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http://www.digitalimagesolutions.de

Stroketool-CT is a user friendly MS-Windows based software system for calculation and visualization of enhanced CT perfusion imaging data sets of the brain. It contains features such as quantitative perfusion using SVD algorithms; DICOM compatibility; rapid calculations of rCBF, MTT, rCBV, TTP,Tmax; and interactive and automatic AIF-detection.

Proper citation: Stroketool-CT (RRID:SCR_013611) Copy   

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http://ielvis.pbworks.com/w/page/116347253/FrontPage

Software toolkit consisting of MATLAB and Bash scripts for intracranial electrode localization/visualization. It maps electrodes to various anatomical and functional atlases, and overlays electrode data over functional neuroimaging data. Software for intracranial electrode localization and visualization.

Proper citation: iELVis (RRID:SCR_016109) Copy   

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http://www.ikaros-project.org/

Ikaros is an open infrastructure for system level modeling of the brain including databases of experimental data, computational models and functional brain data. The system makes heavy use of the emerging standards for Internet based information and makes all information accessible through an open web-based interface. In addition, Ikaros can be used as a control architecture for robots which in the extension will lead to the development of a brain inspired robot architecture. The main components of the Ikaros systems are: a platform independent simulation kernel; a set of computational brain models; a set of I/O modules for interfacing with data files and peripheral such as robots or video cameras; tools for building systems of interconnected models; a plug-in architecture that allows new models to be easily added to the system; and a database with data from learning experiments that can be used for validation of the computational models.

Proper citation: Ikaros Project (RRID:SCR_007391) Copy   

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http://blog.wholebraincatalog.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. The blog of the Whole Brain Catalog.

Proper citation: Whole Brain Catalog Blog (RRID:SCR_000582) Copy   

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http://nac.spl.harvard.edu/

Biomedical Technology Resource Center that develops image processing and analysis techniques for basic and clinical neurosciences. The NAC research approach emphasizes both specific core technologies and collaborative application projects. The core activity of the center is the development of algorithms and techniques for postprocessing of imaging data. New segmentation techniques aid identification of brain structures and disease. Registration methods are used for relating image data to specific patient anatomy or one set of images to another. Visualization tools allow the display of complex anatomical and quantitative information. High-performance computing hardware and associated software techniques further accelerate algorithms and methods. Digital anatomy atlases are developed for the support of both interactive and algorithmic computational tools. Although the emphasis of the NAC is on the dissemination of concepts and techniques, specific elements of the core software technologies have been made available to outside researchers or the community at large. The NAC's core technologies serve the following major collaborative projects: Alzheimer's disease and the aging brain, morphometric measures in schizophrenia and schizotypal disorder, quantitative analysis of multiple sclerosis, and interactive image-based planning and guidance in neurosurgery. One or more NAC researchers have been designated as responsible for each of the core technologies and the collaborative projects.

Proper citation: Neuroimage Analysis Center (RRID:SCR_008998) Copy   

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http://learn.genetics.utah.edu/content/addiction/

A physiologic and molecular look at drug addiction involving many factors including: basic neurobiology, a scientific examination of drug action in the brain, the role of genetics in addiction, and ethical considerations. Designed to be used by students, teachers and members of the public, the materials meet selected US education standards for science and health. Drug addiction is a chronic disease characterized by changes in the brain which result in a compulsive desire to use a drug. A combination of many factors including genetics, environment and behavior influence a person's addiction risk, making it an incredibly complicated disease. The new science of addiction considers all of these factors - from biology to family - to unravel the complexities of the addicted brain. * Natural Reward Pathways Exist in the Brain: The reward pathway is responsible for driving our feelings of motivation, reward and behavior. * Drugs Alter the Brain's Reward Pathway: Drugs work over time to change the reward pathway and affect the entire brain, resulting in addiction. * Genetics Is An Important Factor In Addiction: Genetic susceptibility to addiction is the result of the interaction of many genes. * Timing and Circumstances Influence Addiction: If you use drugs when you are an adolescent, you are more likely to develop lifetime addiction. An individual's social environment also influences addiction risk. * Challenges and Issues in Addiction: Addiction impacts society with many ethical, legal and social issues.

