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http://www.talairach.org/

Software automated coordinate based system to retrieve brain labels from the 1988 Talairach Atlas. Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach Atlas.

Proper citation: Talairach Daemon (RRID:SCR_000448) Copy   

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http://www.yandell-lab.org/software/index.html

Sequenced genomes contain a treasure trove of information about how genes function and evolve. Getting at this information, however, is challenging and requires novel approaches that combine computer science and experimental molecular biology. My lab works at the intersection of both domains, and research in our group can be summarized as follows: generate hypotheses concerning gene function and evolution by computational means, and then test these hypotheses at the bench. This is easier said than done, as serious barriers still exist to using sequenced genomes and their annotations as starting points for experimental work. Some of these barriers lie in the computational domain, others in the experimental. Though challenging, overcoming these barriers offers exciting training opportunities in both computer science and molecular genetics, especially for those seeking a future at the intersection of both fields. Ongoing projects in the lab are centered on genome annotation and comparative genomics; exploring the relationships between sequence variation and human disease; and high-throughput biological image analysis. Current software tools available: VAAST (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds upon existing amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unified likelihood-framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-to-use fashion. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST thus has a much greater scope of use than any existing methodology. MAKER 2 (updated 01-16-2012) MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources. RepeatRunner RepeatRunner is a CGL-based program that integrates RepeatMasker with BLASTX to provide a comprehensive means of identifying repetitive elements. Because RepeatMasker identifies repeats by means of similarity to a nucleotide library of known repeats, it often fails to identify highly divergent repeats and divergent portions of repeats, especially near repeat edges. To remedy this problem, RepeatRunner uses BLASTX to search a database of repeat encoded proteins (reverse transcriptases, gag, env, etc...). Because protein homologies can be detected across larger phylogenetic distances than nucleotide similarities, this BLASTX search allows RepeatRunner to identify divergent protein coding portions of retro-elements and retro-viruses not detected by RepeatMasker. RepeatRunner merges its BLASTX and RepeatMasker results to produce a single, comprehensive XML-based output. It also masks the input sequence appropriately. In practice RepeatRunner has been shown to greatly improve the efficacy of repeat identifcation. RepeatRunner can also be used in conjunction with PILER-DF - a program designed to identify novel repeats - and RepeatMasker to produce a comprehensive system for repeat identification, characterization, and masking in the newly sequenced genomes. CGL CGL is a software library designed to facilitate the use of genome annotations as substrates for computation and experimentation; we call it CGL, an acronym for Comparitive Genomics Library, and pronounce it Seagull. The purpose of CGL is to provide an informatics infrastructure for a laboratory, department, or research institute engaged in the large-scale analysis of genomes and their annotations.

Proper citation: Yandell Lab Portal (RRID:SCR_000807) Copy   

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http://fantom.gsc.riken.jp/

International collaborative research project and database of annotated mammalian genome. Used to improve estimates of total number of genes and their alternative transcript isoforms in both human and mouse. Consortium to assign functional annotations to full length cDNAs that were collected during Mouse Encyclopedia Project at RIKEN.

Proper citation: Functional Annotation of the Mammalian Genome (RRID:SCR_000788) Copy   

