypotheses difficult to formulate otherwise. The alignment strategies provided in this study constitute a basic starting point for first-order, user-guided data migration between PW and S reference spaces along three dimensions that is potentially extensible to other spatial reference systems for the rat brain.http://journal.frontiersin.org/article/10.3389/fnsys.2018.00007/fullstereotaxicstereotacticatlasdata migrationregistrationcomputer vision |