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https://github.com/cwatson/braingraph/

Software R package for performing graph theory analyses of brain MRI data.

Proper citation: brainGraph (RRID:SCR_017260) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/ABCDreport

Software application as a simple system to review study progress. Used in ABCD study.

Proper citation: ABCDreport (RRID:SCR_016030) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/normalizefov

FSoftware for field-of-view normalization to minimize mismatch in different subjects' images. It aids that streamline analysis of large-scale brain MRI datasets.

Proper citation: NeuroImage Field-of-View Normalization Tool (RRID:SCR_015957) Copy   

•   Source: SciCrunch Registry

http://braintissuebank.dal.ca

A biomaterial supply resource which supplies brain tissue for researchers studying dementia and other neurodegenerative diseases. The Maritime Brain Tissue Bank archives tissues related to Alzheimer's Disease, mixed dementias, Lewy Body Disease, and Huntington's Disease, among others.

Proper citation: Maritime Brain Tissue Bank (RRID:SCR_013838) Copy   

•   Source: SciCrunch Registry

http://www.brainbank.nl

A biomaterial supply resource which collects, stores, and disseminates diseased and healthy brain tissue. The Netherlands Brain Bank currently contains more than 3600 samples, and each sample includes a neuropathological report and donor medical history. The samples can additionally be matched with ante-mortem parameters and post-mortem parameters upon request. Sample types include cortex, spinal cord, cerebrospinal fluid, plasma, and DNA, among others. Database mining is available with a financial contribution.

Proper citation: Netherlands Brain Bank (RRID:SCR_013841) Copy   

•   Source: SciCrunch Registry

http://www.ncl.ac.uk/ion/about/facilities/nbtr/

A biomaterial supply resource which archives and disseminates brain tissue for the study of normal brain aging and brain disorders. Researchers must create an account in order to browse the database of available tissue. Samples are distributed to researchers in such a way that the identity and personal information of donors is protected.

Proper citation: Newcastle Brain Tissue Resource (RRID:SCR_013843) Copy   

•   Source: SciCrunch Registry

http://autopatcher.org/

Software tool for neuronal recording in intact brain.

Proper citation: Autopatcher (RRID:SCR_017464) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/fmridatacenter/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community.

Proper citation: fMRI Data Center (RRID:SCR_007278) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank-handbook/tissue-arrays

Offer high-throughput analysis of tissue histology and protein expression for the biogerontology research community. Each array is a 4 micron section that includes tissue cores from multiple tissues at multiple ages on one slide. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. Ages are chosen to span the life from young adult to very old age. (available ages: 4, 12, 18, 24 and 28 months of age) Images of H&E stained punches are available for Liver, Cardiac Muscle, and Brain. The NIA aged rodent tissue arrays were developed with assistance from the National Cancer Institute (NCI) Tissue Array Research Program (TARP), led by Dr. Stephen Hewitt, Director. NCI TARP contains more information on tissue array construction, protocols for using arrays, and references. Preparation and Product Description Tissue arrays are prepared in parallel from different sets of animals so that experiments can be conducted in duplicate, with each array using unique animals with a unique product number. The product descriptions page describes each array, including: * Strain * Gender * Ages * Tissues * Animal Identification Numbers

Proper citation: Aged Rodent Tissue Arrays (RRID:SCR_007332) Copy   

•   Source: SciCrunch Registry

http://human.brain-map.org/static/brainexplorer

Multi modal atlas of human brain that integrates anatomic and genomic information, coupled with suite of visualization and mining tools to create open public resource for brain researchers and other scientists. Data include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is desktop software application for viewing human brain anatomy and gene expression data in 3D.

