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http://pepr.cnmcresearch.org/

An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ).

Proper citation: Public Expression Profiling Resource (RRID:SCR_007274) Copy   

•   Source: SciCrunch Registry

http://www.geneatlas.org/gene/main.jsp

This website allows visitors to search for genes of interest based on their spatial expression patterns in the Postnatal Day 7 mouse brain. Geneatlas provides two searching tools: A graphical interface for customized spatial queries; A textual interface for querying annotated structures. Geneatlas is the product of a collaboration between researchers at Baylor College of Medicine, Rice University, and University of Houston.

Proper citation: Gene Atlas (RRID:SCR_008089) 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.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://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.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://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.nitrc.org/projects/broccoli/

A software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. If BROCCOLI is running on a GPU, it can perform non-linear spatial normalization to a 1 mm brain template in 4-6 s and run a second level permutation test with 10,000 permutations.

Proper citation: BROCCOLI (RRID:SCR_014093) Copy   

•   Source: SciCrunch Registry

http://brain.io/

A startup research, development and innovation company based in The Grand Duchy of Luxembourg working on four major areas: Open Research, as Information Hub; Information Technology, as The Common Brain; Collective Awareness, as Manifesto; and Biophysics, as Human Extensibility. The Information Hub researches a methodology to conduct open research using a collaborative approach designed for multi-disciplinary interventions, multi-scope goal alignment, advanced analytics and a unified research experience for international cooperation. The Common Brain researches an open source intelligent architecture for future internet, one that is deeply sustainable over a highly distributed hybrid network, self-governed, heterogenous, and logical. Manifesto researches a methodology for a collaborative approach for policy making, open standardization, accreditation, verification and compliance. Human Extensibility researches the establishment of the scientific ground for a field of science concerned with the study of the physics and physiology of the human being, to provide techniques and genetic algorithms for human extensibility.

Proper citation: Brain.io (RRID:SCR_014527) Copy   

•   Source: SciCrunch Registry

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

Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain.

Proper citation: brainlife.io (RRID:SCR_016513) Copy   

•   Source: SciCrunch Registry

https://www.med.upenn.edu/sbia/brats2017.html

Organization that provides a conference about the methods for the segmentation of brain tumors in magnetic resonance imaging (MRI) scans. Its conferences utilize multi-institutional pre-operative MRI scans and focus on the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas.

Proper citation: BraTS (RRID:SCR_016214) Copy   

•   Source: SciCrunch Registry

https://www.drugabuse.gov

Portal provides list of genetic resources such as Brain Atlases and genomes for various species provided by National Institute of Drug Abuse.

Proper citation: Compilation of Genetics Resource Databases (RRID:SCR_017501) Copy   

•   Source: SciCrunch Registry

https://cic.ini.usc.edu/

Project to create complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks.

Proper citation: Mouse Connectome Project (RRID:SCR_017313) Copy   

•   Source: SciCrunch Registry

http://www.morf-brain.com/

Portal devoted to suite of MORF reporter mice labels of Cre positive neurons and glia distributed stochastically throughout brain and can be imaged with endogenous fluorescence (mNeonGreen in MORF1 and EGFP in TIGRE-MORF) or stained for multivalent immunoreporter (Spaghetti Monster fluorescent protein V5, or smFP-V5, in MORF3). MORF technology used to label and reconstruct thousands genetically defined cells per brain for large scale, unbiased classification and quantitative analyses of CNS cell types brainwide.

Proper citation: Mononucleotide Repeat Frameshift Portal (RRID:SCR_021125) Copy   

•   Source: SciCrunch Registry

http://www.madsci.org/cgi-bin/cgiwrap/~lynn/image?return=http://www.google.com/custom?domains&name=a_vm1110&show_all=1&search

Portal for learning resources about the brain. It includes information and interactive images of transverse brain sections.

Proper citation: Visible Human Transverse Section Through the Head (RRID:SCR_001966) Copy   

•   Source: SciCrunch Registry

http://connectir.projects.nitrc.org

An R-based package to conduct brain connectivity analyses with a focus on a novel approach to conducting Connectome-Wide Association Studies (CWAS) using functional connectivity.

Proper citation: Connectir (RRID:SCR_000863) Copy   

•   Source: SciCrunch Registry