Proper citation: New Science of Addiction: Genetics and the Brain (RRID:SCR_002770) Copy   

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http://www.cnl.salk.edu/

The long range goal of this laboratory is to understand the computational resources of brains from the biophysical to the systems levels. The central issues being addressed are how dendrites integrate synaptic signals in neurons, how networks of neurons generate dynamical patterns of activity, how sensory information is represented in the cerebral cortex, how memory representations are formed and consolidated during sleep, and how visuo-motor transformations are adaptively organized. Additionally, new techniques have been developed for modeling cell signaling using Monte Carlo methods (MCell) and the blind separation of brain imaging data into functionally independent components (ICA).

Proper citation: Computational Neurobiology Laboratory at the Salk Institute (RRID:SCR_002809) Copy   

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http://www.fmrib.ox.ac.uk/fsl/

Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas.

Proper citation: FSL (RRID:SCR_002823) Copy   

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http://www.rbwb.org/

The Rodent Brain WorkBench is the portal to atlases, databases and tools developed by the Neural Systems and Graphics Computing Laboratory (NeSys) at the Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway. The Rodent Brain WorkBench presents a collection of brain mapping and atlasing oriented database applications and tools. The main category of available data is high resolution mosaic images covering complete histological sections through the rat and mouse brain. A highly structured relational database system for archiving, retrieving, viewing, and analysing microscopy and imaging data, aiming at presentation in standardized brain atlas space, is used to present a series of web applications for individual research projects. * Brain Connectivity * Atlases of Mouse Brain Promoter Gene Expression * General Brain Atlas and Navigation Systems * Downloadable tools for 3-DVisualization Open Access: * Atlas 3D * Cerebro-Cerebellar I * Cerebro-Cerebellar II * Neurotransporter Atlas * Rat Hippocampus * Tet-Off Atlas I (PrP) * Tet-Off Atlas II (PrP/CamKII) * Whole Brain Connectivity Atlas The data presented have been produced in collaboration with a large number of laboratories in Europe and the United States.

Proper citation: Rodent Brain WorkBench (RRID:SCR_002727) Copy   

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http://sumsdb.wustl.edu/sums/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures

Proper citation: SumsDB (RRID:SCR_002759) Copy   

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http://sncid.stanleyresearch.org/

A database of 1749 neuropathological markers measured in 12 different brain regions from 60 brains in the Consortium Collection from the Stanley Medical Research Institute combined with microarray data and statistical tools. Fifteen brains each are from patients diagnosed with schizophrenia, bipolar disorder, or major depression, and unaffected controls. The four groups are matched by age, sex, race, postmortem interval, pH, side of brain, and mRNA quality. A Repository of raw data is also included. Users must register for access.

Proper citation: Stanley Neuropathology Consortium Integrative Database (RRID:SCR_002749) Copy   

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http://studyforrest.org

An MRI data repository that holds a set of 7 Tesla images and behavioral metadata. Multi-faceted brain image archive with behavioral measurements. For each participant a number of different scans and auxiliary recordings have been obtained. In addition, several types of minimally preprocessed data are also provided. The full description of the data release is available in a dedicated publication. This project invites anyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging by documenting how much (scientific) value can be generated out of a single data release by publication of scientific findings derived from a dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and integration of new data.

Proper citation: studyforrest.org (RRID:SCR_003112) Copy   

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http://www.fly-trap.org/

Flytrap is an interactive database for displaying gene expression patterns, in particular P(GAL4) patterns, via an intuitive WWW based interface. This development consists of two components, the first being the HTML interface to the database and the second, a tool-kit for constructing and maintaining the database. The browser component of the project is entirely platform independent; based on javascript and HTML and therefore only requires a "standard" browser. This is to facilitate CD-ROM distribution and off-line browsing. Whether on-line or on CD, the basic browser structure does not reply on any server based scripts. Basic searching is now available. The search page uses javascript and will work off-line (i.e. from a CD-ROM copy). The construction tool-kit is UNIX based and requires an on-line web server. The tool-kit is used to compile the HTML browser interface from a simple database. The tool-kit part comprises a forms based HTML interface to the datasets allowing new information to b e added and updated very simply. We are also developing a java interface for the tool-kit that will enable us to edit and annotate images on-line. The basic browser interface is complete and a demonstration version can be accessed via the website. The first working version of the tool-kit is now on-line and is available for use.

