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http://mialab.mrn.org/index.html
MIALAB, headed by Dr. Vince Calhoun, focuses on developing and optimizing methods and software for quantitative analysis of structure and function in medical images with particular focus on the study of psychiatric illness. We work with many types of data, including functional magnetic resonance imaging (fMRI), diffusion tensor imaging (DTI), electroencephalography (EEG), structural imaging and genetic data. Much of our time is spent working on new methods for flexible analysis of brain imaging data. The use of data driven approaches is very useful for extracting potentially unpredictable patterns within these data. However such methods can be further improved by incorporating additional prior information as constraints, in order to benefit from what we know. To this end, we draw heavily from the areas of image processing, adaptive signal processing, estimation theory, neural networks, statistical signal processing, and pattern recognition.
Proper citation: MIALAB - Medical Image Analysis Lab (RRID:SCR_006089) Copy
http://www.brain-map.org/api/index.html
API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service
Proper citation: Allen Brain Atlas API (RRID:SCR_005984) Copy
A web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications.
Proper citation: Viking Viewer for Connectomics (RRID:SCR_005986) Copy
http://www.nitrc.org/projects/abc
A comprehensive processing pipeline developed and used at University of North Carolina and University of Utah for brain MRIs. The processing pipeline includes image registration, filtering, segmentation and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program. The image segmentation algorithm is based on the EMS software developed by Koen van Leemput.
Proper citation: ABC (Atlas Based Classification) (RRID:SCR_005981) Copy
http://www.fmriconsulting.com/brodmann/
An atlas that facilitates fMRI analysis understanding by providing access to all of the functions that have been associated with each of the 52 Brodmann's areas or corresponding gyri. Links to main publications supporting the findings are provided in PubMed ID format. Brodmann's areas with similar functions and locations have been collapsed into a single page. The word left or right has been added indicating a lateralized function. All the abstracts published on PubMed on fMRI and brain PET studies in which the Brodmann's area or its anatomical correlate were mentioned have been reviewed up to August 2008. Abstracts with poorly described experimental methods or findings clearly conflicting with established knowledge provided by the clinical model were excluded. Studies on patients were also excluded.
Proper citation: Brodmann's Interactive Atlas (RRID:SCR_006368) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Project to advance understanding of the neural mechanisms of vocal learning by providing a quantitative description of the relationship between physiological variables and vocal performance over the course of development in a songbird, the zebra finch. They propose to study vocal learning dynamically across neuronal and peripheral subsystems, using a novel collaborative approach that will harness the combined expertise of several investigators. Their proposed research model will 1) provide simultaneous measurements of acoustic, articulatory and electrophysiological data that will document the detailed dynamics of the vocal imitation process in a standardized learning paradigm; and 2) incorporate these measurements into a theoretical/computational framework that simultaneously provides a phenomenological description and attempts to elucidate the mechanistic basis of the learning process.
Proper citation: Zebra Finch Song Learning Consortium (RRID:SCR_006356) Copy
http://brainvis.wustl.edu/wiki/index.php/Caret:About
Software package to visualize and analyze structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. Runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems.
Proper citation: Computerized Anatomical Reconstruction and Editing Toolkit (RRID:SCR_006260) Copy
A collection of images of the human nervous system focusing on disease and injury.
Proper citation: Human Nervous System Disease and Injury (RRID:SCR_006370) Copy
Initiative to assemble a multicenter team of expert neuroscientists to evaluate the late effects of Traumatic brain injury (TBI), including single and repetitive TBI of varying severity, and Chronic Traumatic Encephalopathy (CTE), using histological examination of postmortem bio specimens and neuroimaging tools as a foundation to develop in vivo diagnostics. As a first aim, this proposal will bring together a team of 5 accomplished neuropathologists in neurodegenerative disease to establish consensus criteria for the post-mortem diagnosis of CTE. This team will also define the stages of CTE pathology, the features that differentiate CTE from other neurodegenerations and the effects of substance abuse, and the characteristics of posttraumatic neurodegeneration after single TBI. As a second aim, this proposal will establish a national bio specimen and data bank for TBI (Understanding Neurological Injury and Traumatic Encephalopathy (UNITE) bio bank) by developing a nationwide brain donor registry and hotline to acquire high quality bio specimens and data. The UNITE bank will use strictly standardized protocols and a web-based interface to ensure that tissue and data are readily available to qualified investigators. Comprehensive retrospective clinical data including clinical symptoms, brain trauma and substance abuse history, and medical records (including common data elements) will be entered into a secure database. Behavioral/ mood dysfunction, cognitive changes, substance abuse and traumatic exposure will be correlated with quantitative assessment of the multifocal tauopathy, Ass deposition and axonal injury. As a third aim, neuroimaging signatures of the neuropathology will be determined in post-mortem tissue using high spatial resolution diffusion tensor imaging (DTI) and autoradiography using a highly selective PET ligand for tau. Quantitative assessment of axonal injury, tau, and Ass will be correlated with ex vivo DTI abnormalities and tau ligand autoradiography. Pilot neuroimaging studies of individuals at high risk for the development of CTE will also be conducted in the final 2 years of the proposal. This proposal will determine the clinical and neuroimaging correlates of CTE and posttraumatic neurodegeneration and create the groundwork for establishing their incidence and prevalence. This study will have a tremendous impact on public health of millions of Americans and greatly increase our understanding of the latent effects of brain trauma.
