Volumetric atlasing in the rodent brain: connecting experimental image data to standard anatomical space
AbstractA major challenge for understanding the brain in health and disease is related to combining information about the brain from many different sources. Spatial analysis and comparison of 2D and 3D brain images with the aim to discover new structural and functional features in the data requires mapping the images to a common anatomical space. For rodent models, widely used anatomical reference atlases have until recently been published in a book format that hinders effective comparison across images acquired at different angles and dimensions. The ambition of this study is to advance digital atlasing of the rodent brain towards a new generation of volumetric atlases that facilitate integration of whole-brain image data from multiple modalities. We present the first comprehensive anatomical reference atlas of the Sprague Dawley rat brain based on magnetic resonance imaging. To ensure interoperability with other atlases, we applied the Waxholm Space standard in the rat brain for the first time, and created a mapping against the widely used stereotaxic space. For connecting experimental data to the new reference atlas, we established standard anatomical landmarks for image registration across different levels of structural detail, and created a workflow for section to volume alignment and spatial analysis of brain-wide microscopic image series. Open access to the results of this work has enabled localization of signal in functional and structural image volumes, integration of 2D image series, and development of new atlases of various features of the brain.
List of papers
|Paper I. Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG Waxholm Space atlas of the Sprague Dawley rat brain NeuroImage 97 (2014) 374-386. DOI: 10.1016/j.neuroimage.2014.04.001 The paper is available in DUO: http://hdl.handle.net/10852/60986|
|Addendum to paper I: Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG Addendum to “Waxholm Space atlas of the Sprague Dawley rat brain” [NeuroImage 97 (2014) 374-386] NeuroImage 105 (2015) 561–562. DOI: 10.1016/j.neuroimage.2014.10.017 The paper is not available in DUO due to publisher restrictions. The published version is available at: https://doi.org/10.1016/j.neuroimage.2014.10.017|
|Paper II. Sergejeva M, Papp EA, Bakker R, Gaudnek MA, Okamura-Oho Y, Boline J, Bjaalie JG, Hess A Anatomical landmarks for registration of experimental image data to volumetric rodent brain atlasing templates Journal of Neuroscience Methods 240 (2015) 161-169. DOI: 10.1016/j.jneumeth.2014.11.005 The paper is not available in DUO due to publisher restrictions. The published version is available at: https://doi.org/10.1016/j.jneumeth.2014.11.005|
|Paper III. Papp EA, Leergaard TB, Csucs G, Bjaalie JG Brain-wide mapping of axonal connections: workflow for automated detection and spatial analysis of labeling in microscopic sections Frontiers in Neuroinformatics (2016) 10:11 DOI: 10.3389/fninf.2016.00011 The paper is available in DUO: http://hdl.handle.net/10852/53449|