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http://neuromab.ucdavis.edu/

A national mouse monoclonal antibody generating resource for biochemical and immunohistochemical applications in mammalian brain. NeuroMabs are generated from mice immunized with synthetic and recombinant immunogens corresponding to components of the neuronal proteome as predicted from genomic and other large-scale cloning efforts. Comprehensive biochemical and immunohistochemical analyses of human, primate and non-primate mammalian brain are incorporated into the initial NeuroMab screening procedure. This yields a subset of mouse mAbs that are optimized for use in brain (i.e. NeuroMabs): for immunocytochemical-based imaging studies of protein localization in adult, developing and pathological brain samples, for biochemical analyses of subunit composition and post-translational modifications of native brain proteins, and for proteomic analyses of native brain protein networks. The NeuroMab facility was initially funded with a five-year U24 cooperative grant from NINDS and NIMH. The initial goal of the facility for this funding period is to generate a library of novel NeuroMabs against neuronal proteins, initially focusing on membrane proteins (receptors/channels/transporters), synaptic proteins, other neuronal signaling molecules, and proteins with established links to disease states. The scope of the facility was expanded with supplements from the NIH Blueprint for Neuroscience Research to include neurodevelopmental targets, the NIH Roadmap for Medical Research to include epigenetics targets, and NIH Office of Rare Diseases Research to include rare disease targets. These NeuroMabs will then be produced on a large scale and made available to the neuroscience research community on an inexpensive basis as tissue culture supernatants or purified immunoglobulin by Antibodies Inc. The UC Davis/NIH NeuroMab Facility makes NeuroMabs available directly to end users and is unable to accommodate sales to distributors for third party distribution. Note, NeuroMab antibodies are now offered through antibodiesinc.

Proper citation: NeuroMab (RRID:SCR_003086) Copy   

•   Source: SciCrunch Registry

http://www.genepaint.org/MapP7_01.htm

Abbreviated reference atlas for the P56 mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).

Proper citation: GenePaint P7 Atlas (RRID:SCR_002787) Copy   

•   Source: SciCrunch Registry

http://sleep.alleninstitute.org

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.

Proper citation: Allen Institute for Brain Science Sleep Study (RRID:SCR_002983) Copy   

•   Source: SciCrunch Registry

http://www.virtualflybrain.org

An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain.

Proper citation: Virtual Fly Brain (RRID:SCR_004229) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/unc_brain_atlas

Human brain atlases for adult, pediatric and elderly populations, by iterative joint deformable registration of training datasets into a single unbiased average image. Atlases packages include T1-weighted images, tissue priors (WM,GM,CSF), lobar parcellation maps and subcortical structures. Current available atlases: * Adult atlas: Symmetric atlas generated from 50+ healthy adult subjects (20-59 year old). * UNC-MNI Pediatric 1-year-old atlas: Symmetric atlas generated from 104 1-year-old subjects, combining children at high familial risk of autism and controls. * Pediatric 4-year-old atlas: Symmetric atlas generated from 10 4-year-old healthy subjects. * Elderly atlas: Atlas generated from 27 healthy elderly subjects (60+ years old). Additional information and acknowledgment for their usage can be found by clicking on the release notes.

Proper citation: UNC Human Brain Atlas (RRID:SCR_002606) Copy   

•   Source: SciCrunch Registry

http://cvr.yorku.ca/home/

The Centre for Vision Research focuses on interdisciplinary research into human and machine vision and visual processes, into vision's interactions with other senses and with motor and cognitive processes, and in applications such as visually-guided robotics or clinical diagnosis and treatment. The Centre for Vision Research includes the following major research themes: - Human Visual Performance - Visual Human-Computer Interaction, Graphics and Virtual Reality - Visual Psychophysics - Eye Movements and Hand-Eye Coordination - Computational Modeling and Computer Vision - Electrophysiology - Clinical and Developmental Studies - Brain Imaging

Proper citation: Centre for Vision Research (RRID:SCR_002879) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/neurolabels

This resource was created to host descriptions of protocols, definitions and rules for the reliable identification and localization of human brain anatomy and discussions of best practices in brain labeling. Project for manual anatomical labeling of human brain MRI data, and the visual presentation of labeled brain images.

Proper citation: BrainColor: Collaborative Open Labeling Online Resource (RRID:SCR_006377) Copy   

•   Source: SciCrunch Registry

http://www.nih.gov/science/brain/

Project aimed at revolutionizing understanding of human brain, to show how individual cells and complex neural circuits interact, enable rapid progress in development of new technologies and data analysis tools to treat and prevent brain disorders. BRAIN Initiative encourages collaborations between neurobiologists and scientists from disciplines such as statistics, physics, mathematics, engineering, and computer and information sciences. Institutes and centers contributing to NIH BRAIN Initiative support those research efforts.

