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http://brain-development.org/

brain-development.org hosts data and resources used in computational analysis of brain development, including MRI data sets of developing human, software tools, atlases, protocols and software. Several different atlas datasets are available including: * Adult * Pediatric * Neonatal (T2 Templates, Probability Maps) * Neonatal (High-definition, T1 and T2 Templates, Probability Maps) * Fetal (High-definition, T2 Templates, Probability Maps) * Atlas software Anatomical segmentation protocols are available, as well as an Image Registration Toolkit.

Proper citation: brain-development.org (RRID:SCR_005838) Copy   

•   Source: SciCrunch Registry

http://brain-development.org/ixi-dataset/

Data set of nearly 600 MR images from normal, healthy subjects, along with demographic characteristics, collected as part of the Information eXtraction from Images (IXI) project available for download. Tar files containing T1, T2, PD, MRA and DTI (15 directions) scans from these subjects are available. The data has been collected at three different hospitals in London: * Hammersmith Hospital using a Philips 3T system * Guy''s Hospital using a Philips 1.5T system * Institute of Psychiatry using a GE 1.5T system

Proper citation: IXI dataset (RRID:SCR_005839) Copy   

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http://riodb.ibase.aist.go.jp/brain/index.php?LANG=ENG

Atlas of magnetic resonance images and histological sections of a Japanese monkey brain, Rhesus monkey and human. The Brain Explorer allows for display, magnification, and comparison these images. Other formats include a collection of .jpg images, Quicktime VR (allow user to zoom in), and EmonV, a voxel viewer for MacOS X.

Proper citation: Brain Atlas Database of Japanese Monkey for WWW (RRID:SCR_006104) Copy   

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http://songbirdtranscriptome.net/

Database containing cDNA clone information of the brains of songbirds. These clones are annotated with behavioral information, as well as links to information of homologous genes of other species. The database includes over 91,000 zebra finch brain cDNAs (2009) sequenced by Duke, ESTIMA, and Rockefeller research groups. The project is a collaborative effort of the Jarvis Laboratory of Duke University, Duke Bioinformatics, and The Genomics group of RIKEN, with Erich D. Jarvis as P.I. and Kazuhiro Wada as Co-P.I. Microarrays with the cDNAs in this database are available at Duke http://mgm.duke.edu/genome/dna_micro/core/spotted.htm and through the NIH Neurosciences Microarray Consortium http://arrayconsortium.tgen.org/np2/public/overview.jsp

Proper citation: Songbird Brain Transcriptome Database (RRID:SCR_006182) Copy   

•   Source: SciCrunch Registry

http://www.mouseimaging.ca/

A unique resource and comprehensive imaging facility combining the latest state-of-the-art digital medical imaging technologies for the characterization of mouse functional genomics. The goals of the Mouse Imaging Centre are: * To provide a variety of medical imaging technologies adapted to studying genetically modified mice. These technologies include magnetic resonance (MR) imaging, micro computed tomography (micro-CT), ultrasound biomicroscopy (UBM), and optical projection tomography (OPT). * To screen large numbers of mice for models of human diseases. * To image an individual mouse over time to observe development, disease progression and responses to experimental treatment. * To develop an exciting team of investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. * To work by collaboration with researchers throughout the world. When we look for human diseases in the human population, we make extensive use of medical imaging. Therefore, it makes sense to have available the same imaging capabilities as we investigate mice for models of human disease. The Mouse Imaging Centre (MICe) has developed high field magnetic resonance imaging microscopy, ultrasound biomicroscopy, micro computed tomography, and optical techniques. With these imaging tools, MICe is screening randomly mutagenized mice to look for phenotypes that represent human diseases and is taking established human disease models in mice and using imaging to follow the progression of disease and response to treatment over time. It is clear that imaging has a major contribution to make to phenotyping genetic variants and to characterizing mouse models. MICe is staffed by an exciting new team of about 30 investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. The Mouse Imaging Centre (MICe) is not a fee-for-service facility but works through collaborations. Services include: * Projects involving MicroCT are available as a fee for service. * We will eventually move to the same model above with MRI. * Ultrasound Biomicroscopy is used for cardiac, embryo and cancer studies and is available as fee for service at $100 per study or in some cases on a collaborative basis. * Optical Projection Tomography has only limited availability on a collaborative basis. Mouse Atlas As our images are inherently three-dimensional, we will be able to make quantitative measures of size and volume. With this in mind, we are developing a mouse atlas showing the normal deviation of organ sizes. This atlas is an important resource for biologists as it has the potential to eliminate the need to sacrifice as many controls when making comparisons with mutants. Mouse Atlas Examples: * Variational Mouse Brain Atlas * Cerebral Vascular Atlas of the CBA Mouse * Neuroanatomy Atlas of the C57Bl/6j Mouse * Vascular Atlas of the Developing Mouse Embryo * Micro-CT E15.5 Mouse Embryo Atlas

