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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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BluePyOpt Resource Report Resource Website 10+ mentions |
BluePyOpt (RRID:SCR_014753) | simulation software, software application, software resource | An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms. | python, optimization, framework, library, brain, model parameter, neuroscience | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | European Union FP7 604102 | Acknowledgement requested | http://www.nitrc.org/projects/bluepyopt/ | SCR_014753 | SciCrunch Registry | Blue Brain Python Optimization Library, Blue Brain Python Optimisation Library (BluePyOpt), Blue Brain Python Optimisation Library | 2026-10-31 12:16:17 | 31 | |||||||
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openMINDS controlledTerms metadata model Resource Report Resource Website |
openMINDS controlledTerms metadata model (RRID:SCR_026247) | openMINDS_controlledTerms, openMINDS controlledTerms | data or information resource, narrative resource, software resource, source code, standard specification | Software repository is part of open Metadata Initiative for Neuroscience Data Structures (openMINDS). It contains the schema-templates as well as corresponding terminologies (as JSON-LDs) for all terms that are defined and maintained centrally in this repository. Where applicable, the defined terms are connected to a matching ontological term. Schemas of openMINDS_core as well as openMINDS_SANDS reference to these controlled terms. | metadata schema, graph metadata model, schema-templates, corresponding terminologies, |
is related to: openMINDS metadata framework is related to: openMINDS SANDS metadata model is related to: EBRAINS |
European Union’s Horizon 2020 Framework Programme for Research and Innovation - Human Brain Project SGA1 720270; European Union’s Horizon 2020 Framework Programme for Research and Innovation - Human Brain Project SGA2 785907; European Union’s Horizon 2020 Framework Programme for Research and Innovation - Human Brain Project SGA3 945539; European Union’s Research and Innovation Program Horizon Europe - EBRAINS 2.0 101147319; Helmholtz International BigBrain Analytics and Learning Laboratory (HIBALL) |
Free, Available for download, Freely available | https://openminds-documentation.readthedocs.io/en/latest/schema_specifications/controlledTerms.html | SCR_026247 | SciCrunch Registry | 2026-10-31 12:24:04 | 0 | |||||||
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Gannet Resource Report Resource Website 100+ mentions |
Gannet (RRID:SCR_016049) | data analysis software, data processing software, software application, software resource, source code | Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data. | mri, magnetic resonance spectroscopy, mrs, batch, analysis, matlab, neuroscience, brain | PMID:25548816 | https://www.nitrc.org/projects/gannet/, https://markmikkelsen.github.io/Gannet-docs/index.html | http://www.gabamrs.com/about | SCR_016049 | SciCrunch Registry | Gannet - Batch Analysis of Edited Magnetic Resonance Spectroscopy (MRS) Data | 2026-10-31 12:16:38 | 167 | ||||||||
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BRAINSMush Resource Report Resource Website |
BRAINSMush (RRID:SCR_009485) | BRAINSMush | data processing software, image analysis software, segmentation software, software application, software resource | Tool to generate brain volume mask from input of T1 and T2-weighted images alongside a region of interest brain mask. This volume mask omits dura, skull, eyes, etc. The program is built upon ITK and uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. | analyze, application, bsd license, bsd/mit-style open source license, c++, console (text based), dicom, magnetic resonance, nifti, nrrd, segmentation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155702 | http://www.nitrc.org/projects/brainsmush | SCR_009485 | SciCrunch Registry | 2026-10-31 12:14:57 | 0 | |||||||
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PreSurgMapp Resource Report Resource Website 1+ mentions |
