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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Synapse Web Reconstruct Resource Report Resource Website 50+ mentions |
Synapse Web Reconstruct (RRID:SCR_002716) | Reconstruct | image analysis software, software application, data processing software, software resource | A Windows (Win32) software application for montaging, aligning, tracing, measuring, and reconstructing objects from serial microscopic section images. The software is designed for microscopy in which section resolution is much less than section thickness, such as transmitted electron microscopy (EM) where the resolution is a few nanometers while the section thickness is many tens of nanometers. Reconstruct can easily handle series with hundreds of very large, high-resolution section images. It facilitates image cropping, scaling and alignment. Multiple images can be placed side-by-side to make a montage of a section from a mosaic of images. The alignment of adjacent sections can be rapidly compared by either blending the two sections or by flickering between them. Sections can be moved while blended. Reconstruct aids in the calibration of image size. Images taken at different magnifications can be combined, calibrated and aligned. Tools for tracing and editing of objects on sections are provided. Objects can be surfaced from the traces and previewed in an OpenGL-based 3D scene window. The 3D scene can be saved as a bitmap or as a VRML file. | electron microscopy, align, alignment, calibrate, image cropping, measure, microscopy, montage, reconstruct, scale, serial section image, trace, image, crop | has parent organization: University of Texas at Austin; Texas; USA | NICHD P30 HD18655; NIBIB R01 EB 002170 |
Free, Available for download, Freely available | nif-0000-23420 | SCR_002716 | 2026-02-17 10:00:02 | 73 | |||||||
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LONI Inspector Resource Report Resource Website 1+ mentions |
LONI Inspector (RRID:SCR_004923) | LONI Inspector | software application, data processing software, software resource | A Java application for reading, displaying, searching, comparing, and exporting metadata from medical image files: AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI. | analyze, dicom, java, minc, magnetic resonance, nifti, os independent, win32 (ms windows), workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
LONI Software License | nlx_155785 | http://www.nitrc.org/projects/inspector | http://www.loni.ucla.edu/Software/LONI-Inspector | SCR_004923 | 2026-02-17 10:00:51 | 3 | |||||
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Neuroscience Gateway Resource Report Resource Website 10+ mentions |
Neuroscience Gateway (RRID:SCR_008915) | NSG | data or information resource, project portal, portal, software resource | Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists. | Large, scale, modeling, data, computing, neuroscience, neuron, BRAIN Initiative |
is recommended by: BRAIN Initiative lists: ModelRun is related to: XSEDE - Extreme Science and Engineering Discovery Environment is related to: NEURON is related to: GENESIS Neural Database and Modelers Workspace has parent organization: San Diego Supercomputer Center has parent organization: Neuroscience Information Framework has parent organization: Yale School of Medicine; Connecticut; USA |
NSF 1458840; NSF 1458495; BBSRC N005236; NIBIB R01 EB023297; NSF 1339856; NSF 1146949 |
Free, Freely available | nlx_151553, SCR_015767 | http://www.nitrc.org/projects/nsg/ | SCR_008915 | Neuroscience Gateway - A Portal for Computational Neuroscience, Neuroscience Gateway, Neuroscience Gateway (NSG) Portal | 2026-02-17 10:01:19 | 23 | |||||
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Brain Computer Interface 2000 Software Package Resource Report Resource Website 100+ mentions |
Brain Computer Interface 2000 Software Package (RRID:SCR_007346) | software application, data processing software, software resource | BCI2000 is a general-purpose system for brain-computer interface (BCI) and adaptive neurotechnology research. It can also be used for data acquisition, stimulus presentation, and brain monitoring applications. The mission of the BCI2000 project is to facilitate research and applications in the areas described. Their vision is that BCI2000 will become a widely used software tool for diverse areas of real-time biosignal processing. In order to achieve this vision, BCI2000 system is available for free for non-profit research and educational purposes. BCI2000 supports a variety of data acquisition systems, brain signals, and study/feedback paradigms. During operation, BCI2000 stores data in a common format (BCI2000 native or GDF), along with all relevant event markers and information about system configuration. BCI2000 also includes several tools for data import/conversion (e.g., a routine to load BCI2000 data files directly into Matlab) and export facilities into ASCII. BCI2000 also facilitates interactions with other software. For example, Matlab scripts can be executed in real-time from within BCI2000, or BCI2000 filters can be compiled to execute as stand-alone programs. Furthermore, a simple network-based interface allows for interactions with