Proper citation: MICe - Mouse Imaging Centre (RRID:SCR_006145) Copy   

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http://neuroviisas.med.uni-rostock.de/neuroviisas.html

An open framework for integrative data analysis, visualization and population simulations for the exploration of network dynamics on multiple levels. This generic platform allows the integration of neuroontologies, mapping functions for brain atlas development, and connectivity data administration; all of which are required for the analysis of structurally and neurobiologically realistic simulations of networks. What makes neuroVIISAS unique is the ability to integrate neuroontologies, image stacks, mappings, visualizations, analyzes and simulations to use them for modelling and simulations. Based on the analysis of over 2020 tracing studies, atlas terminologies and registered histological stacks of images, neuroVIISAS permits the definition of neurobiologically realistic networks that are transferred to the simulation engine NEST. The analysis on a local and global level, the visualization of connectivity data and the results of simulations offer new possibilities to study structural and functional relationships of neural networks. neuroVIISAS provide answers to questions like: # How can we assemble data of tracing studies? (Metastudy) # Is it possible to integrate tracing and brainmapping data? (Data Integration) # How does the network of analyzed tracing studies looks like? (Visualization) # Which graph theoretical properties posses such a network? (Analysis) # Can we perform population simulations of a tracing study based network? (Simulation and higher level data integration) neuroVIISAS can be used to organize mapping and connectivity data of central nervous systems of any species. The rat brain project of neuroVIISAS contains 450237 ipsi- and 175654 contralateral connections. A list of evaluated tracing studies are available. PyNEST script generation does work using WINDOWS OS, however, the script must be transferred to a UNIX OS with installed NEST. The results file of the NEST simulation can be visualized and analyzed by neuroVIISAS on a WINDOWS OS.

Proper citation: neuroVIISAS (RRID:SCR_006010) Copy   

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http://www.rad.upenn.edu/sbia/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. Software package used to simulate brain images with local growth / atrophy within a prescribed spherical region. Specifically, given an input image and its segmented image, the location of the center of the spherical region, and the radius of that sphere, it simulates new images that have tissue growth or shrinkage within that pre-specified brain region according to given rates (atrophy for rates less than one and growth for rates greater than one). The algorithm uses an iterative procedure that tries to achieve the given level of volumetric change for brain tissues within the region, by seeking a smooth deformation field, whose Jacobian determinants match the prescribed volume change rate within the region. Note that in the current software, the simulation of growth or atrophy for brain tissue requires that the input spherical region has to cover some CSF or background regions.

Proper citation: Atrophy Simulation Package (RRID:SCR_006046) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/toads-cruise/

A collection of software plug-ins developed for the automatic segmentation of magnetic resonance brain images. The tools include multiple published algorithms developed at Johns Hopkins University. The SPECTRE algorithm performs brain extraction. The TOADS algorithm generates a topology-preserving tissue classification into cortical, subcortical, and cerebellar structures. The CRUISE algorithm produces inner, central, and outer cortical surfaces suitable for computing thickness and other geometric measures. Tools are also included for performing gyral labeling, lesion segmentation, thickness computation, surface visualization, and surface file conversion. All tools are released as plug-ins for the MIPAV software package and were developed using the Java Image Science Toolkit (both available at NITRC: http://nitrc.org). They are therefore cross-platform and compatible with a wide variety of file formats.