Proper citation: flytrap (RRID:SCR_003075) Copy   

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http://brainmap.org/

A community database of published functional and structural neuroimaging experiments with both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates (x,y,z) in Talairach or MNI space. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data. The goal of BrainMap is to develop software and tools to share neuroimaging results and enable meta-analysis of studies of human brain function and structure in healthy and diseased subjects. It is a tool to rapidly retrieve and understand studies in specific research domains, such as language, memory, attention, reasoning, emotion, and perception, and to perform meta-analyses of like studies. Brainmap contains the following software: # Sleuth: database searches and Talairach coordinate plotting (this application requires a username and password) # GingerALE: performs meta-analyses via the activation likelihood estimation (ALE) method; also converts coordinates between MNI and Talairach spaces using icbm2tal # Scribe: database entry of published functional neuroimaging papers with coordinate results

Proper citation: brainmap.org (RRID:SCR_003069) Copy   

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http://www.genepaint.org

Digital atlas of gene expression patterns in developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features virtual microscope tool that enables zooming into images down to cellular resolution.

Proper citation: GenePaint (RRID:SCR_003015) Copy   

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http://braininfo.rprc.washington.edu

Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures.

Proper citation: BrainInfo (RRID:SCR_003142) Copy   

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http://developingmouse.brain-map.org/

Map of gene expression in developing mouse brain revealing gene expression patterns from embryonic through postnatal stages. Provides information about spatial and temporal regulation of gene expression with database. Feature include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases may be viewed alongside in situ hybridization (ISH) data as well as by itself.

Proper citation: Allen Developing Mouse Brain Atlas (RRID:SCR_002990) Copy   

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http://niftilib.sourceforge.net

Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. nifti-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. Niftilib currently has C, Java, MATLAB, and Python libraries; we plan to add some MATLAB/mex interfaces to the C library in the not too distant future. Niftilib has been developed by members of the NIFTI DFWG and volunteers in the neuroimaging community and serves as a reference implementation of the nifti-1 file format. In addition to being a reference implementation, we hope it is also a useful i/o library. Niftilib code is released into the public domain, developers are encouraged to incorporate niftilib code into their applications, and, to contribute changes and enhancements to niftilib. Please contact us if you would like to contribute additonal functionality to the i/o library.

Proper citation: Niftilib (RRID:SCR_003355) Copy   

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https://www.msu.edu/~brains/index.html

The Brain Biodiversity Bank refers to the repository of images of and information about brain specimens contained in the collections associated with the National Museum of Health and Medicine at the Armed Forces Institute of Pathology in Washington, DC. Atlases and brain sections are available for a variety of mammals, and we are also developing a series of labeled atlases of stained sections for educators, students, and researchers. These collections include, besides the Michigan State University Collection, the Welker Collection from the University of Wisconsin, the Yakovlev-Haleem Collection from Harvard University, the Meyer Collection from the Johns Hopkins University, and the Huber-Crosby and Crosby-Lauer Collections from the University of Michigan. What we are doing currently at Michigan State is a series of demonstration projects for publicizing the contents of the collections and ways in which they can be used. For example, the images from the collection can be used for comparative brain study. We have prepared databases of the contents of the collections for presentation and use on this site, as well as for downloading by users in several formats. We are also developing a series of labeled atlases of stained sections for educators, students, and researchers. This internet site is associated with the Comparative Mammalian Brain Collections site. All of the images are in JPEG or GIF format.

Proper citation: Michigan State University Brain Biodiversity Bank (RRID:SCR_003289) Copy   

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http://www.brainbank.mclean.org/

Biomaterial supply resource that acquires, processes, stores, and distributes postmortem brain specimens for brain research. Various types of brain tissue are collected, including those with neurological and psychiatric disorders, along with their parents, siblings and offspring. The HBTRC maintains an extensive collection of postmortem human brains from individuals with Huntington's chorea, Alzheimer's disease, Parkinson's disease, and other neurological disorders. In addition, the HBTRC also has a collection of normal-control specimens.

Proper citation: Harvard Brain Tissue Resource Center (RRID:SCR_003316) Copy   

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