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http://phm.utoronto.ca/~jeffh/neuromouse.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17, 2023.Toolbook(tm) based, interactive graphical database which provides structural, molecular, and genetic information on the adult murine nervous system; and its relevance to human neurobiology. This resource is primarily designed as a platform for users to interact, each sharing knowledge on their own area of expertise, which is compiled to a master database. This hypertext atlas presently comprises more than 1000 pages and is designed to provide a flexible integrated resource for the description and discussion of all forms mammalian neurologic data. Version 4.0 of the NeuroMouse program extends the program's basic framework to include a number of areas in modern molecular neurobiology. This system provides an integrated resource for the characterization and description of mammalian neurological data. Major divisions include: Neural Atlas, Molecular Atlas, Genetics/Surgical Lesion Atlas. Neuromouse has been integrated into our strain-specific three dimensional MRI and surgical atlases of the murine CNS. Database contents: Neural Atlas: - Rotational representation of the murine brain. - Neural structures: visual and alphabetic point and click index of neural structures, pathways and systems. - Brain atlas:photographic serial sections in the coronal, sagittal, and horizontal planes (average plate distance - 300 um). Physical brain distances are also provided as are meta-index grids to allow rapid movement between different planes and regions. # Catalog of primary and immortalized neural cells indexed to relevant neural structures. Molecular Atlas: - Index of neurotransmitters: Acetylcholine, GABA, Glutamate, Aspartate, Glycine, Dopamine, Norepinephrine, Epinephrine, Serotonin (synthesis, distribution, degradation, molecular modules, receptors, subunits, agonists, antagonists, gene structure, localization, physical properties and transgenics are indicated for each item). - Index of neurotrophins / neurokines: NGF, BDNF, NT-3, NT-4/5, CNTF, LIF, Onostain M, IL-6, GDNF, FGF's, S100b (ligand, receptors, expression pattern, physical properties, homologous factors, transgenics/knockouts, chromosomal location, effects of agent, and effects of factors on agent are indicated for each item). - Index of additional neural agents: Bcl-2, TNF/Fas, TGF-beta, P53/Rb, PDGF, EGF family (ligand, receptor, expression patterns, physical properties, homologous factors, transgenics/ knockouts, chromosomal location, effects of agent, effects of factors on agent are indicated for each item). - Molecular biology: Molecular biology of important neural genes with integrated l links, plus selected neural topics (ex. programmed cell death, inducible gene systems, protein motifs, neural gene elements, and selected signal transduction pathways). Genetics Atlas: - Lesion paradigms: Index of common neuronal structural and chemical lesion paradigms. - Selected procedures: description of common neurosurgical, cell tracing, culturing and laboratory procedures. - Neurologic syndromes: Index of important human neurologic syndromes and appropriate animals models. - Neural mutant database: Index and description of naturally occurring and genetically modified murine neurologic mutations; including pages on double knockout animals. Interactive maps of each murine chromosome and human syntenic maps.

Proper citation: NeuroMouse Database (RRID:SCR_001143) Copy   

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http://brainethics.org/

There are a lot of fine blogs out there covering the avalance of current neuroscience research. With this blog Thomas Rams��y & Martin Skov want to highlight the many consequences of this growing understanding of the human brain. We are especially interested in two types of consequences: Tinkering with the brain and What is it like to be a human being? * Tinkering with the brain: First and foremost, with an understanding of how the brain works comes the possibility of tinkering with it. We already use billions of dollars every year on psychopharmocologia trying to treat depression, schizophrenia, obsessive-compulsive disorder and other mental diseases. But should we also use our knowledge of the brain to treat undesirable mental traits such as pedophilia or sociopathy? And what about enhancing normal brains? Clearly, evolution hasn''t endowed us with the most efficient brain imaginable. Shouldn''t we do something about its many shortcomings? * What is it like to be a human being?: Secondly, our view of human behavior is sure to change with our improved understanding of the human brain. Our knowledge of core human faculties such as language, social reasoning, aesthetics, and economics is already being challenged by modern neuroscience, yielding multiple hard questions. Do we have a free will? Is the mind innate or plastic? If people are not responsible for their actions (since all actions are caused by blind molecular processes) does our legal system still make sense? In short, will modern neuroscience come to completely redefine human nature? We try to discuss contemporary research literature, not just news reports. Although we will occasionally also target popular science reports, since we believe they play an important role in dissemining lessons from the lab. And in the future we plan to also post interviews with interesting researchers, as well as link to our own publications in journals and books. Additionally, the latest and most important books in the multidisciplinary field of neuroscience, cognition, psychology, ethics and economics are presented.

