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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
7T Structural MRI scans ATAG
 
Resource Report
Resource Website
1+ mentions
7T Structural MRI scans ATAG (RRID:SCR_014084) atlas, data or information resource, data set Data sets from the atlasing of the basal ganglia (ATAG) consortium, which provides ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. They include whole-brain and reduced field-of-view MP2RAGE and T2 scans with ultra-high resolution at a sub millimeter scale. The data can be used to develop new algorithms that help building new high-resolution atlases both in the basic and clinical neurosciences. They can also be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinsons disease and neuropsychiatric diseases. 7t mri, data set, atlas, basal ganglia, structural mri scan, brain, human brain, probabilistic atlas is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Amsterdam; Amsterdam; Netherlands
Available for download SCR_014084 2026-02-10 09:56:46 7
Single Cell Portal
 
Resource Report
Resource Website
100+ mentions
Single Cell Portal (RRID:SCR_014816) SCP portal, data or information resource Portal specializes in visualizing and disseminating single cell data. Allows you to use natural language and faceted search to discover other scientists’ research and share your own findings. Each study includes information on cell types, singular or multiple gene expression, and spatial transcriptomics. Interactive visualizations allow to explore cell clusters and search for related genes. Single cell data visualization, disseminating single cell data, single cell data, brain, RNA, rna seq, multiple gene expression, spatial transcriptomics, open science is used by: BRAIN Initiative
is used by: BICCN
is related to: BICCN Anatomy and Morphology Project
is related to: Allen Institute for Brain Science
has parent organization: Broad Institute
has organization facet: Terra
Free, Available for download, Freely available https://portals.broadinstitute.org/single_cell?utf8=✓&search_terms=e+coli&order=&commit= SCR_014816 Single-Cell RNA-Seq Portal for Brain Research 2026-02-10 09:56:59 222
brainhack.org
 
Resource Report
Resource Website
1+ mentions
brainhack.org (RRID:SCR_000195) brainhack.org portal, data or information resource Forum for collaborative projects in the field of brain science. Everyone is invited to submit projects, either existing ones that you want to see featured or new ones that you want launch and work on in a collaborative, open way. magnetic resonance imaging assay, image, fmri, brain, science, neuroimaging, project is affiliated with: HBM Hackathon
has parent organization: Neuro Bureau
PMID:27042293
PMID:33932337
The community can contribute to this resource nlx_149390 SCR_000195 BrainHack 2026-02-10 09:54:18 1
Mindboggle
 
Resource Report
Resource Website
100+ mentions
Mindboggle (RRID:SCR_002438) Mindboggle software resource, software application, data processing software Mindboggle (http://mindboggle.info) is open source software for analyzing the shapes of brain structures from human MRI data. The following publication in PLoS Computational Biology documents and evaluates the software: Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B, Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human brains. PLoS Computational Biology 13(3): e1005350. doi:10.1371/journal.pcbi.1005350 analyze, anatomic, atlas application, console (text based), labeling, python, magnetic resonance, os independent, region of interest, segmentation, brain, label, mri, anatomy, cerebral cortex, human brain, parcellation, morphometry, shape measures, cortical thickness, cortical depth, Laplace-Beltrami spectra, Zernike moments is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) NIMH MH084029-02 Free, Available for download, Freely available nlx_155813 http://www.nitrc.org/projects/mindboggle SCR_002438 2026-02-10 09:54:42 196
Allen Institute for Brain Science Sleep Study
 
Resource Report
Resource Website
1+ mentions
Allen Institute for Brain Science Sleep Study (RRID:SCR_002983) Allen Sleep Study atlas, data or information resource, data set Collection of gene expression data in mouse brain for five different conditions of sleep and wakefulness to understand sleep deprivation and dynamic changes underlying sleep and wake cycles. Platform to generate cellular resolution expression data. gene, expression, brain, data, image, mice, microarray, nissl, sleep, deprivation, wake, cycle, wakefulness, neuroanatomy is listed by: 3DVC
has parent organization: Allen Institute for Brain Science
Free, Public nif-0000-00507 SCR_002983 Sleep Study 2026-02-10 09:54:49 2
EPMBA.ORG: Electronic Prenatal Mouse Brain Atlas
 
