A brain flatmap data visualization tool for mouse, rat, and human

Here we provide open‐access brain data flatmap visualization and analysis tools for the mouse, rat, and human. The present work stems from a previous JCN Toolbox article that introduced a novel flatmap of the mouse brain and substantially enhanced flatmaps of the rat and human brain. These brain flatmap data visualization tools enable computer‐generated graphical flatmap representation of tabulated user‐entered data. For mouse and rat, they are designed to accommodate data resolved spatially up to the level of gray matter regions, supported by parcellation and nomenclature defined in current brain reference atlases. For human, Brodmann cerebral cortical parcellation is emphasized, and all other major brain divisions are represented. A comprehensive user guide is included along with several use examples. These brain data visualization tools enable the tabulation and automatic graphical flatmap representation of any type of mouse, rat, or human brain data that is spatially localized. The formalized presentation afforded by these graphical tools facilitates comparative analysis between data sets within or between the represented species.

[1]  O. Sporns,et al.  Structure–function subsystem model and computational lesions of the central nervous system’s rostral sector (forebrain and midbrain) , 2022, Proceedings of the National Academy of Sciences of the United States of America.

[2]  E. Lundberg,et al.  The emerging landscape of spatial profiling technologies , 2022, Nature Reviews Genetics.

[3]  Hongkui Zeng.  What is a cell type and how to define it? , 2022, Cell.

[4]  Hong-wei Dong,et al.  Macroscale connections of the mouse lateral preoptic area and anterior lateral hypothalamic area , 2022, The Journal of comparative neurology.

[5]  B. Forstmann,et al.  A unified 3D map of microscopic architecture and MRI of the human brain , 2022, Science advances.

[6]  O. Sporns,et al.  Subsystem macroarchitecture of the intrinsic midbrain neural network and its tectal and tegmental subnetworks , 2021, Proceedings of the National Academy of Sciences.

[7]  R. Portugues,et al.  Visualizing anatomically registered data with brainrender , 2021, eLife.

[8]  Liya Ding,et al.  Cellular anatomy of the mouse primary motor cortex , 2020, Nature.

[9]  L. Ng,et al.  The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas , 2020, Cell.

[10]  Nicholas N. Foster,et al.  An open access mouse brain flatmap and upgraded rat and human brain flatmaps based on current reference atlases , 2020, The Journal of comparative neurology.

[11]  Nicholas N. Foster,et al.  Connectivity characterization of the mouse basolateral amygdalar complex , 2019, Nature Communications.

[12]  L. Swanson,et al.  A model for mapping between the human and rodent cerebral cortex , 2019, The Journal of comparative neurology.

[13]  Olaf Sporns,et al.  Macroscale intrinsic network architecture of the hypothalamus , 2019, Proceedings of the National Academy of Sciences.

[14]  L. Swanson.  Brain maps 4.0—Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps , 2018, The Journal of comparative neurology.

[15]  Hongkui Zeng,et al.  Neuronal cell-type classification: challenges, opportunities and the path forward , 2017, Nature Reviews Neuroscience.

[16]  Jeffrey R Moffitt,et al.  High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing , 2016, Proceedings of the National Academy of Sciences.

[17]  Allan R. Jones,et al.  Comprehensive cellular‐resolution atlas of the adult human brain , 2016, The Journal of comparative neurology.

[18]  J. Lichtman,et al.  From Cajal to Connectome and Beyond. , 2016, Annual review of neuroscience.

[19]  L. Swanson.  Brain maps online: Toward open access atlases and a pan‐mammalian nomenclature , 2015, The Journal of comparative neurology.

[20]  Larry W. Swanson,et al.  Neuroanatomical Terminology: A Lexicon of Classical Origins and Historical Foundations , 2014 .

[21]  Allan R. Jones,et al.  The Allen Human Brain Atlas Comprehensive gene expression mapping of the human brain , 2012, Trends in Neurosciences.

[22]  Allan R. Jones,et al.  An anatomically comprehensive atlas of the adult human brain transcriptome , 2012, Nature.

[23]  L. Swanson,et al.  Foundational model of structural connectivity in the nervous system with a schema for wiring diagrams, connectome, and basic plan architecture , 2010, Proceedings of the National Academy of Sciences.

[24]  Larry W. Swanson,et al.  The neuron classification problem , 2007, Brain Research Reviews.

[25]  Larry W Swanson,et al.  From gene networks to brain networks , 2003, Nature Neuroscience.

[26]  A. Colman,et al.  Optimal number of response categories in rating scales: reliability, validity, discriminating power, and respondent preferences. , 2000, Acta psychologica.

[27]  Zehdreh Allen-Lafayette,et al.  Flattening the Earth, Two Thousand Years of Map Projections , 1998 .

[28]  Steven M. Horvath,et al.  Alpha-2 macroglobulin is genetically associated with Alzheimer disease , 1998, Nature Genetics.

[29]  Larry W. Swanson,et al.  Mapping the human brain: past, present, and future , 1995, Trends in Neurosciences.

[30]  James R. Lewis,et al.  Multipoint scales: Mean and median differences and observed significance levels , 1993, Int. J. Hum. Comput. Interact..

[31]  Larry W. Swanson,et al.  Brain Maps: Structure of the Rat Brain , 1992 .

[32]  Patrick R Hof,et al.  In search of the definitive Brodmann's map of cortical areas in human , 2015, The Journal of comparative neurology.

[33]  Larry W. Swanson,et al.  Developmental brain maps : structure of the embryonic rat brain , 1996 .