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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   

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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://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   

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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   

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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   

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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://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   

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http://www.medschool.lsuhsc.edu/epilepsy_center/

The LSU Epilepsy Center of Excellence is dedicated to providing state-of-the-art, comprehensive epilepsy treatment, enhancing access to epilepsy education for patients and physicians, and promoting multidisciplinary epilepsy research in pharmacology, neuroelectrophysiology, neuroimaging, neurosurgery, neuropsychology, biomedical engineering and public health. The center''s team of professionals offers diagnostic and presurgical monitoring, the strategic use of antiepileptic medications, specialized epilepsy neuroimaging, vagus nerve stimulator implantation, ketogenic diet management, neuropsychological testing, psychiatric support and epilepsy surgery for adults and children. The Center also hosts several clinical research trials each year for investigational medications and devices. The following are the treatment methods currently available at this center: - Epilepsy Brain Implants - Responsive Neurostimulator (RNS) - Medications - Medication blood level monitoring - Vagus Nerve Stimulators (VNS) - Epilepsy Surgery - Ketogenic Diet - Psychiatric Services - Radiosurgery Epilepsy Center Sections: *Electrophysiology *Neuroimaging *Neuropsychology *Neuroscience *Neurosurgery *Pharmacology *Psychiatry *Research

Proper citation: Louisiana State University School of Medicine, Health Sciences Center: Epilepsy Center (RRID:SCR_006519) Copy   

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http://www.mitre.org/news/digest/archives/2002/neuroinformatics.html

This resource''s long-term goal is to develop informatics methodologies and tools that will increase the creativity and productivity of neuroscience investigators, as they work together to use shared human brain mapping data to generate and test ideas far beyond those pursued by the data''s originators. This resource currently has four major projects supporting this goal: * Database tools: The goal of the NeuroServ project is to provide neuroscience researchers with automated information management tools that reduce the effort required to manage, analyze, query, view, and share their imaging data. It currently manages both structural magnetic resonance image (MRI) datasets and diffusion tensor image (DTI) datasets. NeuroServ is fully web-enabled: data entry, query, processing, reporting, and administrative functions are performed by qualified users through a web browser. It can be used as a local laboratory repository, to share data on the web, or to support a large distributed consortium. NeuroServ is based on an industrial-quality query middleware engine MRALD. NeuroServ includes a specialized neuroimaging schema and over 40 custom Java Server Pages supporting data entry, query, and reporting to help manage and explore stored images. NeuroServ is written in Java for platform independence; it also utilizes several open source components * Data sharing: DataQuest is a collaborative forum to facilitate the sharing of neuroimaging data within the neuroscience community. By publishing summaries of existing datasets, DataQuest enables researchers to: # Discover what data is available for collaborative research # Advertise your data to other researchers for potential collaborations # Discover which researchers may have the data you need # Discover which researchers are interested in your data. * Image quality: The approach to assessing the inherent quality of an image is to measure how distorted the image is. Using what are referred to as no-reference or blind metrics, one can measure the degree to which an image is distorted. * Content-based image retrieval: NIRV (NeuroImagery Retrieval & Visualization) is a work environment for advanced querying over imagery. NIRV will have a Java-based front-end for users to issue queries, run processing algorithms, review results, visualize imagery and assess image quality. NIRV interacts with an image repository such as NeuroServ. Users can also register images and will soon be able to filter searches based on image quality.

Proper citation: MITRE Neuroinformatics (RRID:SCR_006508) Copy   

•   Source: SciCrunch Registry

http://brainatlas.mbi.ufl.edu/ImageGallery.php

Image Gallery of a 3D MRI Atlas of an Adult C57BL/6J Mouse Brain showing Slice Animation and 3D Animation including Axial, Coronal, Sagittal views. RealPlayer or Windows Media Player needs to be installed for viewing these animations.

Proper citation: MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery (RRID:SCR_007032) Copy   

•   Source: SciCrunch Registry

http://www.nybb.hs.columbia.edu/

A brain bank which collects postmortem human brains to meet the needs of neuroscientists investigating specific psychiatric and neurological disorders. NYBB disburses tissue samples to investigating clinicians or scientists whose research has been approved by their Institutional Review Board. The tasks of the NYBB include: collection and processing of human postmortem brain samples for research; neuropathological evaluation and diagnosis; storage and computerized inventory of brain samples; and distribution of brain samples to investigating clinicians and scientists. Brains from individuals without neurological or psychiatric disorders are used as normal controls.

