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THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The Laboratory of Experimental Neuropathology is engaged in the study of neurodegenerative disease, including Alzheimer's, Parkinson's, and the dementia of HIV encephalitis. It contains a large bank of materials available to fellow investigators including images, publications, and lab safety. Fellow Investigators and Collaborators may request materials from the brain bank. Technologies employed by the laboratory include immunocytochemistry, neurochemistry, molecular genetics, transgenic models of disease, and imaging by scanning laser confocal microscopy.
Proper citation: UCSD Experimental Neuropath Laboratory (RRID:SCR_004906) Copy
Portal touching on all aspects of neuroscience from molecules to the mind, from the laboratory bench to the patient's bedside. Members study the normal structure and workings of the nervous system, its development, its cognitive functions, its derangement by disease and injury, and the means of its repair and protection. Projects span traditional disciplinary boundaries, as do graduate and postdoctoral training programs. Its major achievement has been to foster and improve multidisciplinary collaborations which has increasingly permitted the identification of pathogenic mechanisms and the formulation of new therapeutic approaches.
Proper citation: Brain Research Institute (RRID:SCR_004988) Copy
Neuron Navigator (NNG) integrates a 3D neuron image database into an easy-to-use visual interface. Via a flexible and user-friendly interface, NNG is designed to help researchers analyze and observe the connectivity within the neural maze and discover possible pathways. With NNG''s 3D neuron image database, researchers can perform volumetric searches using the location of neural terminals, or the occupation of neuron volumes within the 3D brain space. Also, the presence of the neurons under a combination of spatial restrictions can be shown as well. NNG is a result of a multi-discipline collaboration between neuroscientists and computer scientists, and NNG has now been implemented on a coordinated brain space for the Drosophila (fruit fly) brain. Account is required.
Proper citation: Neuron Navigator (RRID:SCR_005063) Copy
https://github.com/ABCD-STUDY/DEAP
Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States.
Proper citation: DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) Copy
Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility.
Proper citation: NeMOarchive (RRID:SCR_016152) Copy
Research project examining how biological, psychological, and environmental factors during adolescence may influence brain development and mental health. Using brain imaging and genetics, the project will help develop prevention strategies and improved therapies for mental health disorders in the future., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: IMAGEN (RRID:SCR_016045) Copy
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
Web interface that facilitates open science for neuroscience community by simplifying global access to and sharing of datasets and tools. Portal internalizes typical data cycle of research project, beginning with data acquisition, followed by data processing with published tools, and ultimately publication of results with link to original dataset. Platform to form interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing. Provides unified interface to Canadian neuroscience research community. Open neuroscience research with sharing of both data and methods, to create large-scale databases, development of standards for sharing, facilitation of advanced analytic strategies, open dissemination to global community of neuroscience data and methods, and establishment of training programs for next generation of computational neuroscience researchers.
Proper citation: Canadian Open Neuroscience Platform (RRID:SCR_016433) Copy
https://github.com/nighres/nighres
Software package for processing of high-resolution neuroimaging data. Nighres is a community-developed project that aims to make neuroscience data tools easier to install, use and extend.
Proper citation: Nighres (RRID:SCR_016287) Copy
Project whose goal is to improve health care and lessen the global burden of TBI through the discovery of causal relationships between treatments and clinically meaningful outcomes. InTBIR seeks to encourage well-designed, hypothesis-driven studies that include the collection of high quality data followed by rigorous statistical analysis.
Proper citation: International Initiative for Traumatic Brain Injury Research (RRID:SCR_016237) Copy
http://www.nitrc.org/projects/mica/
Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.
Proper citation: masked ICA (mICA) Toolbox (RRID:SCR_016349) Copy
http://www.nitrc.org/projects/uf2c/
Software tool to standardize and facilitate connectivity studies through a graphical user interface and validated preset parameters.
Proper citation: User Friendly Functional Connectivity - UF²C (RRID:SCR_016550) Copy
http://jefferis.github.io/nat/
Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures.
Proper citation: NeuroAnatomy Toolbox (RRID:SCR_016716) Copy
https://github.com/PatternRecognition/OpenBMI
Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time.
Proper citation: OpenBMI (RRID:SCR_016876) Copy
https://github.com/NeurophysVis/SpectraVis
Web based neuroscience application for analyzing task-related functional networks over time and frequency. Interactive visualization tool for exploring functional brain connectivity.
Proper citation: SpectraVis (RRID:SCR_016691) Copy
Software tool for data management in clinical studies to improve care for patients with Traumatic Brain Injury (TBI). Used to search and find study variables with the associated information and export study data for further analysis.
Proper citation: INCF-Neurobot (RRID:SCR_017004) Copy
Project between Inria, Inserm, CNRS, and University of Rennes for biomedical image analysis for understanding neurological disease. Used to diagnose, monitor and deliver treatment for mental, neurological and substance use disorders by establishing multidisciplinary team between information sciences and medicine in medical imaging, neuroinformatics and population cohorts.
Proper citation: Empenn (RRID:SCR_017074) Copy
Provides Prism softwares and services that integrate advanced imaging into the clinical workflow for brain mapping from acquisition through processing, visualization, and export to PACS. Prism integrates functional MRI, diffusion MRI, perfusion, MR spectroscopy, and PET/CT into a unified workflow for diagnosis and treatment planning in brain disorders. Processing is also available as a cloud deployed service, Prism Serve. Research support includes import/export for imaging and derived quantitative data in both DICOM and research formats such as AFNI and Trackviz.
Proper citation: Prism Clinical Imaging (RRID:SCR_016977) Copy
https://www.mbfbioscience.com/neuroinfo
Software for automatic identification and delineation of brain regions within experimental mouse brain sections. NeuroInfo registers serial section images of any orientation to Allen Mouse Brain Atlas, corrects for distortion due to histological processing, delineates anatomies in experimental section, and detects and reports on cell number within selected anatomies.
Proper citation: NeuroInfo (RRID:SCR_017346) Copy
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
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