external programs written in any programming language. For example, a robotic arm application that is external to BCI2000 may be controlled in real time based on brain signals processed by BCI2000, or BCI2000 may use and store along with brain signals behavioral-based inputs such as eye-tracker coordinates. Because it is based on a framework whose services can support any BCI implementation, the use of BCI2000 provides maximum benefit to comprehensive research programs that operate multiple BCI2000 installations to collect data for a variety of studies. The most important benefits of the system in such situations are: - A Proven Solution - Facilitates Operation of Research Programs - Facilitates Deployment in Multiple Sites - Cross-Platform and Cross-Compiler Compatibility - Open Resource Sponsors: BCI2000 development is sponsored by NIH/NIBIB R01 and NIH/NINDS U24 grants. Keywords: General, Purpose, Systems, Brain, Computer, Interface, Research, Application, Brain, Diverse, Educational, Laboratory, Software, Network, Signals, Behavioral, Eye, Tracker, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institutes of Health |
NIBIB R01 EB026439; NINDS U24 NS109103; NIBIB P41 EB018783 |
nif-0000-00251 | http://www.nitrc.org/projects/bci2000 http://www.bci2000.org https://www.neurotechcenter.org/software |
SCR_007346 | BCI2000 | 2026-02-17 10:01:02 | 166 | ||||||||
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LONI Java Image I/O Plugins Resource Report Resource Website |
LONI Java Image I/O Plugins (RRID:SCR_008277) | software application, data processing software, software resource | Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.The plugins use Java Image I/O interfaces to read and write metadata and image data and can read and write AFNI, ANALYZE 7.5, DICOM, ECAT 7.2, GE 5.0, INTERFILE (including hrrt), MINC, NIFTI, and UCLA PACS file formats. All source code is provided and usage examples are included. | plugin, MRI, software, visualization, data processing |
is related to: Laboratory of Neuro Imaging has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Available for educational and research purposes only | nif-0000-23320 | SCR_008277 | 2026-02-17 10:01:06 | 0 | ||||||||
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Homer2 Resource Report Resource Website 100+ mentions |
Homer2 (RRID:SCR_009586) | image analysis software, software application, data processing software, software resource | Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data. | Analysis, optical, imaging, fnirs, map, brain, activation, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NIRx2nirs: A NIRx to .nirs data converter |
NIBIB EB025145; NIBIB R01 EB006385; NCRR P41 RR14075 |
Free, Available for download, Freely available | nlx_155773 | http://www.nitrc.org/projects/homer2 https://homer-fnirs.org/ |
SCR_009586 | HOMER1, Photon Migration Imaging toolbox | 2026-02-17 10:01:24 | 223 | ||||||
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TRACULA Resource Report Resource Website 10+ mentions |
TRACULA (RRID:SCR_013152) | TRACULA | software application, data processing software, software resource | Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons. | tractography, white matter tract, white matter pathway, diffusion weighted image, diffusion magnetic resonance imaging, white matter, brain, reconstruct, diffusion tensor imaging |
is related to: FreeSurfer has parent organization: Harvard Medical School; Massachusetts; USA |
Aging | NIH Blueprint for Neuroscience Research ; Ellison Medical Foundation ; NIBIB EB008129; NIMH U01-MH093765; NCRR P41-RR14075; NCRR U24-RR021382; NIBIB R01-EB006758; NIA R01-AG022381; National Center for Complementary and Alternative Medicine RC1-AT005728; NINDS R01-NS052585; NINDS R21-NS072652; NINDS R01-NS070963 |
PMID:22016733 | nlx_143919 | SCR_013152 | TRACULA - TRActs Constrained by UnderLying Anatomy, TRACULA: TRActs Constrained by UnderLying Anatomy, TRActs Constrained by UnderLying Anatomy | 2026-02-17 10:02:22 | 17 | |||||
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CAWorks Resource Report Resource Website 1+ mentions |
CAWorks (RRID:SCR_014185) | image analysis software, software application, data processing software, software resource | A software application developed to support computational anatomy and shape analysis. The capabilities of CAWorks include: interactive landmark placement to create segmentation (mask) of desired region of interest; specialized landmark placement plugins for subcortical structures such as hippocampus and amygdala; support for multiple Medical Imaging data formats, such as Nifti, Analyze, Freesurfer, DICOM and landmark data; Quadra Planar view visualization; and shape analysis plugin modules, such as Large Deformation Diffeomorphic Metric Mapping (LDDMM). Specific plugins are available for landmark placement of the hippocampus, amygdala and entorhinal cortex regions, as well as a browser plugin module for the Extensible Neuroimaging Archive Toolkit. | image analysis software, computational anatomy, shape analysis, plugin, subcortex, landmark placement |
is used by: Northwestern University Schizophrenia Data and Software Tool (NUSDAST) is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
