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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Limelight Resource Report Resource Website 10+ mentions |
Limelight (RRID:SCR_014254) | data analysis software, data processing software, software application, time-series analysis software, resource, data acquisition software, software resource | A video tracking system designed for high-throughput behavioral experiments. LimeLight can track up to 4 arenas at once and can collect images at up to 30 frames per second for one animal or up to 8 frames per second when tracking 4 arenas at once. The tracking system has 2 different hardware configurations: the 1-camera system can be used to record 1 to 4 animals at once, while for multiple animals, each one is placed in a separate arena in one quadrant of the image. The software contains productivity features such as flexible arena setup, user-defined behavior scoring, stimulus control, and various analytical functions for quantifying behavior. The program is designed for experiments such as Open Field, Plus Maze, Radial Arm Maze, Zero Maze, Novel Object Recognition, Conditioned Place Preference, and Barnes Maze. | data acquisition software, time series analysis software, data analysis software, video tracking system, behavioral experiment, high throughput, hardware, instrument, equipment | is related to: FreezeFrame | Account required | SCR_014254 | 2026-08-13 09:28:59 | 17 | ||||||||||
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Lightweight Data Pipeline Resource Report Resource Website |
Lightweight Data Pipeline (RRID:SCR_014135) | workflow software, data processing software, software resource, software application | A lightweight framework for setting up dependency-driven processing pipelines. The tool is essentially a configurable shell script (sh/bash), which can be included in other scripts and primarily provides a small number of utility functions for dependency checking and NFS-safe file locking for cluster processing. | workflow software, framework, processing pipeline, configurable shell script, cluster processing |
is used by: NCANDA: Data Integration Component is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
NIAAA U01 AA021697; NIBIB R01 EB008381 |
Available to the research community | SCR_014135 | 2026-08-13 09:28:58 | 0 | |||||||||
|
Journalysis Resource Report Resource Website |
Journalysis (RRID:SCR_014015) | data or information resource, database, software resource, collaboration tool | A database where researchers can read and post reviews of publishing experiences with scientific journals. When writing comments, reviewers are adivsed to provide facts where possible, be specific, be honest, check the review, and offer constructive criticism when writing a negative report. Journalysis collates submitted reviews and data for each journal and provides useful summary information (metrics). Authors wanting to find out more about specific journals can search its databases and find the best journal for their next manuscript submission. Journals can use these reviews and metrics to demonstrate high publishing standards, or to improve standards where reviews may be negative. | database, review, journal review, review logistics, collaboration tool |
is listed by: Connected Researchers is related to: Connected Researchers |
Free, Public, The community can contribute to this resource | SCR_014015 | 2026-08-13 09:28:57 | 0 | ||||||||||
|
CMIND PY Resource Report Resource Website |
CMIND PY (RRID:SCR_014097) | data processing software, software application, software toolkit, image analysis software, software resource | A python toolbox for analysis of MRI images. It relies on calls to a number of widely tested algorithms from the FMRIB software library (FSL) and the advanced normalization tools (ANTS) to provide analysis of simultaneously acquired ASL/BOLD fMRI data. It was developed for analyzing the datasets collected as part of the Cincinnati MR Imaging of NeuroDevelopment (C-MIND) project. | python, toolbox, software toolkit, image analysis software, mri |
uses: FSL uses: ANTS - Advanced Normalization ToolS is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Public | https://research.cchmc.org/c-mind-db/py-doc/html/ | SCR_014097 | CMIND-PY | 2026-08-13 09:28:57 | 0 | ||||||||
|
Useful Science Resource Report Resource Website |
Useful Science (RRID:SCR_013968) | data or information resource, knowledge environment, database, catalog, portal | A collection of concise summaries of scientific articles that link back to the physical article. Users can contribute resources to the site and may choose to provide a summary; if they do not, Useful Science will do so. Summaries are then tagged with the appropriate topic. Topics that relate to everday life such as health, fitness, nutrition, and sleep are the main focus of the site. | catalog, knowledge environment resource, summary, layman, lay person |
is listed by: Connected Researchers is related to: Connected Researchers |
Free, Public, The community can contribute to the resource | SCR_013968 | 2026-08-13 09:28:56 | 0 | ||||||||||
|
PLOS Article-Level Metrics Resource Report Resource Website 1+ mentions |
PLOS Article-Level Metrics (RRID:SCR_014022) | PLOS ALMs | topical portal, data or information resource, portal | A portal which provides access to article level metrics, PLOS news, and videos and presentations. PLOS ALMs provides altmetrics for every article published in PLOS. Researchers can stay up-to-date with their published work and share information about the impact of their publications with collaborators, funders, institutions, and the research community at large. | portal, altmetrics, article level metrics, PLOS |
lists: Plum Analytics lists: ImpactStory is listed by: Connected Researchers |
Sloan Foundation | PMID:19918558 | Free, Public | SCR_014022 | PLOS Article Level Metrics | 2026-08-13 09:28:56 | 1 | ||||||
|
NeuriteTracer Resource Report Resource Website 10+ mentions |