PreSurgMapp (RRID:SCR_014427) | software resource, software toolkit | A MATLAB toolbox for processing the functional areas of the brain using multi-modal fMRI data for pre-surgical mapping. It is composed of three types of individual-level ICA analyses for user use. Traditional ICA (task) can be used for task fMRI. Either Traditional ICA (rest) or ICA with DICI (rest) can be used for rs-fMRI. Traditional ICA (rest) is designed for users who already have a hypothesis of the pattern of the target component and want to have manually set components by themselves. ICA with DICI (rest) is completely automatic, given that the user provides a template (provided). The software utilizes an automatic component identification method that is based on the discriminatory-index. All the components from multiple ICA runs with multiple component settings are ranked and compiled. | fmri, ica, dici, rs-fmri, dici, matlab, software toolkit, toolbox, multi modal, pre surgical, map | uses: MATLAB | Open source | http://restfmri.net/forum/node/2382. | SCR_014427 | SciCrunch Registry | 2026-10-31 12:21:28 | 4 | |||||||||
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Letswave Resource Report Resource Website 10+ mentions |
Letswave (RRID:SCR_016414) | data processing software, data visualization software, software application, software resource, software toolkit | Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals. | process, visualise, EEG, MEG, data, neurophysiological, signal, brain, neuroscience | is related to: MATLAB | Free, Available for download, Freely available | https://www.letswave.org/ | SCR_016414 | SciCrunch Registry | 2026-10-31 12:18:32 | 27 | |||||||||
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AutoStereota Resource Report Resource Website 1+ mentions |
AutoStereota (RRID:SCR_022330) | data or information resource, instrument resource, portal, project portal | Automated surgical instrument for brain tissue aspiration.Instrument for microendoscope implantation. Utilizes robotic control of needle connected to vacuum pump to aspirate brain tissue. System consists of robotic surgical instrument built around commercially available stereotaxic instrument and open source MATLAB-based GUI for control. | OpenBehavior, Instrument, brain tissue aspiration, microendoscope implantation | is listed by: OpenBehavior | DOI:10.1016/j.jneumeth.2018.10.013 | Free, Freely available | https://github.com/liang-bo/AutoStereota | SCR_022330 | SciCrunch Registry | 2026-10-31 12:18:45 | 3 | ||||||||
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Brainstorm Resource Report Resource Website 500+ mentions |
Brainstorm (RRID:SCR_001761) | Brainstorm | data analysis software, data processing software, data visualization software, software application, software resource | Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis. | MEG, EEG, data, magnetoencephalography, electroencephalography, visualization, processing, analysis, brain, recording, fNIRS, ECoG, electrophysiology |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: OpenMEEG is related to: Open MEG Archive is related to: MATLAB has parent organization: University of Southern California; Los Angeles; USA |
CNRS ; McGill University ; NIBIB R01 EB000473; NIBIB R01 EB002010; NIBIB R01 EB009048; NIBIB R01 EB026299 |
PMID:21584256 | Free, Available for download, Freely available | nif-0000-10267 | http://www.nitrc.org/projects/bst, https://github.com/brainstorm-tools/brainstorm3 | SCR_001761 | SciCrunch Registry | brainstorm3 | 2026-10-31 12:12:56 | 622 | ||||
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Cellarium Resource Report Resource Website 1+ mentions |
Cellarium (RRID:SCR_025438) | software resource | Software platform to annotate cell types. | machine learning open source software, infrastructure, annotate cell types, |
is used by: BRAIN Initiative Cell Atlas Network has parent organization: Broad Institute |
NIH | Free, Freely available | https://github.com/10XGenomics/cell-annotation-service-client | SCR_025438 | SciCrunch Registry | 2026-10-31 12:23:34 | 1 | ||||||||
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Eelbrain Resource Report Resource Website 10+ mentions |
Eelbrain (RRID:SCR_014661) | data analysis software, data processing software, software application, software resource | Statistical analysis toolbox for MEG and EEG. There are three primary data-objects: Factor for categorical variables, Var for scalar variables, and NDVar for multidimensional data. Factor is a container for one-dimensional, categorial data – each case is described by a string label. Var is a container to associate one-dimensional numpy.ndarray objects with a name. NDVars offer numpy functionality that takes into account the dimensions. There is also a Dataset class which acts as a vessel for variable objects (Factor, Var and NDVar) describing the same cases. | statistical analysis, analysis toolbox, electrical brain activity, meg, eeg | is hosted by: GitHub | NYU Abu Dhabi Institute G1001 | Open source, Acknowledgement requested | https://github.com/christianbrodbeck/Eelbrain | SCR_014661 | SciCrunch Registry | 2026-10-31 12:16:18 | 14 | ||||||||