Proper citation: Allen Human Brain Atlas (RRID:SCR_007416) Copy   

•   Source: SciCrunch Registry

http://www.neurolens.org/NeuroLens/

An integrated environment for the analysis and visualization of functional neuroimages. It is intended to provide extremely fast and flexible image processing, via an intuitive user interface that encourages experimentation with analysis parameters and detailed inspection of both raw image data and processing results. All processing operations in NeuroLens are built around a Plugin architecture, making it easy to extend its functionality. NeuroLens runs on Apple computers based on the G4, G5, or Intel chipsets and running MacOSX 10.4 (Tiger) or later. It is available free for academic and non-profit research use. * Operating System: MacOS * Programming Language: Objective C * Supported Data Format: AFNI BRIK, ANALYZE, COR, DICOM, MGH/MGZ, MINC, Other Format

Proper citation: NeuroLens (RRID:SCR_007372) Copy   

•   Source: SciCrunch Registry

https://med.uth.edu/nrc/

The Neuroscience Research Center (NRC) is a university-wide center where diverse and multidisciplinary research is conducted to further the understanding of neural and behavioral disorders. Whether conducting cellular research in laboratories or clinical trials in patient care settings, the work of NRC researchers may someday contribute to preventing and treating such devastating disorders as: * Dementias resulting from Alzheimer''s disease and stroke * Mental retardation and other learning disabilities * Mental illnesses, including schizophrenia and manic-depressive illness * Alcoholism and other substance abuse problems * Inability to process knowledge due to factors such as aging and head trauma * Disabilities due to disorders of the developing nervous system More than 280 faculty hold NRC appointments, and are on the faculties of the Medical School, School of Public Health, School of Nursing, Dental Branch, and School of Biomedical Informatics. Departments with significant NRC research activities within the Medical School include Neurobiology and Anatomy; Neurology; Neurosurgery; Ophthalmology and Visual Science; Psychiatry and Behavioral Sciences and Radiology. NRC activities are guided by an executive committee appointed by the President of the Health Science Center. The Neuroscience Research Center (NRC) is affiliated with educational opportunities at the graduate and postdoctoral levels.

Proper citation: UTHealth at Houston Neuroscience Research Center (RRID:SCR_007486) Copy   

•   Source: SciCrunch Registry

http://www.nibb.ac.jp/brish/indexE.html

Database of detailed protocols for single and double in situ hybridization (ISH) method, probes used by Yamamori lab and others useful for studies of brain, and many photos of mammalian (mostly mouse and monkey) brains stained with various gene probes. Also includes a brain atlas of gene expression. Currently, the atlas comprises a series of un-annotated images showing the localization of a particular probe or molecule, e.g., AChE.

Proper citation: BraInSitu: A homepage for molecular neuroanatomy (RRID:SCR_008081) Copy   

•   Source: SciCrunch Registry

http://sig.biostr.washington.edu/projects/brain/

The UW Integrated Brain Project is one project within the national Human Brain Project, a national multi-agency effort to develop informatics tools for managing the exploding amount of information that is accumulating about the human brain. The objective of the UW Integrated Brain Project effort is to organize and integrate distributed functional information about the brain around the structural information framework that is the long term goal of our work. This application therefore extends the utility of the Digital Anatomist Project by using it to organize non-structural information. The initial driving neuroscience problem that is being addressed is the management, visualization and analysis of cortical language mapping data. In recent years, advances in imaging technology such as PET and functional MRI have allowed researchers to observe areas of the cortex that are activated when the subject performs language tasks. These advances have greatly accelerated the amount of data available about human language, but have also emphasized the need to organize and integrate the sometimes contradictory sources of data, in order to develop theories about language organization. The hypothesis is that neuroanatomy is the common substrate on which the diverse kinds of data can be integrated. A result of the work done by this project is a set of software tools for generating a 3-D reconstruction of the patient''s own brain from MRI, for mapping functional data to this reconstruction, for normalizing individual anatomy by warping to a canonical brain atlas and by annotating data with terms from an anatomy ontology, for managing individual lab data in local laboratory information systems, for integrating and querying data across separate data management systems, and for visualizing the integrated results. Sponsors: This Human Brain Project research is funded jointly by the National Institute on Deafness and Other Communication Disorders, the National Institute of Mental Health, and the National Institute on Aging.

