## Human developmental Atlas - [Developmental MRI tepmplate][1] [[Sanchez et al., 2011]][2]: MRI brain templates (2 weeks, 3, 4.5, 6, 7.5, 9, 12, 15, 18 months, 2, 2.5, 3, 4 years). ## Human Genetic Atlas - [abagen: A toolbox for the Allen Brain Atlas genetics data][3] [[Markello et al., 2021]][4]: a Python interface for fetching and working with the Allen Human Brain Atlas (AHBA) microarray expression data. [[Related tweets]][5] - [MAGICC][6]: The atlas was generated using the Allen Human Brain Atlas. To create a dense transcriptomic atlas of the cortex, we used AHBA microarray measures of gene expression for 20,781 genes in each of 1304 cortical samples from six donor left cortical hemispheres. [[Wagstyl et al., 2024]][7] - [Whole-brain 3D maps of cellular abundance for six canonical cell-types in humans][8]: High-resolution imputed maps of spatial cell-type distributions can be used to study variations in cell-type density in relation to macroscale phenotypes ## Human Atlas & Template - [Automated Anatomical Labeling (AAL3)][9] [[Rolls et al., NeuroImage, 2020]][10]: 86 cortical regions + 84 subcortical regions - [Atlas of Lateralized visuospatial Attentional Networks (ALANs)][11]: This repository introduces the ALANs atlas, which encompasses 95 specifically selected regions underpinning the anatomical and functional bases of visuo-spatial attention in humans. - Brainstem Navigator [[Hansen et al., Nat Neuro, 2024]][12] - Desikan-Killiany Atlas 2006 [\[Desikan et al., NeuroImage, 2006\]][13] : 68 (34 /hemisphere) cortical regions used in FreeSurfer - Destrieux Atlas 2009 [\[Destrieux et al., NeuroImage, 2010\]][14] : 148 (74 /hemisphere) corticl regions used in FreeSurfer - HarvardOxford Atlas[ \[Makris et al., 2006][15]; [Frazier et al., 2005][16]; [Desikan et al., 2006][17]; [Goldstein et al., 2007\] : 48 cortical regions + 21 subcortical regions ][18] - [HCP MMP 1.0][19] [\[Glasser et al., Nature, 2016\]][20]: 360 (180 /hemisphere) cortical regions - [NextBrain][21]: a next-generation probabilistic atlas of the human brain using histological sections of five full human hemispheres with manual annotations for 333 regions of interest. - [Penn Hippocampus Atlas][22] [[Adler et al., 2018]][23] ## Non-human primate Atlas & Template - [A MRI brain template for the macaque brain][24] [[Seidlitz et al., NeuroImage, 2019]][25] - [BSI-NI Marmoset-3D Brain Atlas][26] [[Woodward et al., Sci Data, 2018]][27] - [Chimpanzee tractography protocols][28] [[Bryant et al., Plos Biol., 2020]][29]: A atlas of white matter tracts in the chimpanzee. - [Macaque brainnetome atlas][30]: Macaque Brainnetome Atlas (MBA) is a new macaque monkey atlas characterized by the anatomical connectivity of 304 subregions accompanied with the structural and the resting functional connectome. ## Mouse Atlas, Template & Registration - [Australian Mouse Brain Mapping Consortium (AMBMC)][31] - [D-LMBmap][32]: An end-to-end package providing an integrated workflow containing three modules based on novel deep-learning algorithms for whole-brain connectivity mapping. - [Flexible annotation atlas (FAA) of the mouse brain][33] [[Takata et al., bioArxiv, 2020]][34] the model based on [the Allen Brain Reference Atlas][35]. - [MouseX-DW-Allen-Atlas][36]: Overcoming sex bias in preclinical research needs not