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http://transgenicmouse.alleninstitute.org/

A comprehensive characterization of expression patterns of genetically-controlled markers or tool genes in the brains of transgenic mice generated by the Allen Institute as well as the broad scientific community. Providing standardized, detailed, anatomical profiling of transgene expression throughout the brain, this dataset is intended to reveal the potential of each transgenic mouse line and help researchers choose the appropriate tools for their studies. Transgenic mice are valuable tools to label selective neuronal or non-neuronal populations, modulate gene expression in these cells or manipulate activity of these cells for the study of neural circuits and brain function. The Allen Institute has launched a project to generate a variety of transgenic mouse lines, mainly using the Cre/lox system, to express fluorescent probes or neuronal activity manipulating tools in a variety of cell types in the brain. At the same time, utilizing Allen Institute's unique high-throughput capability, a pipeline is set up to characterize the ability in directing cell type specific expression in the brains of various transgenic mice generated by the Allen Institute as well as the broad scientific community. Through standardized, detailed, anatomical profiling of the transgene expression in the entire mouse brain, this dataset is intended to provide a comprehensive evaluation of the potential of each transgenic mouse line and help researchers choose the appropriate transgenic tools to study the function of different regions and/or cell types of the brain. This data release adds additional data to the existing set of new Cre-reporter lines generated at the Allen Institute that have stronger expression than other commonly used reporter lines are used to characterize approximately a dozen Cre-driver lines. The types of characterization data include digitized images (of sections sampling the entire brain) of colorimetric in situ hybridization (CISH), double fluorescent in situ hybridization (DFISH), native fluorescence of XFP (generic term for fluorescent proteins of different colors), and immunohistochemical (IHC) labeling of marker genes.

Proper citation: Allen Institute for Brain Science Transgenic Mouse Study (RRID:SCR_002999) Copy   

•   Source: SciCrunch Registry

http://www.callisto-science.org/NSI/Neuroscience_Image_Database/Rat_Brain_Atlas.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 27,2025. Compact 3rd edition of The Rat Brain Atlas of Paxinos & Watson published in 1997, it is the most widely used stereotaxic reference system for rat brain. The illustrations and nomenclature of the atlas have become standard tools used by almost all research neuroscientists who deal with anatomy, physiology, or function. It has been subsequently updated, with the 6th edition being the most recent. The 3rd edition is the most recent one available online for free. The program runs in Adobe Acrobat Reader.

Proper citation: Rat Brain Atlas of Paxinos and Watson (RRID:SCR_006369) Copy   

•   Source: SciCrunch Registry

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

A reference atlas of standard macaque monkey magnetic resonance images. The template brain volume that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual macaque monkeys and studies. We have used MRI volumes from a group of 25 normal adult macaque monkeys (18 Macaca fascicularis, 7 Macaca mulatta) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous macaque brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the MNI macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format.

Proper citation: McConnell Brain Imaging Center MNI Macaque Atlas (RRID:SCR_005265) Copy   

•   Source: SciCrunch Registry

http://neurosynth.org

Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image.

Proper citation: NeuroSynth (RRID:SCR_006798) Copy   

•   Source: SciCrunch Registry

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

Center dedicated to understanding and treatment of neurological diseases by creating and using imaging methods to study human nervous system. Dedicated to research imaging of human brain. Brain structure is imaged using anatomical Magnetic Resonance Imaging (aMRI) while brain physiology is imaged using Positron Emission Tomography (PET), Magnetic Resonance Spectroscopy (MRS), functional MRI (fMRI) and magnetoencephalography (MEG). BIC maintains linkages with clinical, clinical research and basic research communities within Montreal Neurological Institute (MNI), McGill University and has collaborations across Quebec, Canada, USA and internationally.