Proper citation: TOADS-CRUISE Brain Segmentation Tools (RRID:SCR_005977) Copy   

•   Source: SciCrunch Registry

https://www.braintest.org/brain_test/BrainTest

A portal of online studies that encourage community participation to tackle the most challenging problems in neuropsychiatry, including attention-deficit / hyperactivity disorder, schizophrenia, and bipolar disorder. Our approach is to engage the community and try to recruit tens of thousands of people to spend an hour of their time on our site. You folks will provide data in both brain tests and questionnaires, as well as DNA, and in return, we will provide some information about your brain and behavior. You will also be entered to win amazon.com gift cards. While large collaborative efforts were made in genetics in order to discover the secrets of the human genome, there are still many mysteries about the behaviors that are seen in complex neuropsychiatric syndromes and the underlying biology that gives rise to these behaviors. We know that it will require studying tens of thousands of people to begin to answer these questions. Having you, the public, as a research partner is the only way to achieve that kind of investment. This site will try to reach that goal, by combining high-throughput behavioral assessment using questionnaires and game-like cognitive tests. You provide the data and then we will provide information and feedback about why you should help us achieve our goals and how it benefits everyone in the world. We believe that through this online study, we can better understand memory and attention behaviors in the general population and their genetic basis, which will in turn allow us to better characterize how these behaviors go awry in people who suffer from mental illness. In the end, we hope this will provide better, more personalized treatment options, and ultimately prevention of these widespread and extremely debilitating brain diseases. We will use the data we collect to try to identify the genetic basis for memory and impulse control, for example. If we can achieve this goal, maybe we can then do more targeted research to understand how the biology goes awry in people who have problems with cognition, including memory and impulse control, like those diagnosed with ADHD, Schizophrenia, Bipolar Disorder, and Autism Spectrum Disorders. By participating in our research, you can learn about mental illness and health and help researchers tackle these complex problems. We can''t do it without your help.

Proper citation: Brain Test (RRID:SCR_006212) Copy   

•   Source: SciCrunch Registry

http://www.callisto-science.org/NSI/Neuroscience_Image_Database/Images%20of%20the%20Human%20Nervous%20System%20-%20Neuroanatomy.html

Data set of images of the human nervous system focusing on neuroanatomy.

Proper citation: Human Nervous System Neuroanatomy (RRID:SCR_006371) Copy   

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http://vinovia.ncl.ac.uk/emagewebapp/pages/eadhb_home.jsf

Database of a set of standard 3D virtual models at different stages of development from Carnegie Stages (CS) 12-23 (approximately 26-56 days post conception) in which various anatomical regions have been defined with a set of anatomical terms at various stages of development (known as an ontology). Experimental data is captured and converted to digital format and then mapped to the appropriate 3D model. The ontology is used to define sites of gene expression using a set of standard descriptions and to link the expression data to an ''''anatomical tree''''. Human data from stages CS12 to CS23 can be submitted to the HUDSEN Gene Expression Database. The anatomy ontology currently being used is based on the Edinburgh Human Developmental Anatomy Database which encompasses all developing structures from CS1 to CS20 but is not detailed for developing brain structures. The ontology is being extended and refined (by Prof Luis Puelles, University of Murcia, Spain) and will be incorporated into the HUDSEN database as it is developed. Expression data is annotated using two methods to denote sites of expression in the embryo: spatial annotation and text annotation. Additionally, many aspects of the detection reagent and specimen are also annotated during this process (assignment of IDs, nucleotide sequences for probes etc). There are currently two main ways to search HUDSEN - using a gene/protein name or a named anatomical structure as the query term. The entire contents of the database can be browsed using the data browser. Results may be saved. The data in HUDSEN is generated from both from researchers within the HUDSEN project, and from the wider scientific community. The HUDSEN human gene expression spatial database is a collaboration between the Institute of Human Genetics in Newcastle, UK, and the MRC Human Genetics Unit in Edinburgh, UK, and was developed as part of the Electronic Atlas of the Developing Human Brain (EADHB) project (funded by the NIH Human Brain Project). The database is based on the Edinburgh Mouse Atlas gene expression database (EMAGE), and is designed to be an openly available resource to the research community holding gene expression patterns during early human development.