Proper citation: BrainEthics (RRID:SCR_005530) Copy   

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http://hnrc.hivresearch.ucsd.edu/

The mission of the HIV Neurobehavioral Research Center (HNRC) is to increase our understanding of how HIV and other diseases affect the human nervous system. The HNRC conducts local, national, and international research devoted to advancing our knowledge of the prevention, diagnosis and treatment of HIV-related diseases as they affect the brain and nervous system, and result in impairment of everyday functioning. Research areas of the Center include: - The incidence, prevalence, and features of neurocognitive impairment caused by HIV - The attributes of the virus, host, and host-virus interactions that determine the presentation of HIV-associated neurocognitive disorders - Possible molecular and cellular mechanisms of nervous system impairment, including the mechanisms by which host-virus factors generate neural injury and neurobehavioral disorders - The cerebrospinal fluid (CSF) as a window on CNS events * The role of co-pathogens and comorbidities in neuroAIDS (e.g., hepatitis C infection, methamphetamine abuse) - Real life implications of neurocognitive impairment in terms of work, daily life, and survival - The effects of HIV disease and neurocognitive impairment on family and social adaptation - NeuroAIDS in resource limited settings - Treatments for neurocognitive impairment and behavioral interventions HNRC also has a Developmental Grants Program (DGP), the primary goal of which is the initiation of innovative studies by junior faculty and trainees at UCSD or affiliated institutions with the following objectives: 1. Recruitment to neuroAIDS research of new investigators or established investigators without prior experience in the field; 2. Generation and pilot testing of new research initiatives; 3. Fostering collaboration among investigators from throughout Southern California. The program provides to qualified investigators and trainees any appropriate combination of the following forms of support: 1. Small, 1-2 year grants to support pilot studies; 2. Access to HNRC core resources such as data, specimens, participants, equipment, administrative support, or expert consultation and technical assistance. Lastly, The the NHRC Mentored Investigator Program recruits, supports, and follows the progress of graduate students, postdoctoral (Ph.D. or M.D.) fellows, and junior faculty in disciplines relevant to HNRC research. The HNRC is committed to tailoring our training opportunities to the backgrounds and interests of candidates from a variety of disciplines who join us with various levels of training and experience in research. We have and will continue to provide training and mentoring of medical students, doctoral students in clinical psychology, and postdoctoral fellows in Medicine, Psychiatry, Neurology, and Psychology. Sponsors: The Center is supported by public funding from the National Institutes of Health, the State of California, and other sources.

Proper citation: HIV Neurobehavioral Research Center (RRID:SCR_005370) Copy   

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http://fcon_1000.projects.nitrc.org/

Collection of resting state fMRI (R-fMRI) datasets from sites around world. It demonstrates open sharing of R-fMRI data and aims to emphasize aggregation and sharing of well-phenotyped datasets.

Proper citation: 1000 Functional Connectomes Project (RRID:SCR_005361) Copy   

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http://www.med.harvard.edu/AANLIB/

An atlas of normal and abnormal brain images intended as an introduction to basic neuroanatomy, with emphasis on the pathoanatomy of several leading central nervous system diseases that integrates clinical information with magnetic resonance (MR), x-ray computed tomography (CT), and nuclear medicine images. A range of brain abnormalities are presented including examples of certain brain disease presented with various combinations of image type and imaging frequency. Submissions of concise, exemplary, clinically driven examples of neuroimaging are welcome.

Proper citation: Whole Brain Atlas (RRID:SCR_005390) Copy   

•   Source: SciCrunch Registry

http://www.bscs.org/science-mental-illness

A set of lessons for students used to gain insight into the biological basis of mental illnesses and how scientific evidence and research can help us understand its causes and lead to treatments and, ultimately, cures. Both the Web version and the free supplement are available. It is a creative, inquiry-based instruction program designed to promote active learning and stimulate student interest in medical topics. This curriculum supplement aims to help students experience the process of scientific inquiry and develop an enhanced understanding of the nature and methods of science.