Proper citation: McConnell Brain Imaging Center (RRID:SCR_008364) Copy   

•   Source: SciCrunch Registry

http://www.uab.edu/cnc

The overall mission of the Comprehensive Neuroscience Center (CNC) is to promote and support interdisciplinary neuroscience research, clinical care and education at UAB. Despite significant advances over the last 15 years in understanding many basic neurological processes, development of more effective treatments for neurological and psychiatric diseases have been identified as the largest and fastest growing unmet medical need in this country. The institutions that can most rapidly and creatively establish the necessary neuroscience initiatives to facilitate the translation of basic research discoveries into effective therapies will be positioned to lead neurological and psychiatric disease research into the future. The Center integrates a variety of disciplines, including neurology, psychiatry, neurobiology, neurosurgery, psychology, vision science, and biomedical engineering. Faculty from the Schools of Medicine, Optometry, Social and Behavioral Sciences, Dentistry, Engineering, Health Professions, and Public Health are affiliated with the Center. The need to address neuroscience research is great: one in three Americans are affected by nervous system diseases including brain and spinal cord injury, dementing illnesses, schizophrenia, depression, movement disorders, multiple sclerosis, and autism. The burden of these diseases has an estimated economic cost of 500 billion per year in the United States. Center Research: The CNC serves as a vital center for neuroscience research at UAB and oversees six thematic programs of investigation: neurodevelopment and neurogenetics, neurodegeneration and experimental therapeutics, neuroregeneration and plasticity, behavioral and cognitive health, glial biology in medicine, and neuroimaging. The CNC helps coordinate the efforts of multiple neuroscience related centers at UAB, such as the Center for Glial Biology in Medicine, the Evelyn F. McKnight Brain Institute, the Civitan International Research Center, and the Alzheimers Disease Research Center. By interacting directly with these centers and establishing coalitions of centers and neuroscience subdisciplines, the CNC aids the UAB neuroscience community in meeting the challenges of modern neuroscience investigation. The CNC builds on other recent advances in neuroscience at UAB, including an 8.6 million grant from the National Institutes of Health to establish the Alabama Neuroscience Blueprint Core Center Facility awarded in September 2006. The Neuroscience Blueprint establishes research infrastructure on campus that is shared by investigators from institutions across Alabama and the Southeast. UAB has also added dynamic new leadership in the neuroscience fields including the following new chairs: Ray L. Watts, MD, Neurology (from Emory University); David Sweatt, PhD, Neurobiology (from Baylor College of Medicine); and James Meador-Woodruff, MD, Psychiatry (from the University of Michigan).

Proper citation: UAB Comprehensive Neuroscience Center (RRID:SCR_007195) Copy   

•   Source: SciCrunch Registry

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

A reference atlas of cynomolgus macaque monkey magnetic resonance images. The template brain volume that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual cynomolgus monkeys and studies. We have used MRI volumes from a group of 18 normal adult cynomulgus monkeys (Macaca fascicularis) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous cynomolgus monkey brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the cynomolgus macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format.

Proper citation: McConnell Brain Imaging Center MNI Cynomolgus Macaque Atlas (RRID:SCR_008793) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj2

An unbiased magnetic resonance imaging template brain volume for pediatric data from birth to 4.5y age range. These volumes were created using 317 scans from 108 children enrolled in the NIH-funded MRI study of normal brain development (Almli et al., 2007, Evans and Group 2006). Templates are constructed for different age ranges. Each age range includes an average T1w, T2w, PDw maps normalized between 0 and 100. Also each age range includes a binary brain mask. Tools for using these atlases can be found in the Software section.

Proper citation: NIHPD Objective 2 atlases (birth - 4.5 years) (RRID:SCR_008795) Copy   

•   Source: SciCrunch Registry

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

A reference atlas of rhesus macaque monkey magnetic resonance images that offers a common stereotaxic reference frame. The atlas can be used to localize anatomical and functional information in an organized and reliable way for comparison across individual rhesus monkeys and studies. We have used MRI volumes from a group of 7 normal adult rhesus monkeys (Macaca mulatta) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous rhesus monkey brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the rhesus macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format.

Proper citation: McConnell Brain Imaging Center MNI Rhesus Macaque Atlas (RRID:SCR_008790) Copy   

•   Source: SciCrunch Registry

http://www.neurobiologie.fu-berlin.de/beebrain

Standard brain atlas of the honeybee presented as an interactive three-dimensional surface model with integrated neuron and neuronal tracts. The standard atlas was created as an average-shape atlas of 22 neuropils, calculated from 20 individual immunostained whole-mount bee brains. After correction for global size and positioning differences by repeatedly applying an intensity-based nonrigid registration algorithm, a sequence of average label images was created. The Honeybee, Apis mellifera has been studied extensively with respect to its sensory and neural capacities in navigation, communication, visual and olfactory learning and memory processing. The goal is to integrate the entirety of information into a Virtual Atlas of the Honeybee Brain. This common spatial reference map will potentiate the representation of structural and functional data obtained in different experiments and from different individuals.

Proper citation: Virtual Atlas of the Honeybee Brain (RRID:SCR_007133) Copy   

•   Source: SciCrunch Registry

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

An interactive 3D rendering and neuroanatomical analysis package developed for analyzing focal brain lesions and functional brain imaging data (Damasio and Frank, 1991; Frank, Damasio and Grabowski, 1997).

Proper citation: Brainvox (RRID:SCR_009448) Copy   

•   Source: SciCrunch Registry

http://brancusi.usc.edu/bkms/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7th, 2019. BAMS is an online resource for information about neural circuitry. The BAMS Nested Regions view focuses on the major brain regions and their relationships.

