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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
https://doi.org/10.1016/j.neuroimage.2018.07.046
Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions.
Proper citation: nonparametricGGC_toolbox (RRID:SCR_016539) 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
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
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
Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.
Proper citation: BECA (RRID:SCR_015846) Copy
Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains.
Proper citation: BICCN (RRID:SCR_015820) Copy
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
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
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
Consortium studying the regulation and alternative splicing of gene expression in multiple tissues from human brains. The UKBEC dataset comprises of brains from individuals free of neurodegenerative disorders.
Proper citation: UK Brain Expression Consortium (RRID:SCR_015889) 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://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
https://github.com/Mark-Kramer/Seizure-Waves
Analysis and modeling code for waves of seizure activity.
Proper citation: Seizure-Waves (RRID:SCR_017455) 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
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