Resource Report
Resource Website
1+ mentions
EPMBA.ORG: Electronic Prenatal Mouse Brain Atlas (RRID:SCR_001882) EPMBA atlas, data or information resource The Electronic Prenatal Mouse Brain Atlas, EPMBA, at present consists of two sets of annotated images of coronal sections from Gestational Day (GD) 12 heads and GD 16 brains of C57BL/6J mice. Ten micron thick sections were stained with hematoxylin and eosin. Images were prepared at various resolutions for annotations and for high resolution presentation. A subset of sections were annotated and linked to anatomical terms. Additionally, horizontal sections of a GD 12 head were aligned and re-assembled into a 3D volume for digital sectioning in arbitrarily oblique planes. These images were captured using a Nikon E800 stereomicroscope with a 10X objective. The resolution is 1.35 pixels/micrometer. The PC program used to grab the images, Microbrightfield's Neurolucida (version 6), stitched together a mosaic of between 10 and 50 high-res images for each tissue slice, while the user focused the scope for each mosaic tile. Since the nature of optic lenses is to focus on one central point, it was difficult to obtain a uniformly-focused field of vision; as such, small areas of these images are blurred. Images were then transferred to a Macintosh and processed in Adobe Photoshop (version 7). Color levels were adjusted for maximum clarity of the tissue, and areas surrounding the tissue were cleared of artifacts. Each image is approximately 3350 pixels wide by 2650 pixels high. A scale bar with a length of 1350 pixels/mm is visible in the lower right-hand corner of each image. The annotations have been completed for the Atlas of Developing Mouse Brain Gestational (Embryonic) Day 12 (7/5/07) as well as the Atlas of Developing Mouse Brain Embryonic Day 16 (4/26/07). The 3D EPMBA data set has been mounted on a NeuroTerrain Atlas Server (NtAS). (6/27/07). embryonic, brain, c57bl/6j, coronal, developing, developmental, gestational, head, horizontal sections, image, mouse, prenatal has parent organization: East Tennessee State University; Tennessee; USA Human Brain Project ;
NIMH 263-MD-414639
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10452 SCR_001882 EPMBA.org, Electronic Prenatal Mouse Brain Atlas 2026-02-10 09:54:36 1
Zebrafinch Brain Architecture Project
 
Resource Report
Resource Website
1+ mentions
Zebrafinch Brain Architecture Project (RRID:SCR_004277) Zebrafinch Brain Architecture Project atlas, data or information resource Atlas of high resolution Nissl stained digital images of the brain of the zebra finch, the mainstay of songbird research. The cytoarchitectural high resolution photographs and atlas presented here aim at facilitating electrode placement, connectional studies, and cytoarchitectonic analysis. This initial atlas is not in stereotaxic coordinate space. It is intended to complement the stereotaxic atlases of Akutegawa and Konishi, and that of Nixdorf and Bischof. (Akutagawa E. and Konishi M., stereotaxic atalas of the brain of zebra finch, unpublished. and Nixdorf-Bergweiler B. E. and Bischof H. J., A Stereotaxic Atlas of the Brain Of the Zebra Finch, Taeniopygia Guttata, http://www.ncbi.nlm.nih.gov.) The zebra finch has proven to be the most widely used model organism for the study of the neurological and behavioral development of birdsong. A unique strength of this research area is its integrative nature, encompassing field studies and ethologically grounded behavioral biology, as well as neurophysiological and molecular levels of analysis. The availability of dimensionally accurate and detailed atlases and photographs of the brain of male and female animals, as well as of the brain during development, can be expected to play an important role in this research program. Traditionally, atlases for the zebra finch brain have only been available in printed format, with the limitation of low image resolution of the cell stained sections. The advantages of a digital atlas over a traditional paper-based atlas are three-fold. * The digital atlas can be viewed at multiple resolutions. At low magnification, it provides an overview of brain sections and regions, while at higher magnification, it shows exquisite details of the cytoarchitectural structure. * It allows digital re-slicing of the brain. The original photographs of brain were taken in certain selected planes of section. However, the brains are seldom sliced in exactly the same plane in real experiments. Re-slicing provides a useful atlas in user-chosen planes, which are otherwise unavailable in the paper-based version. * It can be made available on the internet. High resolution histological datasets can be independently evaluated in light of new experimental anatomical, physiological and molecular studies. nissl stain, sagittal, horizontal plane, transverse plane, myelin stain, brain has parent organization: Brain Architecture Project W. M. Keck Foundation ;
Crick-Clay Professorship ;
NINDS NS50436;
NIGMS R24 GM092842
nlx_143663 SCR_004277 2026-02-10 09:55:03 4
DTI White Matter Atlas
 