Proper citation: BAMS Nested Regions (RRID:SCR_000238) Copy   

•   Source: SciCrunch Registry

http://gbrowse.csbio.unc.edu/cgi-bin/gb2/gbrowse/slep/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of genetic and gene expression data from the published literature on psychiatric disorders. Users can search the accumulated data to find the evidence in support of the involvement of a particular genomic region with a set of important psychiatric disorders, ADHD, autism, bipolar disorder, eating disorder, major depressive disorder, schizophrenia, and smoking behavior. It contains findings from manual reviews of 144 papers in psychiatric genetics, 136 primary reports and 8 meta-analyses. Disorders covered include schizophrenia (44 papers), autism (24 papers), bipolar disorder (24 papers), smoking behavior (24 papers), major depressive disorder and neuroticism (14 papers), ADHD (8 papers), eating disorders (3 papers), and a combined schizophrenia-bipolar phenotype (3 papers). The unbiased searches integrated into SLEP include genomewide linkage (117 papers), genomewide association (15 papers), copy number variation (9 papers), and gene expression studies of post-mortem brain tissue (3 meta-analyses courtesy of the Stanley Foundation). In total, SLEP captures 3,741 findings from these 144 papers. SLEP also contains over 70,000 SignPosts. These annotations derive from many different sources and are designed to try to capture current state of knowledge about disease associations in the human genome. SignPosts can be searched simultaneously with the psychiatric genetics literature in order to integrate these two bodies of knowledge. The SignPosts include: accumulated GWAS findings from the human genetics literature, the OMIM database, candidate gene association study literature, CNV location and frequency data, SNPs that influence gene expression in brain, genes expressed in brain, genes with evidence of imprinting and random monoalleleic expression, genes mutated in breast or colorectal cancer, and pathway data from BioCyc.

Proper citation: Sullivan Lab Evidence Project (RRID:SCR_000753) Copy   

•   Source: SciCrunch Registry

http://brainevolutionnews.blogspot.com/

Brain Evolution in the News pulls in blogs from a variety of resources on topic.

Proper citation: Brain Evolution in the News (RRID:SCR_000592) Copy   

•   Source: SciCrunch Registry

http://www.eideneurolearningblog.blogspot.com/

Weekly articles related to brain-based learning and learning styles, problem-solving and creativity, kids, families, and parenting, gifted and visual learners, dyslexia, attention deficit disorders, autism, and more.

Proper citation: Eide Neurolearning Blog (RRID:SCR_000680) Copy   

•   Source: SciCrunch Registry

http://kymata-atlas.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An online atlas of neural function, maintained by Cambridge University and the MRC Cognition and Brain Sciences Unit (CBSU).

Proper citation: Kymata Atlas (RRID:SCR_000269) Copy   

•   Source: SciCrunch Registry

http://gemma-doc.chibi.ubc.ca/neurocarta/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Neurocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. The system enables automatic and manual curation of evidence supporting each association, as well as user-enabled entry of their own annotations. Phenotypes are recorded using controlled vocabularies such as the Disease Ontology to facilitate computational inference and linking to external data sources. The gene-to-phenotype associations are filtered by stringent criteria to focus on the annotations most likely to be relevant. Neurocarta is constantly growing and currently holds more than 30,000 lines of evidence linking over 6,800 genes to 1,800 different phenotypes. Neurocarta is a one-stop shop for researchers looking for candidate genes for any disorder of interest. In Neurocarta, they can review the evidence linking genes to phenotypes and filter out the evidence they're not interested in. In addition, researchers can enter their own annotations from their experiments and analyze them in the context of existing public annotations. Neurocarta's in-depth annotation of neurodevelopmental disorders makes it a unique resource for neuroscientists working on brain development.

Proper citation: Neurocarta (RRID:SCR_000617) Copy   

•   Source: SciCrunch Registry

http://bodymap.genes.nig.ac.jp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008

Proper citation: BodyMap-Xs (RRID:SCR_001147) Copy   

•   Source: SciCrunch Registry

http://netbio.bgu.ac.il/tissuenet/

Database of human tissue protein-protein interactions (PPIs) that associates each interaction with human tissues that express both pair mates. This was achieved by integrating current data of experimentally detected PPIs with extensive data of gene and protein expression across 16 main human tissues. Users can query TissueNet using a protein and retrieve its PPI partners per tissue, or using a PPI and retrieve the tissues expressing both pair mates. The graphical representation of the output highlights tissue-specific and tissue-wide PPIs. Thus, TissueNet provides a unique platform for assessing the roles of human proteins and their interactions across tissues.

Proper citation: TissueNet - The Database of Human Tissue Protein-Protein Interactions (RRID:SCR_002052) Copy   

•   Source: SciCrunch Registry

http://www.braindonors.org

An Australian brain bank which aims to collect, store, characterize and provide tissue to national and international researchers studying disorders of the brain such as alcohol-related brain damage and mental illness, like schizophrenia. The program encourages those who are medically healthy to donate.

Proper citation: Using our Brains Tissue Donor Program (RRID:SCR_000705) Copy   

•   Source: SciCrunch Registry