NIMH 1R01 MH084803; NIBIB R01 EB008171; NIA 5U01AG033655; NCRR P41 RR015241; NIBIB R01 EB000975 |
Available to the research community | http://www.cis.jhu.edu/software/caworks/ | SCR_014185 | Computational Anatomy Works | 2026-02-17 10:02:31 | 1 | |||||||
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DRIFTER Resource Report Resource Website 10+ mentions |
DRIFTER (RRID:SCR_014937) | image analysis software, software application, data processing software, software resource | Model based Bayesian method for eliminating physiological noise from fMRI data. This algorithm uses image voxel analysis to isolate the cardiac and respiratory noise from the relevant data. | bayesian, physiological noise, fMRI, algorithm, cardiac, respiratory, image anaylsis, bold signal | has parent organization: Aalto University; Espoo; Finland | NICHD R01HD040712; NINDS R01NS037462; NINDS R01NS048279; NCR P41RR014075; NIMH R01MH083744; NIDCD R21DC010060; NIBIB R21EB007298; National Science Council Taiwan NSC 98-2320-B-002-004-MY3; National Science Council Taiwan NSC 100-2325-B-002-046; National Health Research Institute Taiwan NHRI-EX100-9715EC; Academy of Finland 124698; Academy of Finland 125349; Academy of Finland 127624; Academy of Finland 129670; Academy of Finland 218054; Academy of Finland 218248 |
PMID:22281675 | Free, Available for download, Acknowledgement requested | SCR_014937 | DRIFTER Toolbox | 2026-02-17 10:02:20 | 28 | |||||||
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Neural Ideal Resource Report Resource Website |
Neural Ideal (RRID:SCR_017448) | software application, data processing software, software resource | Software package for extracting neural activity codes. | Extracting, neural, activity, code, BRAIN Initiative |
is recommended by: BRAIN Initiative is related to: MATLAB |
NIBIB EB022862 | Free, Available for download, Freely available | SCR_017448 | 2026-02-17 10:03:14 | 0 | |||||||||
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Neuron Tools Resource Report Resource Website 1+ mentions |
Neuron Tools (RRID:SCR_017450) | software application, data processing software, software resource | Software tools for converting data files into persistence diagrams and distance matrices. | Converting, data, file, diagram, distance, matice, BRAIN Initiative | is recommended by: BRAIN Initiative | NIBIB EB022899 | Free, Available for download, Freely available | SCR_017450 | 2026-02-17 10:03:35 | 3 | |||||||||
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Archive of Data on Disability to Enable Policy (ADDEP) Resource Report Resource Website |
Archive of Data on Disability to Enable Policy (ADDEP) (RRID:SCR_016315) | ADDEP | data or information resource, service resource, data repository, storage service resource | Provides access to data including wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of Americans with Disabilities Act and other disability policies. | Data, access, disability | is recommended by: National Library of Medicine | NICHD ; NINDS ; NIBIB |
SCR_016315 | Archive of Data on Disability to Enable Policy | 2026-02-17 10:03:00 | 0 | ||||||||
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BpForms Resource Report Resource Website |
BpForms (RRID:SCR_018653) | data access protocol, web service, software toolkit, software resource | Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts. | Molecular structure description, DNA, RNA, protein, modification, epigenetics, transcriptomics, post transcriptional modification, post translational modification, bio.tools |
uses: BcForms is used by: ObjTables is used by: Datanator is listed by: Debian is listed by: bio.tools is related to: BcForms is related to: ObjTables |
NIBIB P41 EB023912; NSF 1649014; NIGMS R35 GM119771 |
PMID:32423472 | Free, Freely available | biotools:bpforms | https://bio.tools/bpforms | SCR_018653 | 2026-02-17 10:03:49 | 0 | ||||||
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ObjTables Resource Report Resource Website |
ObjTables (RRID:SCR_018652) | data management software, software application, data processing software, software resource, software toolkit | Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort. | Creating reusable dataset, combining spreadsheet with schema, spreadsheet, table, supplementary material, schema, object relational map, validation, bio.tools |
uses: BpForms uses: BcForms is listed by: bio.tools is listed by: Debian is related to: BpForms |
NIBIB P41 EB023912; NSF 1649014; NIGMS R35 GM119771 |
Free, Freely available | biotools:objtables | https://bio.tools/objtables | SCR_018652 | 2026-02-17 10:03:30 | 0 | |||||||
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datasets.datalad.org Resource Report Resource Website 1+ mentions |
datasets.datalad.org (RRID:SCR_019089) | storage service resource, data or information resource, service resource, data set, data repository | DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data. | Version control system, data distribution, super dataset, DataLad dataset, neural data | is related to: DataLad | NSF 1429999; NSF 1912266; NIBIB P41 EB019936 |
Free, Freely available | https://www.datalad.org/datasets.html | SCR_019089 | 2026-02-17 10:03:12 | 8 | ||||||||