only including animals of both sexes, but also developing proper tools to handle such data. [[Martinez-Tazo et al., 2024]][37] - [Templates for In vivo Mouse Brain][38] [[Hikishima et al., Sci. Rep., 2017]][39] - [Turone Mouse Brain Template and Atlas (TMBTA) 2019][40] ## Rat Atlas - [Waxholm Space atlas of the rat brain][41]: [[Kleven et al., Nature, 2023][42]] ## Tools for Atlas - [Cross Atlas Remapping via Optimal Transport (CAROT)][43]: [[Dadashkarimi et al., 2023]][44] Creating connectomes for different atlases when raw data is not available - [DeepSlice][45] [[Carey et al., Nat Commu, 2023][46]]:a python library which automatically aligns mouse histology with the allen brain atlas common coordinate framework (and now rat brain histology to the Waxholm rat brain atlas, though this is in beta). [1]: https://jerlab.sc.edu/projects/neurodevelopmental-mri-database/ [2]: http://%20https://doi.org/10.1002/dev.20579 [3]: https://abagen.readthedocs.io/en/stable/ [4]: https://elifesciences.org/articles/72129 [5]: https://twitter.com/misicbata/status/1470786598681907216 [6]: https://github.com/kwagstyl/magicc [7]: https://elifesciences.org/reviewed-preprints/86933v1 [8]: https://github.com/neuropm-lab/cellmaps [9]: https://www.oxcns.org/aal3.html [10]: https://doi.org/10.1016/j.neuroimage.2019.116189 [11]: https://github.com/loiclabache/ALANs_brainAtlas [12]: https://doi.org/10.1038/s41593-024-01787-0 [13]: https://doi.org/10.1016/j.neuroimage.2006.01.021 [14]: https://doi.org/10.1016/j.neuroimage.2010.06.010 [15]: https://doi.org/10.1016/j.schres.2005.11.020 [16]: https://doi.org/10.1176/appi.ajp.162.7.1256 [17]: https://doi.org/10.1016/j.neuroimage.2006.01.021 [18]: http://%20https://doi.org/10.1016/j.biopsych.2006.06.027 [19]: https://www.lead-dbs.org/helpsupport/knowledge-base/atlasesresources/cortical-atlas-parcellations-mni-space/ [20]: https://doi.org/10.1038/nature18933 [21]: https://github-pages.ucl.ac.uk/NextBrain/#/home [22]: https://www.nitrc.org/projects/pennhippoatlas [23]: https://www.pnas.org/content/115/16/4252 [24]: https://github.com/jms290/NMT/tree/master/NMT_v1.3 [25]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5660669/ [26]: https://brainatlas.brain.riken.jp/marmoset/modules/xoonips/listitem.php?index_id=66 [27]: https://www.nature.com/articles/sdata20189 [28]: https://git.fmrib.ox.ac.uk/rmars/chimpanzee-tractography-protocols [29]: https://doi.org/10.1371/journal.pbio.3000971 [30]: https://molicaca.github.io/atlas/mcqatlas.html [31]: https://imaging.org.au/AMBMC/AMBMC [32]: https://github.com/lmbneuron/D-LMBmap [33]: https://github.com/ntakata/flexible-annotation-atlas [34]: https://www.biorxiv.org/content/10.1101/2020.02.17.953547v1.full [35]: https://atlas.brain-map.org/ [36]: https://github.com/TIB-Lab/MouseX-Allen-Atlas [37]: https://doi.org/10.1016/j.neuroimage.2024.120573 [38]: http://www.nitrc.org/projects/tpm_mouse [39]: https://doi.org/10.1038/s41598-017-00148-1 [40]: https://www.nitrc.org/projects/tmbta_2019 [41]: https://www.nature.com/articles/s41592-023-02034-3 [42]: https://www.nature.com/articles/s41592-023-02034-3 [43]: https://www.carotproject.com/ [44]: https://www.sciencedirect.com/science/article/abs/pii/S136184152300124X [45]: https://github.com/PolarBean/DeepSlice/ [46]: https://doi.org/10.1038/s41467-023-41645-4