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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CMAP Resource Report Resource Website 100+ mentions |
CMAP (RRID:SCR_009034) | CMap | data processing software, software application, data analysis software, software resource | Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, unix, solaris, freebsd, linux, sequence, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite has parent organization: Generic Model Organism Database Project works with: Drug Gene Budger |
PMID:19648141 | GNU General Public License | nlx_153998, OMICS_00933 | https://sourceforge.net/projects/gmod/files/cmap/ | http://www.gmod.org/cmap/, http://gmod.org/wiki/Cmap | SCR_009034 | , GMOD Comparative Mapping (CMap) tool, Comparative Mapping tool, genetic and comparative maps | 2026-08-15 11:23:53 | 417 | ||||
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DNAzip Resource Report Resource Website 1+ mentions |
DNAzip (RRID:SCR_009032) | DNAzip | software resource | DNA sequence compression using a reference genome. |
is listed by: OMICtools has parent organization: University of California at Irvine; California; USA |
OMICS_00954 | SCR_009032 | 2026-08-15 11:23:46 | 1 | ||||||||||
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Index Fungorum Resource Report Resource Website 100+ mentions |
Index Fungorum (RRID:SCR_008975) | Index Fungorum | database, data repository, storage service resource, web service, data access protocol, data or information resource, software resource, service resource | International project database indexing all formal names (scientific names) in the Fungi Kingdom. Index Fungorum provides Life Science Identifiers (LSIDs) for records in its database and indicates the status of a name. In the returns from the search page a currently correct name is indicated in green, while others are in blue (a few, aberrant usages of names are indicated in red). All names are linked to pages giving the correct name, with lists of synonyms. Index Fungorum provides a SOAP protocol web service for searching its database and retrieving records. A WSDL file describing the services is available. (adapted from Wikipedia) | life science identifier, nomenclature, scientific name, FASEB list | is related to: MycoBank | Free, Non-commercial, Acknowledgement required, The community can contribute to this resource | nlx_152066 | SCR_008975 | 2026-08-15 11:23:55 | 181 | ||||||||
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NetOGlyc Resource Report Resource Website 500+ mentions |
NetOGlyc (RRID:SCR_009026) | NetOGlyc | production service resource, data analysis service, software application, software resource, service resource, analysis service resource | Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins. | neural network, predict, mucin, galnac, o-glycosylation site, protein, o-glycosylation, glycoprotein, o-glycoproteome, glycosite, proteome, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: CBS Prediction Servers |
PMID:23584533 | Acknowledgement requested | nlx_153864, biotools:netoglyc | https://bio.tools/netoglyc | SCR_009026 | NetOGlyc Server | 2026-08-15 11:23:53 | 643 | |||||
|
CAMARADES Protocols for Systematic Reviews of Animal Studies Resource Report Resource Website 1+ mentions |
CAMARADES Protocols for Systematic Reviews of Animal Studies (RRID:SCR_008970) | CAMARADES | data repository, experimental protocol, storage service resource, data or information resource, service resource, narrative resource | A site for sharing meta-analysis protocols for translational neuroscience research. Protocols for systematic review of in vivo data modelling human neurological disease. Making the protocol for your systematic review available to the community has a number of benefits; it provides evidence that prespecified analyses were indeed prespecified; allows others to comment on your approach; provides examples for others planning such reviews; and can help you identify if other reviews in similar areas are already in progress. This site was created to foster collaboration. | animal model, in vivo, translational research, meta analysis, stroke | has parent organization: University of Edinburgh; Scotland; United Kingdom | Neurological disease | nlx_152037 | SCR_008970 | Protocols for Systematic Reviews of Animal Studies | 2026-08-15 11:23:53 | 3 | |||||||
|
Biodiversity Heritage Library Resource Report Resource Website 1+ mentions |
Biodiversity Heritage Library (RRID:SCR_008969) | BHL | data or information resource, bibliography, database | Collection of legacy literature in biodiversity assembled by an international consortium of natural history and botanical libraries. It also serves as the foundational literature component of the Encyclopedia of Life. Browse by author, title, subject, collection, map, year, language, and contributor. Taxonomic search using UBio. Also supports data export and a variety of machine interfaces. | literature, taxonomy, scientific illustration, botany, biology, natural history, biodiversity, extinct animal, herbaria, ecology, botanical library, extinct |
