Article
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
(2018)
Abstract
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 PWreference spaces to be aligned to atlas levels from any of the four published editions representing Sreference 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 zaxis 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 PWand Sreference spaces. We show that z-aligned point source data (unpublished hypothalamic microinjection sites) can be migrated from PWto Sspace to a first-order approximation in the mediolateral and dorsoventral dimensions using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 Sspace, 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 PWand Sreference spaces along three dimensions that is potentially extensible to other spatial reference systems for the rat brain.
Keywords
- stereotaxic,
- stereotactic,
- brain atlas,
- rat,
- hypothalamus,
- central injections,
- mapping,
- data migration
Disciplines
Publication Date
Spring May 1, 2018
DOI
https://doi.org/10.3389/fnsys.2018.00007
Citation Information
Khan AM, Perez JG, Wells CE and Fuentes O (2018) 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. Front. Syst. Neurosci. 12:7. doi: 10.3389/fnsys.2018.00007.
Creative Commons license
This work is licensed under a Creative Commons CC_BY International License.