Proper citation: Science of Mental Illness: Grades 6- 8 (RRID:SCR_005612) Copy   

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http://science.education.nih.gov/home2.nsf/feature/index.htm

The NIH Office of Science Education (OSE) coordinates science education activities at the NIH and develops and sponsors science education projects in house. These programs serve elementary, secondary, and college students and teachers and the public. Activities * Develop curriculum supplements and other educational materials related to medicine and research through collaborations with scientific experts at NIH * Maintain a website as a central source of information about NIH science education resources * Establish national model programs in public science education, such as the NIH Mini-Med School and Science in the Cinema * Promote science education reform as outlined in the National Science Education Standards and related guidelines The OSE was established in 1991 within the Office of Science Policy of the Office of the Director of the National Institutes of Health. The NIH is the world''s foremost biomedical research center and the U.S. federal government''s focal point for such research. It is one of the components of the Department of Health and Human Services (HHS). The Office of Science Education (OSE) plans, develops, and coordinates a comprehensive science education program to strengthen and enhance efforts of the NIH to attract young people to biomedical and behavioral science careers and to improve science literacy in both adults and children. The function of the Office is as follows: (1) develops, supports, and directs new program initiatives at all levels with special emphasis on targeting students in grades kindergarten to 16, their educators and parents, and the general public; (2) advises NIH leadership on science education issues; (3) examines and evaluates research and emerging trends in science education and literacy for policy making; (4) works closely with the NIH extramural, intramural, women''s health, laboratory animal research, and minority program offices on science education special issues and programs to ensure coordination of NIH efforts; (5) works with NIH institutes, centers, and divisions to enhance communication of science education activities; and (6) works cooperatively with other public- and private-sector organizations to develop and coordinate activities.

Proper citation: NIH Office of Science Education (RRID:SCR_005603) Copy   

•   Source: SciCrunch Registry

http://www.thehamner.org/technology-and-development/technology-transfer/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. BMDExpress is a Java application used to analyze dose-response data from microarray experiments. The program was designed to perform a stepwise analysis on microarray data that combines bench mark dose (BMD) calculations with gene ontology (GO) classification analysis. The combination provides dose estimates at which different cellular processes are altered at a defined increase in risk based on expression levels in the untreated controls. The fitting of the data to the statistical models (linear, 2 polynomial models, 3 polynomial, and power models) is performed using source code borrowed from the U.S. Environmental Protection Agency''''s BMDS software. The MPPD model is a computational model that can be used for estimating human and rat airway particle dosimetry. The model is applicable to risk assessment, research, and education. The MPPD model calculates the deposition and clearance of monodisperse and polydisperse aerosols in the respiratory tracts of rats and human adults and children (deposition only) for particles ranging in size from ultrafine (0.01 m) to coarse (20 m). The models are based on single-path and multiple-path methods for tracking air flow and calculating aerosol deposition in the lung. The single-path method calculates deposition in a typical path per airway generation, while the multiple-path method calculates particle deposition in all airways of the lung and provides lobar-specific and airway-specific information. Within each airway, deposition is calculated using theoretically derived efficiencies for deposition by diffusion, sedimentation, and impaction within the airway or airway bifurcation. Filtration of aerosols by the head is determined using empirical efficiency functions. The MPPD model includes calculations of particle clearance in the lung following deposition. Eight tutorials are provided so that the user can learn to interact with the software.

Proper citation: The Hamner Institute for Health Sciences: BMDExpress and The multiple-path particle dosimetry (RRID:SCR_005511) Copy   