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Mediation Analysis of Causality under Confounding Resource Report Resource Website |
Mediation Analysis of Causality under Confounding (RRID:SCR_017442) | MACC | data analysis software, software application, data processing software, software resource | Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method. | Casual, mediation, analysis, confounding, correlated, error, data, hierarchical, structure, parameter, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: CRAN |
NIBIB EB022911 | Free, Available for downloads, Freely available | SCR_017442 | Mediation Analysis of Causality under Confounding, macc | 2026-02-17 10:03:35 | 0 | |||||||
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ReproNim/containers Resource Report Resource Website 1+ mentions |
ReproNim/containers (RRID:SCR_018467) | narrative resource, workflow, data or information resource, portal, training material, software resource, software toolkit, knowledge environment resource | Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments. | Containerized environment, reproducible neuroimaging, ReproNim, neuroimaging, dataset, DataLad, imaging, data | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | NIBIB P41 EB019936; NSF 1429999; German Federal Ministry of Education and Research |
Free, Freely available | https://github.com/ReproNim/containers | SCR_018467 | 2026-02-17 10:03:46 | 1 | ||||||||
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GMA Resource Report Resource Website |
GMA (RRID:SCR_009212) | GMA | software application, time-series analysis software, data processing software, data analysis software, software resource | Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure. | Granger, meditation, analysis, time, series, level, GMA, model, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
NIBIB EB022911 | PMID:31070732 | Free, Available for download, Freely available | nlx_154361, biotools:GMA | https://github.com/chaoning/GMA https://bio.tools/GMA |
http://www.montana.edu/kalinowski/GMA/GMA_Home.htm | SCR_009212 | Granger Mediation Analysis | 2026-02-17 10:01:21 | 0 | |||
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Mango Resource Report Resource Website 100+ mentions |
Mango (RRID:SCR_009603) | Mango | data visualization software, software application, image processing software, data processing software, software resource, image analysis software | A viewer for medical research images that provides analysis tools and a user interface to navigate image volumes. There are three versions of Mango, each geared for a different platform: * Mango ? Desktop ? Mac OS X, Windows, and Linux * webMango ? Browser ? Safari, Firefox, Chrome, and Internet Explorer * iMango ? Mobile ? Apple iPad Key Features: * Built-in support for DICOM, NIFTI, Analyze, and NEMA-DES formats * Customizable: Create plugins, custom filters, color tables, file formats, and atlases * ROI Editing: Threshold and component-based tools for painting and tracing ROIs * Surface Rendering: Interactive surface models supporting cut planes and overlays * Image Registration: Semi-automatic image coregistration and manual transform editing * Image Stacking: Threshold and transparency-based image overlay stacking * Analysis: Histogram, cross-section, time-series analysis, image and ROI statistics * Processing: Kernel and rank filtering, arithmetic/logic image and ROI calculators | analyze, atlas application, console (text based), dicom, gifti, java, linux, macos, microsoft, magnetic resonance, nifti, os independent, platform, posix/unix-like, quantification, region of interest, registration, rendering, segmentation, spatial transformation, statistical operation, sunos/solaris, surface analysis, temporal transformation, visualization, volumetric analysis, web environment, win32 (ms windows), windows, windows vista, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA |
NIBIB P01-EB01955; NIBIB R01-EB015314-01a1; NIMH R01-MH074457 |
Free | nlx_155804 | http://www.nitrc.org/projects/mango | SCR_009603 | Multi-image Analysis GUI | 2026-02-17 10:01:31 | 461 | |||||
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iTools Resource Report Resource Website 10+ mentions |
iTools (RRID:SCR_009626) | iTools | data access protocol, storage service resource, data or information resource, database, service resource, software resource, web service, software repository, data repository | An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org). | computational neuroscience, data, experiment control, hardware, imaging genomics, information specification, java, loni pipeline, model, ontology, os independent, metadata |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: National Centers for Biomedical Computing has parent organization: Laboratory of Neuro Imaging |
NIH Roadmap for Medical Research ; NCRR U54-RR021813; NIDA U54-DA021519; NCI U54-CA121852; NHGRI U54-HG004028; NIGMS U54-GM072970; NIBIB U54-EB005149; NLM U54-LM008748 |
PMID:18509477 | GNU Lesser General Public License | nlx_155852 | http://www.nitrc.org/projects/itools http://www.loni.usc.edu/research/software |
http://itools.loni.ucla.edu/ | SCR_009626 | ITools Resourceome, NCBC iTools | 2026-02-17 10:01:25 | 45 |
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