Proper citation: CTE and Post-traumatic Neurodegeneration: Neuropathology and Ex Vivo Imaging (RRID:SCR_006543) Copy
http://www.medschool.lsuhsc.edu/neuroscience/
Research center that takes multidisciplinary approach to neuroscience education and research. Research programs on molecular and cellular bases of neural diseases are the center of the innovative educational programs. Primary mission is to foster and conduct science that advances understanding of brain function and diseases that affect nervous system.
Proper citation: Louisiana State University School of Medicine Neurosciences Center (RRID:SCR_006446) Copy
Platform for Traumatic Brain Injury relevant data. System was developed to share data across entire TBI research field and to facilitate collaboration between laboratories and interconnectivity between informatics platforms. FITBIR implements interagency Common Data Elements for TBI research and provides tools and resources to extend data dictionary. Established submission strategy to ensure high quality and to provide maximum benefit to investigators. Qualified researchers can request access to data stored in FITBIR and/or data stored at federated repositories.
Proper citation: Federal Interagency Traumatic Brain Injury Research Informatics System (RRID:SCR_006856) Copy
Professional networking site dedicated to those working, studying, or simply interested in the science of the brain. Those with personal and professional interests in neuroscience, neurology, psychology, and all related areas -- those studying neural activities in invertebrates up to the human brain, including brain-like systems and networks are welcome. The NeuroNetwork was built to allow students and researchers to find and interact with each other in a professional environment. You may create searchable profiles with your research interests; start a blog; upload poster presentations and videos; post and search job listings; form a virtual group based on your interests, geographical location, etc.; and view, post, and RSVP to upcoming meetings. And don''t just create a profile for yourself -- create one for your organization, institute, society, or even your lab as well.
Proper citation: NeuroNetwork (RRID:SCR_006761) Copy
http://platform.invbrain.neuroinf.jp/
Database of information on nervous systems and behavior of various species of invertebrates and a large body of ancillary material to promote the use of invertebrate systems in research and education and facilitate information transfer to engineers that are looking for mechanisms that may be useful to solve a wide range of technological problems. The database is linked to explanations of the contents to allow users to familiarize themselves with the data and the context in which they were obtained. The platform has four entrance points tailored to different target user groups. The first entrance point is designed for users that are interested in using invertebrates for research purposes, in particular in the field of neuroscience, to assist them in initiating research projects. This includes databases of sensory systems, brains, and behavior of invertebrates, especially insects. The databases contain sensory organ structure and function, photographs and movies documenting insect behavior, data acquisition equipment and other instrumentation, software, material for eduction, and bibliography. A second entrance point is available for those that are concerned with implementations of design principles of invertebrate nervous systems and behavior in industrial applications. The third portal is destined for providing quick access for instructors that intend to use invertebrates for educational purposes and the remaining entrance point facilitates obtaining general comparative information on sensory and central nervous systems and behavior of invertebrates.
Proper citation: Invertebrate Brain Platform (RRID:SCR_006764) Copy
http://neuroade.christakou.org/
At neuroade, a Cognitive Neuroscience Laboratory, we study change in brain and behavior across multiple time-scales. Researchers in the lab combine a variety of methodologies to answer specific questions about typical and atypical behavior and development. We use functional magnetic resonance imaging (fMRI), peripheral psychophysiology (such as skin conductance responses), behavioral testing, genotyping analysis, and computational modeling. Most of our work takes place at the Centre for Integrative Neuroscience and Neurodynamics (CINN), and we all live in the Department of Psychology at the University of Reading. Our research is divided into several distinct yet highly interlinked themes, all converging in their application to understanding psychopathology -- summarised here in no particular order: * Decision-making and the Evaluation of Decision Outcomes * Dimensions of Impulsivity as a Foraging Strategy * Adolescent Development * Computational Modeling Probes of Individual Differences
Proper citation: neuroade (RRID:SCR_006758) Copy
A pan-European scientific association to encourage research across the neurosciences and to translate new knowledge on fundamental disease mechanisms into new medicines and clinical applications. As an interdisciplinary forum for the science and treatment of disorders of the brain, they promote the communication and cross- fertilization of high-quality experimental and clinical research across the field of neuroscience. ECNP is a non-profit member-based association, independently governed and self-funded. ECNP is a public-interest-serving entity.