Proper citation: New York Brain Bank at Columbia University (RRID:SCR_007142) Copy   

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http://brainatlas.mbi.ufl.edu/Database/

Comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. This database consists of: Individual MRI images of mouse brains; three types of atlases: individual atlases, minimum deformation atlases and probabilistic atlases; the associated quantitative structural information, such as structural volumes and surface areas. Quantitative group information, such as variations in structural volume, surface area, magnetic resonance microscopy image intensity and local geometry, have been computed and stored as an integral part of the database. The database augments ongoing efforts with other high priority strains as defined by the Mouse Phenome Database focused on providing a quantitative framework for accurate mapping of functional, genetic and protein expression patterns acquired by a myriad of technologies and imaging modalities. You must register First (Mandatory) and then you may Download Images and Data.

Proper citation: MRM NeAt (Neurological Atlas) Mouse Brain Database (RRID:SCR_007053) Copy   

•   Source: SciCrunch Registry

http://www.stanleyresearch.org/dnn/BrainResearchLaboratory/tabid/195/Default.aspx

It is a widely used resource for researchers trying to find the causes of, and better treatments for, schizophrenia, bipolar disorder and major depression. Brains were collected 1994 to 2005 with the permission of the families in a standardized manner, with half of each specimen being frozen and half fixed in formalin. Currently four cohorts are available for study; the Neuropathology Consortium consisting of 60 cases (15 each schizophrenia, bipolar disorder, depression, and controls), the Array Collection consisting of 105 cases (35 each schizophrenia, bipolar disorder, and controls), the Depression Collection consisting of 36 cases (12 each depression with psychosis, depression without psychosis, and controls), and the Parietal Collection of 48 cases (fixed inferior parietal sections from 24 each schizophrenia and controls). Since 1996, the Stanley Brain Collection has sent over 200,000 sections and 10,000 blocks of brain tissue to 240 research laboratories in 23 states and 20 foreign countries. All tissue has been provided to the researchers without charge. All costs for collecting, processing, and storing the brain tissue have been borne by The Stanley Medical Research Institute as a public service. All reasonable requests for brain tissue (over 90 percent of applications) have been honored. Researchers selected to receive tissue must sign an agreement that sets forth conditions for its use. Results received from researchers become part of the Stanley brain collection data set and will be used for integrative, multivariate analyses. In addition to overseeing the brain collection, the laboratory conducts research on the neuropathology of schizophrenia and bipolar disorder and on brain development. Many studies carried out at the Stanley Brain Research Laboratory are done in cooperation with studies at the Stanley Laboratory of Developmental Neurovirology.

Proper citation: Stanley Brain Collection (RRID:SCR_007062) Copy   

•   Source: SciCrunch Registry

http://www9.biostr.washington.edu/da.html

Atlases of human brain, thoracic viscera and knee designed for teaching gross anatomy. Also provides a neuroanatomy Interactive syllabus, suitable as a laboratory guide, with an instructive caption accompanying each image and interactive quizzes. The Digital Anatomist Project is motivated by the belief that anatomy is the basis of all the biomedical sciences (including clinical medicine). Manifestations of health and disease can be regarded as attributes of anatomical structures ranging in size from molecules to body parts. Therefore DAP''s goal is to represent anatomy in a comprehensive and consistent way, which should meet the needs of all biomedical applications that require anatomical knowledge. DAP has pursued two parallel tracks for representing anatomical information: 1. The generation of graphical models derived from cadaver and clinical imaging data; and 2. Symbolic modeling of the structures and relationships that constitute the human body. It''s initial work with graphical representations of anatomy provided the impetus and motivation for the National Library of Medicine to establish the Visible Human Project, and it''s symbolic modeling has enhanced NLM''s Unified Medical Language System in order to represent deep anatomical knowledge. In collaboration with the knowledge systems group at Stanford, it has now created a very large knowledge base which provides the foundation for the machine-based intelligence needed to remotely interact with biomedical image data.