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nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data. | model, modelling, python, neuroelectrophysiology, object, neuroimaging, analysis, neurophysiology, electrophysiology, BRAIN Initiative | is recommended by: BRAIN Initiative | Human Frontiers Science Program RGY0088; NSF CBET-1351692; NSF IOS-1550994 |
Free, Available for download, Freely available | SCR_016209 | SciCrunch Registry | Nelpy (Neuroelectrophysiology) | 2026-10-31 12:16:33 | 3 | ||||||||
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3D Slicer Resource Report Resource Website 1000+ mentions |
3D Slicer (RRID:SCR_005619) | Slicer | data processing software, data visualization software, image analysis software, software application, software resource | A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl. | birn, diffusion, functional, na-mic (ncbc), nifti-1 support, registration, segmentation, visualization, volume, warping |
uses: 3DSlicerLupusLesionModule uses: ShapePopulationViewer uses: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI uses: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Slicer3 Example Modules is related to: Stereoscopic Atlas of Intrinsic Brain Networks is related to: VMTK in 3D Slicer is related to: Diffusion Tractography with Kalman Filter is related to: Fast Nonlocal Means for MRI denoising is related to: SpineSegmentation module for 3DSlicer is related to: BioImage Suite is related to: NA-MIC Kit is related to: Hammer And WML Modules for 3D Slicer is related to: ABC (Atlas Based Classification) is related to: ARCTIC is related to: Finsler tractography module for Slicer is related to: GAMBIT is related to: GPU based affine registration is related to: GTRACT is related to: LEAD-DBS has parent organization: Harvard University; Cambridge; United States is parent organization of: Level-set Segmentation for Slicer3 is parent organization of: Slicer3 Module Rician noise filter has plug in: MultiXplore works with: UManitoba - JHU Functionally Defined Human White Matter Atlas works with: SlicerMorph |
NIH ; NCRR ; NIBIB ; NCI ; US Army ; Telemedicine and Advanced Technology Research Center |
3D Slicer License | nif-0000-00256 | http://www.nitrc.org/projects/slicer | SCR_005619 | SciCrunch Registry | Slicer, 3D Slicer: A multi-platform free and open source software package for visualization and medical image computing, 3D Slicer, 3DSlicer | 2026-10-31 12:14:17 | 3187 | |||||
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spm_auto_reorient_coregister Resource Report Resource Website |
spm_auto_reorient_coregister (RRID:SCR_017281) | software resource, software toolkit | Open source cross platform for automatic AC-PC realignment, reorientation and coregistration robust to brain damage in Statistical Parametric Mapping. Set of routines to perform auto reorient and auto coregistration in toolbox SPM12. | Nifti Libraries, NeuroImaging, MRI, MRI 3D image, reorientation, coregistration, statistical, parametric, mapping | works with: SPM | FNRS 1124417F | Free, Available for download, Freely available | SCR_017281 | SciCrunch Registry | 2026-10-31 12:21:32 | 0 | |||||||||
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BehaviorDEPOT Resource Report Resource Website 1+ mentions |
BehaviorDEPOT (RRID:SCR_023602) | software resource, source code | Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs. | OpenBehavior, automated behavioral detection, markerless pose tracking, detect frame by frame behavior, video time series, kinematic and postural statistics, |
is listed by: OpenBehavior is related to: SLEAP, LEAP and MotionMapper project works with: DeepLabCut |
Brain and Behavior Research Foundation ; Brain Research Foundation ; NIMH K01MH116264; NIMH K08MH116125; NIMH T32MH073526; NSF ; Simonsen Foundation ; Whitehall Foundation |
PMID:35997072 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/behaviordepot/ | SCR_023602 | SciCrunch Registry | 2026-10-31 12:23:13 | 2 | |||||||
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EEGsynth Resource Report Resource Website 1+ mentions |
EEGsynth (RRID:SCR_018732) | software application, software resource | Open source Python codebase that provides real-time interface between open-hardware devices for electrophysiological recordings like EEG, EMG, and ECG, and analog and digital devices like MIDI, OSC, and analog synthesizers. This allows one to use electrical brain/body activity to flexibly control devices in real-time. | Codebase, electrophysiological recording, interface, analog, digital device, analog synthesizer, device control, electrical brain activity, EEG, EMG, ECG, BCI, Neurofeedback, Biofeedback, Music, MIDI, OSC, Python | Free, Freely available | https://www.eegsynth.org, http://pypi.org/project/eegsynth/ | SCR_018732 | SciCrunch Registry | 2026-10-31 12:21:34 | 2 | ||||||||||