•   Source: SciCrunch Registry

http://fcon_1000.projects.nitrc.org/indi/adhd200/index.html#

A grassroots initiative dedicated to accelerating the scientific community''''s understanding of the neural basis of ADHD through the implementation of open data-sharing and discovery-based science. They believe that a community-wide effort focused on advancing functional and structural imaging examinations of the developing brain will accelerate the rate at which neuroscience can inform clinical practice. The ADHD-200 Global Competition invited participants to develop diagnostic classification tools for ADHD diagnosis based on functional and structural magnetic resonance imaging (MRI) of the brain. Applying their tools, participants provided diagnostic labels for previously unlabeled datasets. The competition assessed diagnostic accuracy of each submission and invited research papers describing novel, neuroscientific ideas related to ADHD diagnosis. Twenty-one international teams, from a mix of disciplines, including statistics, mathematics, and computer science, submitted diagnostic labels, with some trying their hand at imaging analysis and psychiatric diagnosis for the first time. The data for the competition was provided by the ADHD-200 Consortium. Consortium members from institutions around the world provided de-identified, HIPAA compliant imaging datasets from almost 800 children with and without ADHD. A phenotypic file including all of the test set subjects and their diagnostic codes can be downloaded. Winner is presented. The ADHD-200 consortium included: * Brown University, Providence, RI, USA (Brown) * The Kennedy Krieger Institute, Baltimore, MD, USA (KKI) * The Donders Institute, Nijmegen, The Netherlands (NeuroImage) * New York University Medical Center, New York, NY, USA (NYU) * Oregon Health and Science University, Portland, OR, USA (OHSU) * Peking University, Beijing, P.R.China (Peking 1-3) * The University of Pittsburgh, Pittsburgh, PA, USA (Pittsburgh) * Washington University in St. Louis, St. Louis, MO, USA (WashU)

Proper citation: ADHD-200 Sample (RRID:SCR_005358) Copy   

•   Source: SciCrunch Registry

http://www.labman.org

On March 8, 2008 in Havana, the Latin American Network for Brain Mapping (LABMAN) was created with participants from Argentina, Brazil, Colombia, Cuba and Mexico. The focus of LABMAN is to promote neuroimaging and systems neuroscience in the region through the implementation of training and exchange programs, and to increase public awareness of the Latin American potential to contribute both to basic and applied research in human brain mapping. The immediate LABMAN goals are to: * Train specialists in all major imaging techniques. * Expedite the transfer of new scientific and technical knowledge from abroad. * Increase the scientific productivity of the region. * Drastically increase the awareness of local governments, international organizations and of the general public of brain mapping results on potential. * Organize multinational projects in areas of special relevance to the region, e.g. nutrition, pediatric development, neurodegeneration. Latin American Brain Mapping Network (LABMAN) participants : * Cuban Neuroscience Center * University of Buenos Aires * University of Sao Paulo * Universidad del Valle, Cal��, Colombia * UAM Iztapalapa, Mexico City, Mexico

Proper citation: Latin American Brain Mapping Network (LABMAN) (RRID:SCR_005509) Copy   

•   Source: SciCrunch Registry

http://national_databank.mclean.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. A publicly accessible data repository to provide neuroscience investigators with secure access to cohort collections. The Databank collects and disseminates gene expression data from microarray experiments on brain tissue samples, along with diagnostic results from postmortem studies of neurological and psychiatric disorders. All of the data that is derived from studies of the HBTRC collection is being incorporated into the National Brain Databank. This data is available to the general public, although strict precautions are undertaken to maintain the confidentiality of the brain donors and their family members. The system is designed to incorporate MIAME and MAGE-ML based microarray data sharing standards. Data from various types of studies conducted on brain tissue in the HBTRC collection will be available from studies using different technologies, such as gene expression profiling, quantitative RT-PCR, situ hybridization, and immunocytochemistry and will have the potential for providing powerful insights into the subregional and cellular distribution of genes and/or proteins in different brain regions and eventually in specific subregions and cellular subtypes.

Proper citation: National Brain Databank (RRID:SCR_003606) Copy   

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http://www.nimh.nih.gov/educational-resources/index.shtml

A portal to educational resources.