Proper citation: HUDSEN Human Gene Expression Spatial Database (RRID:SCR_006325) Copy   

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http://learn.genetics.utah.edu/content/addiction/drugs/mouse.html

Mouse Party is an interactive website that teaches how various drugs disrupt the synapse by taking a look inside the brains of mice on drugs! Every drug of abuse has its own unique molecular mechanism. Where applicable, this presentation primarily depicts how drugs interact with dopamine neurotransmitters because this website focuses on the brain''s reward pathway. Mouse Party is designed to provide a small glimpse into the chemical interactions at the synaptic level that cause the drug user to feel ''high''. The simplified mechanisms of drug action presented here are just a small part of the story. When drugs enter the body they elicit very complex effects in many different regions of the brain. Often they interact with many different types of neurotransmitters and may bind with a variety of receptor types in a variety of different locations. For example, THC in marijuana can bind with cannabinoid receptors located on the presynaptic and/or postsynaptic cell in a synapse.

Proper citation: Mouse Party (RRID:SCR_006438) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/functionalconnectivitytoolbox/

MATLAB toolbox for performing functional connectivity analyses includes many of the most commonly-used approaches researchers have utilized to date for the identification of condition-dependent functional interactions between fMRI time-series obtained from two or more brain regions. The approaches are either bivariate or multivariate methods defined in time or frequency domains that emphasize distinct features of relationships among the time-series.

Proper citation: Functional Connectivity Toolbox (RRID:SCR_006394) Copy   

•   Source: SciCrunch Registry

http://users.loni.ucla.edu/~shattuck/brainsuite/

Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction

Proper citation: BrainSuite (RRID:SCR_006623) Copy   

•   Source: SciCrunch Registry

https://github.com/bheAI/MonkeyCBP_CLI

Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community.

Proper citation: MonkeyCBP (RRID:SCR_017640) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/brainmaker

Software tool to automatically align sections to visualize brains in 3D. Assists with cell mapping, cytoarchitectonics and other areas requiring characterization of neuronal circuitry to create comprehensive anatomical reference. Automatically creates full resolution, 3D reconstructions of entire brain or any organ from serial sections of whole slide images. Allows to view cells, structures, and lesions, locate neurons expressing particular gene or visualize axonal projections of specific neurons with full anatomical context.

Proper citation: BrainMaker (RRID:SCR_017666) Copy   

•   Source: SciCrunch Registry

http://brainu.org/

A neuroscience training program for Minnesota students and teachers. It provides teachers with three years of neuroscience training, materials, and staff support to bring brain science to their students. In these professional workshops, participants receive updates on the latest in neuroscience research -- discussion is complemented with hands-on activities and lab work. Teachers also receive curriculum materials to aid them in using neuroscience topics in support of Minnesota Intermediate and Middle Level standards. The program was expanded in 2008 to include high school teachers.

Proper citation: BrainU: The Neuroscience Teacher Institute (RRID:SCR_008677) Copy   

•   Source: SciCrunch Registry

https://www.musc.edu/website/research/brainbank/braindonor.html

A brain bank and biospecimen repository that provides research materials to clinicians, scientists and pathologists in South Carolina. The bank provides both control and diseased biospecimens and brain tissue needed for research in Alzheimer's disease, Parkinson's disease and other related neurological disorders. The Campbell Laboratory coordinates the brain tissue donation program, provides post-mortem confirmation of a patient having neurological disorders, and leads research trials. Any South Carolina resident can choose to sign up as a tissue donor and have their brain tissue donated post-mortem to be used for neurological disorder research. The tissue bank will process and analyze these tissue samples and send the results to the deceased person's family.

Proper citation: MUSC Center on Aging Campbell Neuropathology Laboratory (RRID:SCR_008826) Copy   

•   Source: SciCrunch Registry

http://www.mghmind.org

An institute whose mission is to translate laboratory discoveries into prevention, treatment and cures for Alzheimer's, ALS, Huntington's, Parkinson's and other neurodegenerative diseases. MIND seeks to accelerate therapies that lessen the toll of disease on patients and families. Researchers of the institute collaborate, strategize, and share technology to find treatment for these diseases. As promising leads are developed in one area, they are tested in the other neurodegenerative disorders.

Proper citation: MassGeneral Institute for Neurodegenerative Disease (RRID:SCR_008746) Copy   

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http://brainpeps.ugent.be/

Database of blood-brain barrier properties of peptides including structure, method, responses, physicochemical properties and related literature. The database is linked to a manuscript entitled Brainpeps: the blood-brain barrier peptide database, in which the BBB methods and responses are clarified and correlated to each other. Data may be submitted for addition to the database.

Proper citation: BrainPeps (RRID:SCR_008851) Copy   

•   Source: SciCrunch Registry