Proper citation: Digital Anatomist Interactive Atlases Project (RRID:SCR_007060) Copy   

•   Source: SciCrunch Registry

http://www.wholebraincatalog.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. An open source, downloadable, 3d atlas of the mouse brain and its cellular constituents that allows multi-scale data to be visualized in a seamless way, similar to Google earth. Data within the Catalog is marked up with annotations and can link out to additional data sources via a semantic framework. This next generation open environment has been developed to connect members of the neuroscience community to facilitate solutions for today's intractable challenges in brain research through cooperation and crowd sourcing. The client-server platform provides rich 3-D views for researchers to zoom in, out, and around structures deep in a multi-scale spatial framework of the mouse brain. An open-source, 3-D graphics engine used in graphics-intensive computer gaming generates high-resolution visualizations that bring data to life through biological simulations and animations. Within the Catalog, researchers can view and contribute a wide range of data including: * 3D meshes of subcellular scenes or brain region territories * Large 2D image datasets from both electron and light level microscopy * NeuroML and Neurolucida neuronal reconstructions * Protein Database molecular structures Users of the Whole Brain Catalog can: * Fit data of any scale into the international standard atlas coordinate system for spatial brain mapping, the Waxholm Space. * View brain slices, neurons and their animation, neuropil reconstructions, and molecules in appropriate locations * View data up close and at a high resolution * View their own data in the Whole Brain Catalog environment * View data within a semantic environment supported by vocabularies from the Neuroscience Information Framework (NIF) at http://www.neuinfo.org. * Contribute code and connect personal tools to the environment * Make new connections with related research and researchers 5 Easy Ways to Explore: * Explore the datasets across multiple scales. * View data closely at high resolution. * Observe accurately simulated neurons. * Readily search for content. * Contribute your own research.

Proper citation: Whole Brain Catalog (RRID:SCR_007011) Copy   

•   Source: SciCrunch Registry

http://www.neuropat.dote.hu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. A set of human neuroanatomical resources developed at the University of Hungary. Resources include an on-line brain atlas, a neuropathology atlas, functional neuroanatomy for neurologists and an extensive series of links to other neuroanatomy and neurological resources on the web. The original resources developed by this site include a set of neuropathological slides covering many neurological conditions, e.g., Alzheimer's disease, an atlas of normal human neuroanatomy based on unstained brain slices, along with histological images of brainstem and spinal cord. On-line quizzes are also provided. This is an excellent educational site and gateway to neurological resources on the web.

Proper citation: Neuroanatomy and Neuropathology on the Internet (RRID:SCR_007272) Copy   

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http://www.hbpp.org/

An open international project under the patronage of the Human Proteome Organisation (HUPO) that aims: To analyze the brain proteome of human as well as mouse models in healthy, neurodiseased and aged status with focus on Alzheimer's and Parkinson's Disease; To perform quantitative proteomics as well as complementary gene expression profiling on disease-related brain areas and bodily fluids; To advance knowledge of neurodiseases and aging in order to push new diagnostic approaches and medications; To exchange knowledge and data with other HUPO projects and national / international initiatives in the neuroproteomic field; To make neuroproteomic research and its results available in the scientific community and society. Recent work has shown that standards in proteomics and especially in bioinformatics are mandatory to allow comparable analyses, but still missing. To address this challenge, the HUPO BPP is closely working together with the HUPO Proteome Standards Initiative (HUPO PSI).

Proper citation: HUPO Brain Proteome Project (RRID:SCR_007302) Copy   

•   Source: SciCrunch Registry

http://www.nntc.org/

Collects, stores, and distributes samples of nervous tissue, cerebrospinal fluid, blood, and other tissue from HIV-infected individuals. The NNTC mission is to bolster research on the effects of HIV infection on human brain by providing high-quality, well-characterized tissue samples from patients who died with HIV, and for whom comprehensive neuromedical and neuropsychiatric data were gathered antemortem. Researchers can request tissues from patients who have been characterized by: * degree of neurobehavioral impairment * neurological and other clinical diagnoses * history of drug use * antiretroviral treatments * blood and CSF viral load * neuropathological diagnosis The NNTC encourages external researchers to submit tissue requests for ancillary studies. The Specimen Query Tool is a web-based utility that allows researchers to quickly sort and identify appropriate NNTC specimens to support their research projects. The results generated by the tool reflect the inventory at a previous time. Actual availability at the local repositories may vary as specimens are added or distributed to other investigators.

Proper citation: National NeuroAIDS Tissue Consortium (RRID:SCR_007323) Copy   

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http://fmri.wfubmc.edu/software/PickAtlas

A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: WFU PickAtlas (RRID:SCR_007378) Copy   

•   Source: SciCrunch Registry