Resource Report
Resource Website
DTI White Matter Atlas (RRID:SCR_005279) DTI White Matter Atlas atlas, data or information resource DTI white matter atlases with different data sources and different image processing. These include single-subject, group-averaged, B0 correction, processed atlases (White Matter Parcellation Map, Tract-probability maps, Conceptual difference between the WMPM and tract-probability maps), and linear or non-linear transformation for automated white matter segmentation. # Adam single-subject white matter atlas (old version): These are electronic versions of atlases published in Wakana et al, Radiology, 230, 77-87 (2004) and MRI Atlas of Human White Matter, Elsevier. ## Original Adam Atlas: 256 x 256 x 55 (FOV = 246 x 246 mm / 2.2 mm slices) (The original matrix is 96x96x55 (2.2 mm isotropic) which is zerofilled to 256 x 256 ## Re-sliced Adam Atlas: 246 x 246 x 121 (1 mm isotropic) ## Talairach Adam: 246 x 246 x 121 (1 mm isotropic) # New Eve single-subject white matter atlas: The new version of the single-subject white matter atlas with comprehensive white matter parcellation. ## MNI coordinate: 181 x 217 x 181 (1 mm isotropic) ## Talairach coordinate: 181 x 217 x 181 (1 mm isotropic) # Group-averaged atlases: This atlas was created from their normal DTI database (n = 28). The template was MNI-ICBM-152 and the data from the normal subjects were normalized by affine transformation. Image dimensions are 181x217x181, 1 mm isotropic. There are two types of maps. The first one is the averaged tensor map and the second one is probabilistic maps of 11 white matter tracts reconstructed by FACT. # ICBM Group-averaged atlases: This atlas was created from ICBM database. All templates follow Radiology convention. You may need to flip right and left when you use image registration software that follows the Neurology convention. white matter, brain, template, human, magnetic resonance imaging, diffusion tensor imaging, adult human, male, female, cerebellum, mni, talairach has parent organization: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA Normal NCRR P41RR015241 Account required nlx_144313 SCR_005279 2026-02-10 09:55:14 0
Atlas of the Brain
 
Resource Report
Resource Website
1+ mentions
Atlas of the Brain (RRID:SCR_005967) Atlas of the Brain atlas, data or information resource On line labeled atlas of the human brain developed by Dr. Rand Swenson of Dartmouth Medical School. It includes gross anatomical and MRI-generated slices (Axial T1-weighted MRI and Coronal T2 MRI weighted, along with Magnetic resonance arteriogram (MRA) and Magnetic resonance venogram (MRV)images. Labels may be turned on and off. A companion on-line textbook is also available. The site says it is still under construction, although the copyright is 2009. * Atlas of Gross Brain Topography * Atlas of the Brain Stem in Cross Section * Atlas of the Brain in Axial Slices * Atlas of the Brain in Coronal Slices * Atlas of the Head in Axial Slices * Axial T1-weighted MRI * Axial T2-weighted MRI * Coronal T1 MRI * Coronal T2 MRI * Magnetic resonance arteriogram (MRA) * Magnetic resonance venogram (MRV) brain, magnetic resonance imaging, magnetic resonance venogram, magnetic resonance arteriogram, brainstem, radiographic anatomy, axial, coronal is related to: Review of Clinical and Functional Neuroscience
is related to: Review of Clinical and Functional Neuroscience
has parent organization: Dartmouth Medical School; New Hampshire; USA
nlx_151327 SCR_005967 Atlas of the Brain - Structure with functional correlates 2026-02-10 09:55:21 1
Adult Wistar Rat Atlas
 
