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http://research.mssm.edu/cnic/
Center to advance research and training in mathematical, computational and modern imaging approaches to understanding the brain and its functions. Software tools and associated reconstruction data produced in the center are available. Researchers study the relationships between neural function and structure at levels ranging from the molecular and cellular, through network organization of the brain. This involves the development of new computational and analytic tools for imaging and visualization of 3-D neural morphology, from the gross topologic characteristics of the dendritic arbor to the fine structure of spines and their synapses. Numerical simulations of neural mechanisms based on these structural data are compared with in-vivo and in-vitro electrophysiological recordings. The group also develops new theoretical and analytic approaches to exploring the function of neural models of working memory. The goal of this analytic work is to combine biophysically realistic models and simulations with reduced mathematical models that capture essential dynamical behaviors while reproducing the functionally important features of experimental data. Research areas include: Imaging Studies, Volume Integration, Visualization Techniques, Medial Axis Extraction, Spine Detection and Classification, Applications of Rayburst, Analysis of Spatially Complex Structures, Computational Modeling, Mathematical and Analytic Studies
Proper citation: Computational Neurobiology and Imaging Center (RRID:SCR_013317) Copy
Research forum portal to address brain status by acquiring comprehensive, multimodal data from healthy humans across the lifespan to characterize brain status, assess its change over time, and associate composite descriptors of brain status. Specifically, the measurements are acquired noninvasively by existing neuroimaging technologies (structural MRI, functional MRI, magnetic resonance spectroscopy, diffusion MRI, and magnetoencephalography); in addition, genetic, cognitive, language, and lifestyle data are acquired. Goals: * Derive the Brain Health Index- An integrative assessment of brain status derived from multimodal measurements of brain structure, function, and chemistry. * Continue acquiring data to construct the first-ever databank on brain, cognitive, language and genetic measurements for healthy people across the lifespan. * Provide a novel and unique dataset by which to: characterize brain status, assess its change over time, and associate it with genetic makeup, cognitive function, and language abilities. * Forecast future brain health and disease based on current measurements and guide physicians towards new interventions and evaluate interventions as they develop. * Extend to siblings and other family members to further assess the genetic influences and inheritability.
Proper citation: HBP: Healthy Brain Project (RRID:SCR_013137) Copy
Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.
Proper citation: NeMO Analytics (RRID:SCR_018164) Copy
http://www.neuro.uni-jena.de/cat/
Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry.
Proper citation: Computational Anatomy Toolbox for SPM (RRID:SCR_019184) 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
https://github.com/Frederik-D-Weber/cosleep
Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton.
Proper citation: COsleep (RRID:SCR_017053) 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
Searchable table of datasets. Data generated from projects through BRAIN Initiative Cell Census Network. Datasets can be filtered by species, research investigator, grant number or experimental technique. Includes links to data directories at data archives and links to protocols.
Proper citation: BICCN Cell Registry (RRID:SCR_017267) Copy
https://github.com/cwatson/braingraph/
Software R package for performing graph theory analyses of brain MRI data.
Proper citation: brainGraph (RRID:SCR_017260) 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
https://github.com/zuoxinian/CCS
Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies.
Proper citation: Connectome Computation System (RRID:SCR_017342) Copy
Developer of medical software to offer image analysis technologies. Company in Denmark that provides medical image processing software to get quantifiable and accurate insight into brain.
Proper citation: Brainreader (RRID:SCR_017308) Copy
https://www.ibis-network.org/index.html
Research study of brain development in infants and children with autism. Consortium of researchers across North America that work together to discover early changes in brain development of young children with autism. Participants will travel to their closest study location to receive developmental and behavioral assessments, MRI scan of the brain. Participants will be reimbursed for travel and related expenses. Families of children at high risk for developing symptoms of autism will receive assistance with referrals for local services. check if data repository is in the papers
Proper citation: IBIS Network (RRID:SCR_017399) Copy
http://www.brainimagelibrary.org
Repository for confocal microscopy brain imaging data. Data archives that have been established by BRAIN Initiative Data Sharing. National public resource enabling researchers to deposit, analyze, mine, share and interact with large brain image datasets. Operated as partnership between Biomedical Applications Group at Pittsburgh Supercomputing Center, Center for Biological Imaging at University of Pittsburgh and Molecular Biosensor and Imaging Center at Carnegie Mellon University. Provides persistent centralized repository for brain microscopy data.