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Attys project Resource Report Resource Website |
Attys project (RRID:SCR_021461) | data or information resource, instrument resource, portal, project portal | Portal related to biomedical signals.Provides wearable data acquisition device with special focus on biomedical signals such as heart activity (ECG), muscle activity (EMG) and brain activity (EEG).Open source high precision bluetooth data acquisition device. | Biomedical signals acquire, heart activity data acquire, muscle activity data acquire, brain activity data acquire, data acquisition device, bluetooth data acquisition device, OpenBehavior, Instrument | is listed by: OpenBehavior | Free, Freely available | SCR_021461 | SciCrunch Registry | Attys | 2026-10-31 12:18:18 | 0 | |||||||||
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TD_Drive Resource Report Resource Website |
TD_Drive (RRID:SCR_025672) | instrument resource, software resource, source code | Parametric, open-source implant for multi-area electrophysiological recordings in behaving and sleeping rats. 3D-printable implant for rats, capable of symmetric, bilateral wire electrode recordings, currently in up to six distributed brain areas simultaneously. | OpenBehavior, 3D-printable implant, implant, device, multi-area electrophysiological recordings, behaving and sleeping rats, | is listed by: OpenBehavior | Dutch Research Council | PMID:38738884 | https://edspace.american.edu/openbehavior/project/tddrive/ | SCR_025672 | SciCrunch Registry | TD Drive, The TD Drive | 2026-10-31 12:23:41 | 0 | |||||||
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iELVis Resource Report Resource Website 10+ mentions |
iELVis (RRID:SCR_016109) | data processing software, data visualization software, software application, software resource | 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. | electrode, stimulus, visualization, brain, neuroimaging, intracranial, localization, anatomy, functional, BRAIN Initiative | is recommended by: BRAIN Initiative | Natural Sciences and Engineering Research Council of Canada RGPIN-2014-04465; Page and Otto Marx Jr. Foundation ; Swiss National Science Foundation P300P3_148388; Swiss National Science Foundation PBGEP3_139829 |
PMID:28192130 | Open source, Free, Available for download | https://github.com/iELVis/iELVis | SCR_016109 | SciCrunch Registry | iELVis (intracranial electrode visualization), Intracranial ELectrode VISualization | 2026-10-31 12:16:40 | 47 | ||||||
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University College London Sainsbury Wellcome Centre Advanced Microscopy Core Facility Resource Report Resource Website |
University College London Sainsbury Wellcome Centre Advanced Microscopy Core Facility (RRID:SCR_029090) | access service resource, core facility, service resource | Core offers imaging services including design, build, upgrade, and repair optical systems. Provides high-throughput, automated, and custom-built imaging infrastructure and open-source optical tools for neuroscience and biological research. Services include Automated Whole-Brain Imaging, Histology and Spatial Transcriptomics, In-Vivo Microscopy Technical Services. | ABRF, imaging services, custom built imaging infrastructure, |
is listed by: ABRF CoreMarketplace has parent organization: University College London; London; United Kingdom |
Open | ABRF_6234 | https://coremarketplace.org/RRID:SCR_029090/?citation=1 | SCR_029090 | SciCrunch Registry | University College London Sainsbury Wellcome Centre Advanced Microscopy Facility, SWC Advanced Microscopy Facility | 2026-10-31 12:25:08 | 0 | |||||||
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PetaVision Resource Report Resource Website |
PetaVision (RRID:SCR_017451) | OpenPV | simulation software, software application, software resource | Open source software neural simulation toolbox. C++ library for designing and deploying large scale neurally inspired computational models. Object oriented neural simulation toolbox optimized for high performance multi core, multi node computer architectures. | Neural, simulation, computational, model, object, oriented, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1734980 | Free, Available for download, Freely available | http://petavision.github.io/ | SCR_017451 | SciCrunch Registry | 2026-10-31 12:18:40 | 0 |
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