Resource Report
Resource Website
1+ mentions
Adult Wistar Rat Atlas (RRID:SCR_006288) Adult Wistar Rat Atlas atlas, data or information resource Multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). The atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. To access the atlas, click view supplementary materials in CIVMSpace at the bottom of the following webpage. magnetic resonance histology, wistar rat, brain, mri, diffusion tensor imaging, histology, magnetic resonance imaging, neuroanatomy, histology has parent organization: Duke University; North Carolina; USA NIBIB ;
NCRR P41 RR005959
PMID:22634863 Free for academic use, We ask that you provide contact information, Acknowledgement required nlx_151935 SCR_006288 Multidimensional Magnetic Resonance Histology Atlas of the Wistar Rat Brain 2026-02-10 09:55:25 6
BrainNavigator
 
Resource Report
Resource Website
1+ mentions
BrainNavigator (RRID:SCR_008289) BrainNavigator atlas, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips. 3d, 2d, acetylcholinesterase, anatomy, brain, coronal, reconstruction, sagittal, sterotaxic, visualization, molecular neuroanatomy resource, training resource, connection, literature, gene expression, image THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-24037 SCR_008289 Brain Navigator 2026-02-10 09:55:49 5
Registration Software Mitra Lab
 
Resource Report
Resource Website
Registration Software Mitra Lab (RRID:SCR_018353) software resource, software application, data processing software Software package to align brain slice images in atlas free manner. Align, brain, brain slice, brain slice image, atlas free manner Free, Available for download, Freely available SCR_018353 2026-02-10 09:57:43 0
TumorSim
 
Resource Report
Resource Website
1+ mentions
TumorSim (RRID:SCR_002604) simulation software, software resource, software application Simulation software that generates pathological ground truth from a healthy ground truth. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc) and then outputs simulation images. clinical neuroinformatics, magnetic resonance, mri, brain, segmentation, simulation, tumor, ground truth uses: BrainWeb - Simulated Brain Database
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Utah; Utah; USA
Cancer NIBIB R01 EB000219 PMID:19119055 Free, Available for download, Freely available nlx_156007 SCR_002604 2026-02-10 09:54:44 1
MindSeer
 
Resource Report
Resource Website
MindSeer (RRID:SCR_003019) MindSeer data visualization software, software resource, software application, data processing software A cross-platform application for 3D brain visualization for multi-modality neuroimaging data written in Java/Java3D, that runs in both standalone and client-server mode. It supports basic data management capabilities, visualization of 3D surfaces (SPM's output or OFF files), volumes (Analyze, NIFTI or Minc) and label sets. MindSeer has 2 different modes: # Client/Server is designed to allow users to visualize data that is stored centrally and enhance collaboration. # Standalone mode is available to view local data and is built for more performance than Client/Server Both modes have the same interface and support the same features. It has a modular architecture and is designed to be extensible. Requirements: # Java 5.0 or above. # Java Web Start. # Java3D (installed automatically by Web Start). 3d surface, visualization, multimodal, volume, neuroimaging, 3-d volume, surface, java, java3d, brain, brain structure, magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
has parent organization: University of Washington; Seattle; USA
Human Brain Project ;
NIDCD DC02310
PMID:17937818 GNU General Public License, With some, GNU Lesser General Public License, Components (MatFile and NIFTI jar files). nif-0000-00525 http://www.nitrc.org/projects/mindseer SCR_003019 2026-02-10 09:54:49 0
MouseLight Neuron Browser
 
Resource Report
Resource Website
10+ mentions
MouseLight Neuron Browser (RRID:SCR_016669) web application, software resource Interactive web platform for anyone to explore, search, filter and visualize the single neuron reconstructions. explore, search, filter, visualize, single, neuron, reconstruction, mouse, brain has parent organization: Janelia Research
is provided by: MouseLight Project
Free, Freely available, Tutorial available, Acknowledgement required http://mouselight.janelia.org/ SCR_016669 Neuron Browser, NeuronBrowser, MouseLight Neuron Browser 2026-02-10 09:57:22 26
MRIcron
 
