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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | |||||||||
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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 | |||||||
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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 | |||||||||||
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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 | |||||||||
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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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CrimeStat Resource Report Resource Website 10+ mentions |
CrimeStat (RRID:SCR_014243) | data analysis software, data processing software, software resource, software application | A spatial statistics program which provides tools for crime mapping and analyzing crime incident locations. CrimeStat is organized into five sections: data setup, which arranges and organizes the location data; spatial description, which performs analyses such spatial distribution, spatial autocorrelation, and distance and hot spot analysis; spatial modeling, which performs a number of analyses such as Bayesian journey to crime analysis and space-time analysis; crime travel demand modeling, which detects crime patterns and correlations over time and space; and CrimeStat libraries, which are component objects that include all of the routines that were developed through version 2.0 of the regular CrimeStat program. | spacial statistics, data analysis software, crime mapping, crime incident location | has parent organization: University of Michigan; Ann Arbor; USA | National Institute of Justice 1997-IJ-CX-0040; National Institute of Justice 1999-IJ-CX-0044; National Institute of Justice 2002-IJ-CX-0007; National Institute of Justice 2005-IJ-CX-K037 |
Distributed freely for educational or research purposes, May not be re-sold, Acknowledgement requested | http://nij.gov/topics/technology/maps/pages/crimestat.aspx | SCR_014243 | 2026-08-13 09:28:58 | 14 | ||||||||
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Image Synthesis Tools Resource Report Resource Website |
Image Synthesis Tools (RRID:SCR_014123) | image processing software, data processing software, software resource, software application | A collection of software tools developed for medical image synthesis of typically magnetic resonance (MR) brain images. The approaches have been used to create computed tomography (CT) images from MR input. The goal of image synthesis is to recover MR images with a desired optimal contrast for further processing by either registration or segmentation. | image synthesis, image restoration, software, mri, brain image, ct image |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
Available for download | SCR_014123 | 2026-08-13 09:28:57 | 0 | ||||||||||
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HDBIG Resource Report Resource Website |
HDBIG (RRID:SCR_014120) | data processing software, software application, software toolkit, image analysis software, software resource | A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association. | image analysis software, genomics, imaging, joint analysis, toolkit, sparse association, sparse regression |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Indiana University; Indiana; USA |
NLM R01 LM011360; NSF IIS-1117335 |
http://www.iu.edu/~hdbig/ | SCR_014120 | High Dimensional Brain Imaging Genomics Toolkit | 2026-08-13 09:28:58 | 0 | ||||||||
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JMP Resource Report Resource Website 100+ mentions |
JMP (RRID:SCR_014242) | data processing software, data management software, software application, data visualization software, software resource | Statistical software that uses dynamic graphics rather than tables or graphs to visualize raw data. More specific versions of JMP are available for statistical analyses, clinical work, and genomics. Features include statistical modeling, data cleanup, automation and scripting, and experimental design. | statistical software, data visualization, data management, graphic data visualization |
is listed by: Metabolomics Workbench is listed by: SoftCite |
Pay for product, Free trial download is available | SCR_014242 | 2026-08-13 09:29:09 | 207 | ||||||||||
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Living Image software Resource Report Resource Website 1000+ mentions |
Living Image software (RRID:SCR_014247) | workflow software, data processing software, software resource, software application | In vivo imaging software which facilitates workflow for in vivo optical, X-ray and microCT image acquisition, analysis and data organization., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | in vivo imaging software, workflow software, image acquisition, image analysis, data organization | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014247 | 2026-08-13 09:28:59 | 3021 | |||||||||||
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AutoAlign Head Resource Report Resource Website 1+ mentions |
AutoAlign Head (RRID:SCR_014245) | data processing software, software application, image analysis software, alignment software, software resource | Software designed to automatically realign brain images for easier cross patient examination regardless of age, disease or head position. It positions and aligns anatomy-related sagittal, coronal and axial slices using anatomical landmarks. | brain, cross patient examination, anatomical landmark, automatic realignment | Pay for product | SCR_014245 | 2026-08-13 09:29:01 | 2 |
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