is listed by: re3data.org is related to: EOL - Encyclopedia of Life |
MacArthur Foundation via the Encyclopedia of Life ; Gordon and Betty Moore Foundation ; Richard Lounsbery Foundation ; Institute of Museum and Library Services ; Smithsonian Institution ; Atherton Seidell Endowment Fund |
If files in, Public domain, Acknowledgement requested, If files are from a copyrighted work for which we have obtained permission, Then all of the files on http://www.biodiversitylibrary.org are, Creative Commons Attribution-NonCommercial-ShareAlike License, v3, If a work in the BHL is published in 1923 or after, The work may be in copyright. More at, Http://biodivlib.wikispaces.com/Licensing+and+Copyright | nlx_152035 | SCR_008969 | Biodiversity Library | 2026-08-15 11:23:45 | 5 | ||||||
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Slicer3 Module Rician noise filter Resource Report Resource Website 1+ mentions |
Slicer3 Module Rician noise filter (RRID:SCR_009614) | Slicer3:Module:Rician Noise Removal | data processing software, software application, image processing software, software resource | Two Slicer3 modules removing rician noise in diffusion tensor MRI | c++, console (text based), linux, magnetic resonance, posix/unix-like, diffusion mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: 3D Slicer |
NIH Roadmap for Medical Research ; NIBIB U54 EB005149; NCRR 2-P41-RR12553-07 |
PMID:17354881 | GNU General Public License | nlx_155836 | http://www.nitrc.org/projects/dtiricianrem | SCR_009614 | 2026-08-15 11:23:49 | 1 | |||||
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GIFTI Resource Report Resource Website 10+ mentions |
GIFTI (RRID:SCR_009579) | GIfTI | data or information resource, software resource, standard specification, narrative resource | Geometry format under the Neuroimaging Informatics Technology Initiative (NIfTI). Basically, it is the surface-file format complement to the NIfTI volume-file format .nii. Programs which support the Gifti format, intended to allow exchange of each others surface files, include: Freesurfer, Caret, BrainVISA, Brain Voyager, CRkit, VisTrails and AFNI. | algorithm or reusable library, c, computational neuroscience, information resource, magnetic resonance, os independent, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Neuroimaging Informatics Technology Initiative |
nlx_155761 | SCR_009579 | 2026-08-15 11:23:49 | 30 | |||||||||
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NeuroWeb - NeuroImaging Database Resource Report Resource Website 1+ mentions |
NeuroWeb - NeuroImaging Database (RRID:SCR_009610) | NeuroWeb | software resource | Infrastructure for data aggregation, processing, and management in multi-dimensional medical imaging research (i.e., MRI, CT, PET). NeuroWeb is designed for rapid deployment on a small/moderate scale with limited hardware. | computed tomography, magnetic resonance, pet, spect, mri, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155829 | http://www.nitrc.org/projects/neuroweb | SCR_009610 | 2026-08-15 11:23:49 | 1 | ||||||||
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ERPLAB Resource Report Resource Website 100+ mentions |
ERPLAB (RRID:SCR_009574) | ERPLAB | data processing software, software application, data analysis software, software resource | A set of open source, freely available Matlab routines for analyzing Event Related Potential (ERP) data. It is tightly integrated with the EEGLAB Toolbox. ERPLAB routines can be accessed from the Matlab command window and from Matlab scripts in addition to being accessed from the EEGLAB GUI. Consequently, ERPLAB provides the ease of learning of a GUI-based system but also provides the power and flexibility of a scripted system.The development of ERPLAB Toolbox is being coordinated by Steve Luck and Javier Lopez-Calderon at the UC-Davis Center for Mind & Brain, with financial support from NIMH. | anova, eeg, meg, electrocorticography, event related potential, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Bioelectromagnetism Matlab Toolbox has parent organization: University of California at Davis; California; USA |
NIMH | GNU General Public License | nlx_155754 | http://www.nitrc.org/projects/erplab | SCR_009574 | ERPLAB Toolbox | 2026-08-15 11:23:49 | 463 | |||||
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EMSE Suite Resource Report Resource Website 10+ mentions |