Proper citation: NIMH Educational Resources (RRID:SCR_004045) Copy   

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http://brainarchitecture.org/

Evolving portal that will provide interactive tools and resources to allow researchers, clinicians, and students to discover, analyze, and visualize what is known about the brain's organization, and what the evidence is for that knowledge. This project has a current experimental focus: creating the first brainwide mesoscopic connectivity diagram in the mouse. Related efforts for the human brain currently focus on literature mining and an Online Brain Atlas Reconciliation Tool. The primary goal of the Brain Architecture Project is to assemble available knowledge about the structure of the nervous system, with an ultimate emphasis on the human CNS. Such information is currently scattered in research articles, textbooks, electronic databases and datasets, and even as samples on laboratory shelves. Pooling the knowledge across these heterogeneous materials - even simply getting to know what we know - is a complex challenge that requires an interdisciplinary approach and the contributions and support of the greater community. Their approach can be divided into 4 major thrusts: * Literature Curation and Text Mining * Computational Analysis * Resource Development * Experimental Efforts

Proper citation: Brain Architecture Project (RRID:SCR_004283) Copy   

•   Source: SciCrunch Registry

http://neuroandpsych.slu.edu/

The Department of Neurology & Psychiatry aims to 1) provide the best psychiatric and neurological care to patients and their families, 2) discover and investigate new treatments for psychiatric and nervous system disorders, 3) study psychosocial processes in psychiatric and neurological illness, and 4) educate the next generation of practitioners, as well as our patients and the lay community. The Department of Neurology & Psychiatry (DNP) was established on June 1, 2007. The Department has 34 faculty members and is planning continued expansion. There are 7 psychiatrists, 18 neurologists, 4 child neurologists, and 5 NIH-supported PhD investigators. The DNP is one of five departments in the country that combines the disciplines of neurology and psychiatry. We are unique in having two strong residency programs and are the only that attempts to establish a new paradigm in care of patients with neurological and psychiatric disease through co-management initiatives. * Division of Psychiatry: The Psychiatrists work within four areas: Adult, Geriatric, Community, and Forensic Psychiatry. * Division of Neurology: The division has an extremely active stroke/intensive care and general neurology service. We are expanding services in neurocritical care and interventional neurology. * Education: The DNP has approximately 25 residents/fellows in each discipline. * Research: The DNP has robust programs in clinical, basic, and translational research. We emphasize 3 areas in this overview of the DNP. ** Clinical Research Unit ** Psychosocial Processes Group ** Translational Neuromuscular Disease VISION STATEMENT All members of the Saint Louis University Department of Neurology & Psychiatry will collaborate to support state-of-the-art neurological and psychiatric education, compassionate patient care, and a growing research enterprise. The Department will develop the most exciting intellectual environment in the Nation for investigation, treatment, and training in psychiatry and neurology. We will fulfill this Vision in an environment of mutual respect and collaboration.

Proper citation: St. Louis University Department of Neurology and Psychiatry (RRID:SCR_004297) Copy   

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http://www.abc.net.au/rn/allinthemind/default.htm

Radio National''s weekly foray into all things mental a program (podcast) about the mind, brain and behavior, hosted by Lynne Malcolm (previously by Natasha Mitchell). From dreaming to depression, addiction to artificial intelligence, consciousness to coma, psychoanalysis to psychopathy, free will to forgetting ��All in the Mind��explores the human condition through the mind''s eye. All in the Mind brings together unexpected voices, themes and ideas and engages with both leading thinkers and personal stories. Psychology and human behavior are only part of the equation. The program''s scope is considerably broader and explores themes in science, religion, health, philosophy, education, history and pop culture, with the mind as the key focus.

Proper citation: All In The Mind (RRID:SCR_004240) Copy   

•   Source: SciCrunch Registry

http://openconnectomeproject.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go.

Proper citation: Open Connectome Project (RRID:SCR_004232) Copy   

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http://www.cvrgrid.org/

Infrastructure for sharing cardiovascular data and data analysis tools. Human ExVivo heart data set and canine ExVivo normal and failing heart data sets are available. Canine hearts atlas and human InVivo atlases are available.

Proper citation: CardioVascular Research Grid (CVRG) (RRID:SCR_004472) Copy   

•   Source: SciCrunch Registry