Proper citation: University of Washington Integrated Brain Project (RRID:SCR_008075) Copy   

•   Source: SciCrunch Registry

http://mmil.ucsd.edu/

An interdisciplinary group of scientists and clinicians who study the human brain using a variety of imaging, recording, and computational techniques. Their primary goal is to bridge non-invasive imaging technologies to the underlying neurophysiology of brain neuronal circuits for a better understanding of healthy human brain function, and mechanisms of disruption of this function in diseases such as Alzheimer's, epilepsy and stroke. The other goal of the MMIL is to develop and apply advanced imaging techniques to understanding the human brain and its disorders. In order to ground these methodological developments in their underlying neurobiology, invasive studies in humans and animals involving optical and micro physiological measures are also performed. These methodologies are applied to understanding normal function in sleep, memory and language, development and aging, and diseases such as dementia, epilepsy and autism.

Proper citation: Multimodal Imaging Laboratory (RRID:SCR_008071) Copy   

•   Source: SciCrunch Registry

http://enhancer.lbl.gov/

Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth.

Proper citation: VISTA Enhancer Browser (RRID:SCR_007973) Copy   

•   Source: SciCrunch Registry

http://www.buzsakilab.com/

Lab interested in understanding how neuronal circuitries of the brain support its cognitive capacities. Its goal is to provide rational, mechanistic explanations of cognitive functions at a descriptive level. In the lab''s view, the most promising area of cognitive faculties for scientific inquiry is memory, since it is a well-circumscribed term, can be studied in animals and substantial knowledge has accumulated on the molecular mechanisms of synaptic plasticity. Available software: * NeuroScope: NeuroScope can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities. * Klusters: Klusters is a powerful and easy-to-use cluster cutting application designed to help neurophysiologists sort action potentials from multiple neurons on groups of electrodes (e.g., tetrodes or multisite silicon probes). * KlustaKwik: KlustaKwik is a program for automatic cluster analysis, specifically designed to run fast on large data sets. * MATLAB m-files: A selection of MATLAB files developed in the lab., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Buzsaki Lab (RRID:SCR_008020) Copy   

•   Source: SciCrunch Registry

http://www.cmbn.no/ottersen/

A laboratory that investigates the molecular mechanisms involved in the development of acute and chronic neurodegenerative disease, with a focus on the role of glutamate excitotoxicity. It aims at unraveling the molecular basis for cell death and edema development in stroke, and explores the pathophysiology of Alzheimer's disease and temporal lobe epilepsy. The main objective of the LMN is to advance understanding of the role of glutamate, as a transmitter substance in the normal brain and as a mediator of excitotoxicity in pathological conditions such as stroke. To this end the LMN employs several vital and nonvital imaging techniques. Model systems includes organotypic slice cultures and transgenic animals. An important focus of the LMN is to explore the role of DNA damage and repair in the pathogenesis of neurodegenerative disease. LMN is also engaged in research on molecular mechanism underlying brain edema, epilepsy, and Alzheimer's disease.

Proper citation: Laboratory of Molecular Neuroscience, University of Oslo (RRID:SCR_008097) Copy   

•   Source: SciCrunch Registry

http://www.cabiatl.com/mricro/

MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyze MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms. Some features of MRIcro are: - Converts medical images to SPM friendly Analyze format. - View Analyze format images (big or little endian). - Create Analyze format headers (big or little endian). - Create 3D regions of interest (with computed volume & intensity). - Overlap multiple regions of interest. - Rotate images to match SPM template images. - Export images to BMP, JPEG, PNG or TIF format. - Yoked images: linked viewing of multiple images (e.g. view same coordinates of PET and MRI scans). Users familiar with other Windows programs will find that this software is fairly straightforward to use. Resting the mouse cursor over a button will cause a text hint to appear over the button. However, a tutorial with a step by step guide of how to use MRIcro with SPM is available.

Proper citation: MRIcro Software (RRID:SCR_008264) Copy   

•   Source: SciCrunch Registry