EMSE Suite (RRID:SCR_009571) | EMSE Suite | software toolkit, image analysis software, data processing software, software application, software resource | A technically supported modular platform for space-time-frequency analyses of EEG/MEG/ECoG integrated (optionally) with structural MRI and functional hemodynamic measures (fMRI and NIRS). The Locator module uses Polhemus devices to acquire 3D sensor coordinates. Data Editor provides pipelines of spatial and temporal filters, and easy-to-use event pipelines for conditional binning of time, frequency, and time-frequency data across participants, with group results. Coherence, phase synchronication, and quasi-causal information assess connectivity. Source Estimator enables modeling of discrete overdetermined and distributed underdetermined sources, and spatial filtering for 3D brain regions of interest. Statistical nonparametric mapping (SnPM) may be performed for all measures. MR Viewer and Image Processor comprise tools for BEM and FEM volume conductor models, using cortical source space models. See http://www.sourcesignal.com/Features_EMSE_550.pdf for details and a supported free trial. | application, eeg, meg, electrocorticography, eeg modeling, forward - inverse, modeling, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155751 | http://www.nitrc.org/projects/emse | SCR_009571 | 2026-08-15 11:23:56 | 10 | |||||||
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LONI Brain Parser Resource Report Resource Website 1+ mentions |
LONI Brain Parser (RRID:SCR_009572) | Brain Parser | image analysis software, data processing software, software application, software resource, segmentation software | Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest. | analyze, anatomic, application, c++, console (text based), labeling, linux, microsoft, magnetic resonance, posix/unix-like, region of interest, segmentation, sh/bash, unix shell, windows, windows nt/2000, windows vista, 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; NCRR U54 RR021813 |
GNU General Public License, LONI Software License | nlx_155783 | http://www.nitrc.org/projects/brainparser | SCR_009572 | BrainParser | 2026-08-15 11:23:59 | 3 | |||||
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MagVenture: MagPro Magnetic Stimulator Resource Report Resource Website 10+ mentions |
MagVenture: MagPro Magnetic Stimulator (RRID:SCR_009601) | MagPro | instrument resource | A complete line of non-invasive magnetic stimulation systems designed for clinical examinations and for research in the areas of neurophysiology, neurology, cognitive neuroscience, rehabilitation and psychiatry. | experiment control, hardware, magnetic resonance, response monitoring, stimulus presentation, clinical, neurophysiology, neurology, cognitive neuroscience, rehabilitation, psychiatry, instrument, equipment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is provided by: MagVenture |
Commercial license | nlx_155803 | http://www.nitrc.org/projects/magpro | SCR_009601 | MagPro Magnetic Stimulator (TMS) | 2026-08-15 11:23:59 | 10 | ||||||
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Mag Design and Engineering Resource Report Resource Website 1+ mentions |
Mag Design and Engineering (RRID:SCR_009600) | Mag Design & Engineering | commercial organization | A variety of MEG- and fMRI-compatible hardware for research use including typical response collection devices such as joysticks, response pads, mice, as well as stimulation devices such as vibrotactile stimulators, olfactometers, and pressure/force generators. The company also offers custom design and production services for many different applications. | mag, eeg, meg, electrocorticography, experiment control, hardware, magnetic resonance, optical imaging, physiological recording, response monitoring, stimulus presentation, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155802 | http://www.magconcept.com | SCR_009600 | 2026-08-15 11:23:56 | 6 | |||||||
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Rockland Download Link Script Resource Report Resource Website 1+ mentions |
Rockland Download Link Script (RRID:SCR_009513) | Rockland Download Link Script | software resource | Script which points browser to Nathan Kline Institute (NKI) Rockland Sample. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NKI/Rockland Sample |
Creative Commons License | nlx_155675 | SCR_009513 | 2026-08-15 11:23:48 | 1 | ||||||||
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Subject Order-Independent Group ICA Resource Report Resource Website 10+ mentions |
Subject Order-Independent Group ICA (RRID:SCR_009514) | SOI-GICA | software resource | While the traditional temporally concatenated Group ICA (TC-GICA) adopting three steps of PCA reduction, it could result in inconsistent and variable components when different subject orders were used, both for the group- and individual-level results. Such instability can further cause instable and thus unreliable statistical results. Subject Order-Independent Group ICA (SOI-GICA) aims to fix this problem by producing stable and reliable GICA results. For details please see the paper Subject Order-Independent Group ICA (SOI-GICA) for Functional MRI Data Analysis (Zhang et al., 2010, NeuroImage)(http://dx.doi.org/10.1016/j.neuroimage.2010.03.039). MICA is the toolbox inplemented SOI-GICA for convenience of usage. | analyze, gnome, independent component analysis, kde, linux, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, software, statistical operation, win32 (ms windows), windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:20338245 | GNU General Public License | nlx_155676 | SCR_009514 | 2026-08-15 11:23:55 | 18 | |||||||