NeuriteTracer (RRID:SCR_014146) | data acquisition software, data processing software, software resource, software application | A set of ImageJ plugins for fully automated measurement of neurite outgrowth in fluorescence microscopy images of cultured neurons. The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length. NeuriteTracer accurately measures neurite outgrowth from cerebellar, DRG and hippocampal neurons. | plugin, data acquisition software, neurite outgrowth, fluorescence microscopy image, neuron |
is used by: ImageJ is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
PMID:17936365 | Availalble to the research community | http://fournierlab.mcgill.ca/styled-6/NeuriteTracer.html | SCR_014146 | 2026-08-13 09:28:57 | 39 | ||||||||
|
NeuroElf Resource Report Resource Website 100+ mentions |
NeuroElf (RRID:SCR_014147) | data processing software, software application, software toolkit, workflow software, software resource | A Matlab-based toolbox initially created for reading, writing, and processing of BrainVoyager (QX) files in Matlab. | matlab, software toolbox, brainvoyager |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainVoyager |
Freely available | http://neuroelf.net, http://neuroelf.net/wiki/doku.php | SCR_014147 | 2026-08-13 09:28:59 | 155 | |||||||||
|
COPASI Resource Report Resource Website 100+ mentions |
COPASI (RRID:SCR_014260) | COPASI | data analysis software, data processing software, simulation software, software application, standalone software, software resource | Software application for simulation and analysis of biochemical network models and their dynamics. COPASI supports models in the SBML standard and can simulate their behavior using ODEs or Gillespies stochastic simulation algorithm. Arbitrary discrete events can be included in such simulations. Models in COPASI are based on reactions that convert a set of species into another set of species. Simulation can be performed either with stochastic kinetics or with differential equations. COPASI also includes various methods of analysis and data visualization. | standalone software, simulation software, data analysis, biochemical system simulator, biochemical network model, biochemical network dynamics, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/btl485 | Free, Available for download, Acknowledgement requested | biotools:copasi | https://bio.tools/copasi | SCR_014260 | COPASI: Biochemical System Simulator | 2026-08-13 09:29:09 | 445 | |||||
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CYANA Resource Report Resource Website 100+ mentions |
CYANA (RRID:SCR_014229) | data analysis software, data processing software, software resource, software application | Software for automated structure calculation of biological macromolecules on basis of conformational constraints from nuclear magnetic resonance. Program for automated NMR protein structure calculation. CYANA requires a sufficient list of assigned chemical shifts and lists of cross-peak positions and columns from 2D, 3D, or4D NOESY spectra in order to calculate the assignment of the NOESY cross-peaks and the 3D structure of the protein in solution. | protein structure, nmr, noesy, 3d structure, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Goethe University Frankfurt am Main; Hessen; Germany has parent organization: RIKEN |
PMID:15318003 PMID:25801209 |
Available to the academic community, Available to commercial user, Pay for license | SCR_021949, biotools:cyana | http://www.las.jp/english/products/cyana.html, https://bio.tools/cyana, https://dbpedia.org/page/CYANA_(software) | SCR_014229 | 2026-08-13 09:29:09 | 428 | |||||||
|
TopSpin Resource Report Resource Website 5000+ mentions |
TopSpin (RRID:SCR_014227) | data analysis software, data processing software, software application, data acquisition software, software resource | Software package for NMR spectra acquisition, processing, and data analysis. Features include: deconvolution/spectrum simulation/iteration; comprehensive functionalities for processing, displaying and analyzing one and multi-dimensional spectra; and user customization. A full list of features is available on the website. | nmr spectra, data analysis software, data acquisition software | Pay for product | SCR_014227 | 2026-08-13 09:28:58 | 6242 | |||||||||||
|
ExPosition Packages Resource Report Resource Website 1+ mentions |
ExPosition Packages (RRID:SCR_014107) | data analysis software, data processing software, software resource, software application | An R package for descriptive (i.e., fixed-effects) multivariate analysis with singular value decomposition. | data analysis software, r package, multivariate analysis, singular value decomposition |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Texas at Dallas; Texas; USA |
https://cran.r-project.org/web/packages/ExPosition/index.html | SCR_014107 | CRAN Package Exposition | 2026-08-13 09:28:57 | 1 | |||||||||
|
Sparky Resource Report Resource Website 100+ mentions |
Sparky (RRID:SCR_014228) | data analysis software, data processing software, software resource, software application | A graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers. Sparky displays NMR spectra, the peaks of which users may pick, assign, and integrate using a graphical interface. Users can work with any number of 2, 3 or 4 dimensional spectra simultaneously. Spectra for input to Sparky can be produced with processing programs NMRPipe, Felix, VNMR, XWinNMR or UXNMR. Output consists of text peak lists showing assignments, chemical shifts, volumes, line widths, etc. | graphical nmr, protein integration, nucleic acid integration | has parent organization: University of California at San Francisco; California; USA | Free, Acknowledgement requested | SCR_014228 | 2026-08-13 09:29:00 | 488 | ||||||||||
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SciLifeLab Resource Report Resource Website 50+ mentions |