Proper citation: Brain Image Library (RRID:SCR_017272) Copy
https://github.com/Mark-Kramer/Seizure-Waves
Analysis and modeling code for waves of seizure activity.
Proper citation: Seizure-Waves (RRID:SCR_017455) Copy
Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems.
Proper citation: EBRAINS Knowledge Graph (RRID:SCR_017612) Copy
https://www.leicabiosystems.com/histology-equipment/cryostats/leica-cm1520/
Cryostat for routine histology and cryosectioning including critical applications such as Mohs surgery. Brain sectioning. Actively cooled quick freezing shelf with defrost function and refrigeration system are provided.
Proper citation: Leica CM1520 Cryostat (RRID:SCR_017543) Copy
A web-based neuroimaging and neuropsychology software suite that offers versatile, automatable data upload/import/entry options, rapid and secure sharing of data among PIs, querying and export all data, real-time reporting, and HIPAA and IRB compliant study-management tools suitable to large institutions as well as smaller scale neuroscience and neuropsychology researchers. COINS manages over over 400 studies, more than 265,000 clinical neuropsychological assessments, and 26,000 MRI, EEG, and MEG scan sessions collected from 18,000 participants at over ten institutions on topics related to the brain and behavior. As neuroimaging research continues to grow, dynamic neuroinformatics systems are necessary to store, retrieve, mine and share the massive amounts of data. The Collaborative Informatics and Neuroimaging Suite (COINS) has been created to facilitate communication and cultivate a data community. This tool suite offers versatile data upload/import/entry options, rapid and secure sharing of data among PIs, querying of data types and assessments, real-time reporting, and study-management tools suitable to large institutions as well as smaller scale researchers. It manages studies and their data at the Mind Research Network, the Nathan Kline Institute, University of Colorado Boulder, the Olin Neuropsychiatry Research Center (at) Hartford Hospital, and others. COINS is dynamic and evolves as the neuroimaging field grows. COINS consists of the following collaboration-centric tools: * Subject and Study Management: MICIS (Medical Imaging Computer Information System) is a centralized PostgreSQL-based web application that implements best practices for participant enrollment and management. Research site administrators can easily create and manage studies, as well as generate reports useful for reporting to funding agencies. * Scan Data Collection: An automated DICOM receiver collects, archives, and imports imaging data into the file system and COINS, requiring no user intervention. The database also offers scan annotation and behavioral data management, radiology review event reports, and scan time billing. * Assessment Data Collection: Clinical data gathered from interviews, questionnaires, and neuropsychological tests are entered into COINS through the web application called Assessment Manager (ASMT). ASMT's intuitive design allows users to start data collection with little or no training. ASMT offers several options for data collection/entry: dual data entry, for paper assessments, the Participant Portal, an online tool that allows subjects to fill out questionnaires, and Tablet entry, an offline data entry tool. * Data Sharing: De-identified neuroimaging datasets with associated clinical-data, cognitive-data, and associated meta-data are available through the COINS Data Exchange tool. The Data Exchange is an interface that allows investigators to request and share data. It also tracks data requests and keeps an inventory of data that has already been shared between users. Once requests for data have been approved, investigators can download the data directly from COINS.
Proper citation: Mind Research Network - COINS (RRID:SCR_000805) Copy
https://github.com/NOCIONS/letswave6/wiki/Download-and-setup
Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals.
Proper citation: Letswave (RRID:SCR_016414) Copy
http://www.nitrc.org/projects/nutil/
Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems.
Proper citation: Nutil - Neuroimaging utilities (RRID:SCR_017183) Copy
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