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LIBEEP Resource Report Resource Website 1+ mentions |
LIBEEP (RRID:SCR_009591) | LIBEEP | software toolkit, software resource, software library | Software library that deals with reading and writing RIFF-format CNT/AVR-files. This file format is also called EEProbe data format, and is used in the software packages EEProbe, ASA, ASA-Lab, Cognitrace, eemagine EEG, Visor, by ANT Neuro B.V., The Netherlands. The file format provides for storage of EEG/ERP/MEG data as 32-bit values, and includes a very efficient compression algorithm. Encoding/decoding from the compressed data is performed automatically through the LIBEEP interface functions. | eeg, meg, electrocorticography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Libeep EEGLAB plugin has parent organization: SourceForge |
GNU Lesser General Public License, Plus Addendum | nlx_155781 | http://www.nitrc.org/projects/libeep | SCR_009591 | LIBEEP library | 2026-08-15 11:23:49 | 1 | ||||||
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map3d Resource Report Resource Website 1+ mentions |
map3d (RRID:SCR_009628) | map3d | data processing software, data visualization software, software application, software resource | A scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models such as high resolution EEG, MEG, and ECG. | c++, eeg, meg, electrocorticography, forward - inverse, linux, macos, microsoft, modeling, posix/unix-like, visualization, win32 (ms windows), windows, windows 95/98/2000 |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
Map3d License | nlx_155857 | http://www.nitrc.org/projects/map3d | SCR_009628 | 2026-08-15 11:23:57 | 3 | ||||||
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Local Label Learning Segmentation Resource Report Resource Website 1+ mentions |
Local Label Learning Segmentation (RRID:SCR_009504) | LLL Segmentation | image analysis software, data processing software, software application, software resource, segmentation software | Software using a novel local label learning strategy to estimate the target image?s segmentation label using statistical machine learning techniques. They used a support vector machine (SVM) with a K nearest neighbor (KNN) based training sample selection strategy to learn a classifier for each of the target image voxel based on a training dataset consisting of its neighboring voxels in the atlases. Validation experiments on hippocampus segmentation of 117 MR images demonstrated that the method can produce segmentation results consistently better than state-of-the-art label fusion methods. | magnetic resonance, svm, segmentation, local label learning, multi-atlas based segmentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:24151008 | BSD License | nlx_155653 | SCR_009504 | Local Label Learning (LLL) Segmentation | 2026-08-15 11:23:57 | 1 | ||||||
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fMRI Grocer Resource Report Resource Website 1+ mentions |
fMRI Grocer (RRID:SCR_009622) | software toolkit, image analysis software, data processing software, software application, data analysis software, software resource | Software toolbox containing many kinds of kits that you may be interested in during fMRI data analysis. This toolbox is a homebrew kits built during practical ASL(arterial spin labeling) based Cerebral Blood Flow (CBF) data analysis. Meanwhile, this toolbox is also compatible with BOLD data analysis. Everyone would find something useful for their own data analysis! This toolbox is run and tested on SPM8 with MATLAB 7.6.0(R2008a) under the Linux OS. Theoretically, most of the functions (except the menu1&2 which are specially designed for the Batch Editor of SPM8) of this toolbox should be compatible with SPM5 and should also work smoothly under the Windows OS. Feel free to give feedback to authors if you encounter any bugs or problems. Senhua Zhu Center for functional Neuroimaging, University of Pennsylvania 3 W.Gates Bldg, 3400, Philadelphia, PA (19104), United States Email: [email protected] ; [email protected] QQ group number (QQ?): 60524357 Google group: https://groups.google.com/d/forum/fmri-grocer | magnetic resonance, cerebral blood flow, fmri, arterial spin labeling |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania; Philadelphia; USA |
Free, Available for download, Freely available, | nlx_155847 | http://code.google.com/p/fmrigrocer/ | SCR_009622 | 2026-08-15 11:23:49 | 1 |
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