SciLifeLab (RRID:SCR_014078) | graduate program resource, analysis service resource, production service resource, service resource, access service resource | A Swedish national center of research for molecular biosciences with a focus on health and environmental research. Researchers from Sweden can use both the technology and the expertise provided by SciLifeLab. Swedish researchers typically pay only for reagents and other consumables. Users from commercial companies pay the actual costs of the analyses performed. SciLifeLab also provides educational courses, seminars, and programs for PhD students, postdocs, investigators and other employees within all Swedish universities. | molecular biosciences, health and environmental research, analysis service resource, graduate program resource, access service resource, sweden |
has parent organization: Uppsala University; Uppsala; Sweden has parent organization: Karolinska Institute; Stockholm; Sweden has parent organization: Royal Institute of Technology; Stockholm; Sweden has parent organization: Stockholm University; Stockholm; Sweden is parent organization of: FACS is parent organization of: Karolinska Institutet Adaptive Immune Receptor Gene Variant Atlas is parent organization of: SciLifeLab Precision Medicine Portal |
Available to the research community, May be specifically for Sweden-based researchers | SCR_014078 | Science for Life Laboratory | 2026-08-13 09:28:56 | 62 | |||||||||
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Huygens Software Resource Report Resource Website 100+ mentions |
Huygens Software (RRID:SCR_014237) | data processing software, software application, image analysis software, image reconstruction software, software resource | A set of fluorescence microscope image processing packages which perform image restoration, interactive analysis, and volume visualization of 2D and 3D multi channel microscopy images or time series. The restoration is based on different deconvolution algorithms, that permit the recovery of objects from images that are degraded by blurring and noise. Tutorials and documentation are available on the website. | deconvolution, fluorescence microscopy, volume visualization, image analysis software, image restoration | Acknowledgement requested, Freeware is available, Some tools require a license | SCR_014237 | 2026-08-13 09:29:09 | 468 | |||||||||||
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Peptide Synthesis Resource Report Resource Website |
Peptide Synthesis (RRID:SCR_014070) | production service resource, service resource, material service resource, reagent manufacture | A reagent manufacturer which provides custom peptide APIs and custom peptide synthesis services. These products and services include high throughput peptide library/array synthesis, high quality bulk API peptides, bioactive catalog peptides, and cosmetic peptides. | peptide, reagent manufacture, custom | Available to the academic community | SCR_014070 | 2026-08-13 09:28:56 | 0 | |||||||||||
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Advanced Connectivity Analysis (ACA) Resource Report Resource Website 1+ mentions |
Advanced Connectivity Analysis (ACA) (RRID:SCR_014195) | ACA | data acquisition software, data processing software, software resource, software application | A large scale functional connectivity data mining software package which enables large-scale seed-based analysis and brain-behavior analysis. It can examine a large number of seed regions with minimal user input. ACA has a brain-behavior analysis component to delineate associations among imaging biomarkers and one or more behavioral variables. | data mining, data acquisition software, seed based analysis, brain behavior analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available to the research community | SCR_014195 | Advanced Connectivity Analysis (ACA): a large scale functional connectivity data mining environment, Advanced Connectivity Analysis | 2026-08-13 09:29:00 | 1 | ||||||||
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VBM toolbox Resource Report Resource Website 100+ mentions |
VBM toolbox (RRID:SCR_014196) | segmentation software, data processing software, software application, software toolkit, image analysis software, software resource | A collection of extensions to the segmentation algorithm of SPM2, SPM5, and SPM8 to provide voxel-based morphometry. The toolboxes are named according to the SPM version. The software is available to the scientific community under the terms of the GNU General Public License. VBM subpages can be accessed from the VBM website. | software toolbox, segmentation, extension, voxel based morphometry | SCR_014196 | Voxel Based Morphometry Toolbox | 2026-08-13 09:29:09 | 415 | |||||||||||
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Nanoparticle Tracking Analysis Resource Report Resource Website 10+ mentions |
Nanoparticle Tracking Analysis (RRID:SCR_014239) | NTA | data acquisition software, data processing software, software resource, software application | Software which utilizes the properties of both light scattering and Brownian motion to obtain the particle size distribution of samples in liquid suspension. The Nanoparticle Tracking Analysis software tracks many particles individually and calculates their hydrodynamic diameters using the Stokes Einstein equation. | data acquisition software, particle size distribution, liquid suspension | is listed by: SoftCite | Pay for product | SCR_014239 | Nanoparticle Tracking Analysis (NTA) | 2026-08-13 09:28:58 | 29 | ||||||||
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Biomag Discussion Group on Yahoo Resource Report Resource Website |
Biomag Discussion Group on Yahoo (RRID:SCR_014089) | topical portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented December 11, 2015. A discussion group for those actively involved in research into, or applications of, biomagnetism and magnetoencephalography (MEG). | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014089 | 2026-08-13 09:29:08 | 0 |
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