Resource Report
Resource Website
1000+ mentions
MRIcron (RRID:SCR_002403) MRIcron data visualization software, software resource, software application, data processing software Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools is used by: XFSL: An FSL toolbox
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
is listed by: neurodebian
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: Colour maps for brain imaging
has parent organization: University of South Carolina; South Carolina; USA
PMID:17583985
PMID:11568431
BSD License biotools:MRIcron, nif-0000-00122 https://sources.debian.org/src/mricron/
http://www.mccauslandcenter.sc.edu/mricro/
http://www.nitrc.org/projects/mricron
http://neuro.debian.net/pkgs/mricron.html
https://bio.tools/MRIcron
SCR_002403 mricron - magnetic resonance image conversion viewing and analysis 2026-02-10 09:54:42 2157
Virtual brain
 
Resource Report
Resource Website
10+ mentions
Virtual brain (RRID:SCR_002249) tvb simulation software, software resource, software application Simulation software for modeling the entire human brain by combining structural and functional data from empirical neuroimaging data. It can generate local field potentials, EEG, MEG and fMRI BOLD data based on neural mass models. The user can also modify the model parameters to match clinical conditions from focal lesions or degenerative disorders. dti, simulation, modeling, brain is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Toronto; Ontario; Canada
James S. McDonnell Foundation PMID:23442172
PMID:23774395
Free, Freely available nlx_155567 http://www.nitrc.org/projects/tvb SCR_002249 thevirtualbrain.org, The Virtual Brain, thevirtualbrain 2026-02-10 09:54:40 38
Confocal Microscopy Image Gallery - Rat Brain Tissue Sections
 
Resource Report
Resource Website
Confocal Microscopy Image Gallery - Rat Brain Tissue Sections (RRID:SCR_002432) image collection, data or information resource An image gallery of the rat brain labeled via immunofluorescence in coronal, horizontal, and sagittal thick sections using laser scanning confocal microscopy. image collection, gallery, function, amygdala, anatomy, blood vessel, brain, cerebellum, cerebral cortex, coronal, digital image, hippocampus, horizontal, hypothalamus, immunofluorescence, microscopy, model, neuron microscopy, rat, receptor, sagittal, thalamus, tissue is provided by: Olympus Free, Freely available nif-0000-21299 http://www.olympusconfocal.com/gallery/ratbrain/ SCR_002432 Olympus Rat Brain Tissue Sections 2026-02-10 09:54:42 0
CNSforum: Image Bank
 
Resource Report
Resource Website
CNSforum: Image Bank (RRID:SCR_002718) image collection, data or information resource A collection of downloadable central nervous system (CNS) images for teaching, presentations, articles, and other purposes. The following major categories of images are as follows: Brain anatomy, Brain physiology, Anxiety, Depression, Schizophrenia, Dementia, Parkinson's disease, Stroke, and Others. image collection, human brain, brain anatomy, brain physiology, anxiety, depression, schizophrenia, dementia, parkinson's disease, stroke, brain has parent organization: CNS Forum Anxiety, Depressive Disorder, Schizophrenia, Dementia, Parkinson's disease, Stroke, Normal Free, Freely available nif-0000-23576 SCR_002718 CNS Forum Image Bank, Lundbeck Institute CNSforum Image Bank 2026-02-10 09:54:46 0
Brian Simulator
 
Resource Report
Resource Website
10+ mentions
Brian Simulator (RRID:SCR_002998) Brian simulation software, software resource, software application Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator. simulation, spiking, neuron, brain, communication, modelling, computational neuroscience, python, spiking neuron, neural network is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Ecole Normale Superieure; Paris; France
European Union ;
French National Research Agency ;
CNRS ;
Ecole Normale Superieure; Paris; France
DOI:10.7554/eLife.47314
DOI:10.3389/neuro.01.026.2009
DOI:10.7554/eLife.47314
Free, Available for download, Freely available nif-0000-30223 http://www.nitrc.org/projects/brian SCR_002998 Brian 2, Brian spiking neural network simulator, Brian2 2026-02-10 09:54:49 25

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