Proper citation: BRAIN Initiative (RRID:SCR_006770) Copy   

•   Source: SciCrunch Registry

http://senselab.med.yale.edu

The SenseLab Project is a long-term effort to build integrated, multidisciplinary models of neurons and neural systems. It was founded in 1993 as part of the original Human Brain Project, which began the development of neuroinformatics tools in support of neuroscience research. It is now part of the Neuroscience Information Framework (NIF) and the International Neuroinformatics Coordinating Facility (INCF). The SenseLab project involves novel informatics approaches to constructing databases and database tools for collecting and analyzing neuroscience information, using the olfactory system as a model, with extension to other brain systems. SenseLab contains seven related databases that support experimental and theoretical research on the membrane properties: CellPropDB, NeuronDB, ModelDB, ORDB, OdorDB, OdorMapDB, BrainPharmA pilot Web portal that successfully integrates multidisciplinary neurocience data.

Proper citation: SenseLab (RRID:SCR_007276) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009

Unbiased standard magnetic resonance imaging template brain volume for normal population. These volumes were created using data from ICBM project. 6 different templates are available: * ICBM 2009a Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, also T2 relaxometry (T2 values calculated for each subject using single dual echo PD/T2 scan), and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.10.1. * ICBM 2009a Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.10.1. Also included brain mask, eye mask and face mask. * ICBM 2009b Nonlinear Symmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009b Nonlinear Asymmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009c Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.11. Sampling is different from 2009a template. * ICBM 2009c Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.11 Also included brain mask, eye mask and face mask.Sampling is different from 2009a template. All templates are describing the same anatomy, but sampling is different. Also, different versions of N3 algorithm produces slightly different tissue probability maps. Tools for using these atlases can be found in the Software section. Viewing the multiple atlas volumes online requires Java browser support. You may also download the templates - see licensing information.

Proper citation: ICBM 152 Nonlinear atlases version 2009 (RRID:SCR_008796) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1

An unbiased standard magnetic resonance imaging template brain volume for pediatric data from the 4.5 to 18.5y age range. These volumes were created using data from 324 children enrolled in the NIH-funded MRI study of normal brain development (Almli et al., 2007, Evans and Group 2006). Tools for using these atlases can be found in the Software section. To view the atlases online, click on the appropriate JIV2 link in the Download section. You can download templates constructed for different age ranges. For each age range you will get an average T1w, T2w, PDw maps normalized between 0 and 100 and tissue probability maps, with values between 0 and 1. Also each age range includes a binary brain mask.

Proper citation: NIHPD Objective 1 atlases (4.5 - 18.5y) (RRID:SCR_008794) Copy   

•   Source: SciCrunch Registry

http://www.neuroethics.ubc.ca/

It is an interdisciplinary research group dedicated to tackling the ethical, legal, policy and social implications of frontier technological developments in the neurosciences. Our objective is to align innovations in the brain sciences with societal, cultural and individual human values through high impact research, education and outreach. The Core''s major research projects are focused on high impact, high visibility areas including the use of drugs and devices for neuroenhancement, ethics in neurodegenerative disease and regenerative medicine research, international and cross-cultural challenges in brain research, neuroimaging in the private sector, and the ethics of personalized medicine, among others. Members of the Core also lead initiatives aside from their research projects. Sponsors: This Core is supported by the University of Brititsh Columbia.

Proper citation: UBC National Core for Neuroethics (RRID:SCR_008063) Copy   

•   Source: SciCrunch Registry

http://www.nmr.mgh.harvard.edu/DOT/resources/homer2/home.htm

Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data.

Proper citation: Homer2 (RRID:SCR_009586) Copy   

•   Source: SciCrunch Registry

http://hermes.ctb.upm.es/

A toolbox for the Matlab environment designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. This toolbox may be very helpful to all the researchers working in the emerging field of brain connectivity analysis.

Proper citation: HERMES (RRID:SCR_009584) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula

Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons.

Proper citation: TRACULA (RRID:SCR_013152) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/atag_mri_scans/

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.

Proper citation: 7T Structural MRI scans ATAG (RRID:SCR_014084) Copy   

•   Source: SciCrunch Registry

http://rfmri.org/dpabi

Software toolbox for data processing and analysis of brain imaging, evolved from DPARSF (Data Processing Assistant for Resting-State fMRI).

Proper citation: DPABI (RRID:SCR_010501) Copy   

•   Source: SciCrunch Registry

https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405

Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas.

Proper citation: Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/#!Synapse:syn4921369/wiki/235539

Portal of PsychENCODE Consortium to study role of rare genetic variants involved in several psychiatric disorders. Database of regulatory elements, epigenetic modifications, RNA and protein in brain.

Proper citation: PsychENCODE Knowledge Portal (RRID:SCR_017500) Copy   

•   Source: SciCrunch Registry

https://github.com/mitragithub/Registration

Software package to align brain slice images in atlas free manner.

Proper citation: Registration Software Mitra Lab (RRID:SCR_018353) Copy   

•   Source: SciCrunch Registry