Table I.
| Resource | Summary | References or Website |
|---|---|---|
| General Resource to Brain Atlases | ||
| Neuroscience Information Framework | Provides links to many brain atlases | https://www.neuinfo.org/mynif/search.php?q=atlas&t=registry |
| Mouse Brain/CNS Atlases | ||
| Allen Mouse Brain Atlas | Reference Atlas of C57BL/6J adult mouse brain and high resolution gene expression atlas | http://mouse.brain-map.org/ |
| Gene Expression Nervous System Atlas (GENSAT) | An NIH-funded, publicly available, gene expression atlas of the developing and adult CNS in mice. | http://www.gensat.org/index.html |
| Whole Brain Catalog | An open source, downloadable, multi-scale, virtual catalog of the mouse brain and its cellular constituents. | http://wholebraincatalog.org/ |
| Rodent Brain Workbench | A consortium website and portal to atlases, databases, and tools. | http://www.rbwb.org/ |
| Waxholm Standard Space | A coordinate-based reference space for the mapping and registration of neuroanatomical data. | http://incf.org/programs/atlasing/projects/waxholm-space |
| GenePaint | A digital atlas of gene expression patterns in the mouse. | http://www.genepaint.org/Frameset.html |
| Mousebrain Gene Expression Map | A database containing gene expression patterns assembled from mouse nervous tissues at 4 time points throughout brain development, including embryonic (e) day 11.5, e15.5, postnatal (p) day 7 and adult p42. | http://www.stjudebgem.org/web/mainPage/mainPage.ph |
| Mouse Spinal Cord Atlas | A gene expression atlas of mouse spinal cord at P4 and P56 | http://mousespinal.brain-map.org/ |
| The Mouse Brain Library | High-resolution images and databases of brains from many genetically characterized strains of mice. | http://www.mbl.org/ |
| Atlases of the Developing Mouse | ||
| Allen Brain Developing Mouse Brain Atlas | In situ hybridization of developing mouse brain at E11.5, E13.5, E15.5, E18.5, P4, P14, P56 | http://developingmouse.brain-map.org/ |
| Molecular Anatomy of Mouse Embryo Project (MAMEP) | A comprehensive information resource for the functional analysis of pattern formation, tissue development, and organogenesis in mice. Whole-mount in situ hybridizations on mid-gestation mouse embryos are used to assign genes to cell types and organs. | http://mamep.molgen.mpg.de/ |
| EMBRYS | A database of gene expression patterns mapped in the whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which the most striking dynamics in pattern formation and organogenesis is observed. | http://embrys.jp/embrys/html/MainMenu.html |
| Eurexpress | A transcriptome Atlas database for mouse embryo. | http://www.eurexpress.org/ee/ |
| e-mouse Atlas (EMA and EMAGE) | EMA is a 3D anatomical atlas of mouse embryo development with histology. EMAGE is a database of mouse gene expression which can be mapped into EMA 3D space. | http://www.emouseatlas.org/emap/home.html |
| Gene Expression Database | A collection of gene expression information during mouse development | http://www.informatics.jax.org/expression.shtml |
| Mouse Phenome Database (MPD) | A NIH-funded database with characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. | http://phenome.jax.org/db/q?rtn=docs/home |
| Non-Human Primate Brain Atlases | ||
| NIH Blueprint NHP Atlas | A suite of gene expression data, neuroanatomical data, and informatics tools for exploring the cellular and molecular architecture of the developing postnatal rhesus macaque brain. | http://www.blueprintnhpatlas.org/ |
| Rhesus Macaque Brain Atlases | These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. A set of multi-subject atlas templates is constructed specifically for functional and structural imaging studies of rhesus macaque. | http://brainmap.wisc.edu/monkey.html |
| Human Brain Atlases | ||
| Big Brain: An Ultrahigh Resolution 3D Human Brain Model | An Ultrahigh Resolution 3D Human Brain Model | https://bigbrain.loris.ca/main.php |
| Allen Human Brain Atlas | A multi-modal, multi-resolution atlas detailing gene expression across the adult human brain | http://human.brain-map.org/ |
| BrainSpan (Atlas of the Developing Brain) | An atlas describing the transcriptional mechanism of human brain development, which includes RNA sequencing and exon microarray data profiling up to 16 cortical and subcortical structures across the full course of human brain development. Such information is referenced to MRI and diffusion weighted imaging (DWI) data. | http://www.brainspan.org |
| Multiple Species Atlases | ||
| Brain Maps | Interactive multi-resolution brain atlases based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of human, non-human primate, cat, rat, mouse, barn owl, opossum, red jungle fowl, spiny anteaters, platypus and goldfish brains. Brain structures and functions can be quickly queried and retrieved over the internet. | http://brainmaps.org/ |
| The Scalable Brain Atlas | A web based display engine for different atlases created for mouse, macaque, and human | http://scalablebrainatlas.incf.org/main/index.php |
| Laboratory of Neuroimaging Atlas | Website contains brain atlases for fetal and adult human, Alzheimer's, monkey, vervet, mouse, and rat | http://www.loni.ucla.edu/Atlases/ |
| Adult Rat Brain Atlas | ||
| Adult Wistar Rat Brain | Atlas combines the Paxino Watson atlas with magnetic resonance histology and diffusion tensor imaging. | http://www.civm.duhs.duke.edu/neuro2012ratatlas/ |
| Rodent Brain Workbench | A consortium website and portal to atlases, databases, and tools. | http://www.rbwb.org/ |
| Other species | ||
| Atlas of the Drosophila Nervous System Armstrong HD et al 1995 | Atlas of the adult and developing Drosophila central nervous system | http://flybrain.neurobio.arizona.edu/ |
| Zebrafish Brain Atlas | Curated information and images of neuroanatomical structures in the developing zebrafish | http://zebrafishbrain.org/ |
| Wormatlas | A description of anatomical location and function of 302 neurons in the adult C. elegans | http://www.wormatlas.org/hermaphrodite/nervous/Neuroframeset.html |
| Zebra Finch Expression Brain Atlas | A NIH-funded online public repository of in situ hybridization images from a large collection of genes expressed in the brain of adult male zebra finches. | http://www.zebrafinchatlas.org/ |
| Human Connectome | ||
| Human Connectome | A five-year project sponsored by NIH including tween two consortia of research institutions to build a “network map” in order to better understand the anatomical and functional connectivity in healthy subjects. |
http://www.humanconnectome.org/
http://www.humanconnectomeproject.org/ |
| Human Brain Connectivity Database | Curated by the Brain Architecture Project, this is a preliminary database of neuroanatomical connectivity reports specifically for the human brain. | http://mitraweb1.cshl.edu:8080/BrainArchitecture/pages/publications.faces |
| Mouse Connectome | ||
| Mouse Connectome | An NIH-funded online database of neuroanatomical connectivity in the mouse brain. |
http://www.mouseconnectome.org/
http://brainarchitecture.org/ http://connectivity.brain-map.org/ |
| Allen Mouse Brain Connectivity Atlas | A cell-based connectivity map of the C57BL/6J mouse brain | http://connectivity.brain-map.org/ |
| Mouse Brain Architecture Project | A connectivity map of the C57BL/6J mouse brain | http://brainarchitecture.org/mouse |