Proper citation: ECNP (RRID:SCR_000501) Copy
The PEDIATRIC BRAIN TUMOR CONSORTIUM (PBTC) is a multidisciplinary cooperative research organization devoted to the study of correlative tumor biology and new therapies for primary CNS tumors of childhood. PBTC's mission is to contribute rapidly and effectively to the understanding and cure of these tumors through the conduct of multi-center, multidisciplinary, innovative studies with designs and analyses based on uniformly high quality statistical science. While the primary mission of the PBTC is to identify through laboratory and clinical science superior treatment strategies for children with brain cancers, the PBTC investigators recognize their profound responsibility to meet the special needs of the children and families as they face this enormous challenge. Members are committed to working within their institutions and communities to improve support services and follow up care for these patients and their families. The PBTC's primary objective is to rapidly conduct novel phase I and II clinical evaluations of new therapeutic drugs, new biological therapies, treatment delivery technologies and radiation treatment strategies in children from infancy to 21 years of age with primary central nervous system (CNS) tumors. A second objective is to characterize reliable markers and predictors (direct or surrogate) of brain tumors' responses to new therapies. The Consortium conducts research on brain tumor specimens in the laboratory to further understand the biology of pediatric brain tumors. A third objective is to develop and coordinate innovative neuro-imaging techniques. Through the PBTC's Neuro-Imaging Center, formed in May 2000, research to evaluate new treatment response criteria and neuro-imaging methods to understand regional brain effects is in progress. These imaging techniques can also advance understanding of significant neuro-toxicity in a developing child's central nervous system. The Neuro-Imaging Center is supported in part by private sources - grants from foundations and non-profit organizations - in addition to the NCI. As an NCI funded Consortium, the Pediatric Brain Tumor Consortium (PBTC) is required to make research data available to other investigators for use in research projects. An investigator who wishes to use individual patient data from one or more of the Consortium's completed and published studies must submit in writing a description of the research project, the PBTC studies from which data are requested, the specific data requested, and a list of investigators involved with the project and their affiliated research institutions. A copy of the requesting investigator's CV must also be provided. Participating Institutions: Children's Hospital of Philadelphia, Children's National Medical Center (Washington, DC), Children's Memorial Hospital (Chicago), Duke University, National Cancer Institute, St. Jude Children's Research Hospital, Texas Children's Cancer Center, University of California at San Francisco, and University of Pittsburgh.
Proper citation: Pediatric Brain Tumor Consortium (RRID:SCR_000658) Copy
http://www.nitrc.org/projects/atp
Autism research program that makes available post-mortem brain tissue to qualified scientists all over the world. Working directly with tissue banks, organ procurement agencies, medical examiners and the general public, this is the largest program dedicated to increasing and enhancing the availability of post-mortem brain tissue for basic research in autism. To date, the ATP has collected and stored more than 170 brains in their repositories at Harvard (US) and Oxford (UK). These brains are processed by formalin fixation and/or snap frozen to properly provide high quality tissue of all brain regions, in support of biological research in autism. The ATP is unique in that they diligently pursue all available clinical data (pre and post mortem) on tissue donors in order to create the most biologically relevant brain repository for autism research. These data, together with tissue resources from both banks and associated repositories, are presented to all interested researchers through their extensive web-based data portal (login required). The ATP is not a brain bank, but works directly with the Harvard Brain Tissue Resource Center in Boston (HBTRC), Massachusetts to serve as its tissue repository. This program augments brain bank functions by: * Creating the most biologically relevant brain tissue repository possible * Fully covering all costs associated with brain extraction and transfer to the repositories at Harvard (US and Canada) and Oxford (UK). * Providing scientific oversight of tissue distributions * Overseeing and managing all tissue grants * Clinically phenotyping and acquiring extensive medical data on all of their donors * Providing continuing family support and communication to all of their donors * Directly supporting researchers to facilitate autism research * Maintaining a robust web based data management and secure on-line global interface system * Developing and supporting ATP established scientific initiatives * Actively providing public outreach and education The ATP is not a clinical organ procurement agency, but rather they facilitate the wishes of donors and families to donate their tissue to autism research. Through the ATP's established international infrastructure, they work with any accredited tissue bank, organ procurement agency, or medical examiner that receives a family's request to donate their loved one's tissue to the program. Once contacted, the ATP will insure that the family's request to donate their loved one's tissue is faithfully met, covering all costs to the family and partnering agency as well as ensuring the tissues' proper and rapid transport to the ATP's repository at the Harvard Brain Tissue Resource Center (HBTRC) in Boston, Massachusetts.
Proper citation: Autism Tissue Program (RRID:SCR_000651) Copy
http://mitraweb1.cshl.edu:8080/BrainArchitecture/pages/publications.faces
Preliminary database of neuroanatomical connectivity reports specifically for the human brain, which have been manually curated. It includes details (based on manual literature curation) of tract tracing or related connectivity studies conducted in human brain tissue. This database and user interface will be expanded and improved in the near future.
Proper citation: Human Brain Connectivity Database (RRID:SCR_001594) Copy
http://incf.org/programs/atlasing/projects/waxholm-space
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files.
Proper citation: Waxholm Space (RRID:SCR_001592) Copy
http://www.neurologychannel.com/
A topical portal which provides information about conditions that affect the nervous system (brain, spinal cord, nerves, and muscles), such as stroke (brain attack), Alzheimer's disease, and back pain. It is a physician developed and monitored source of neurology information for consumers. Additionally, it contains comprehensive condition and treatment information, as well as interactive tools.
Proper citation: Neurologychannel (RRID:SCR_001597) Copy
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