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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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L-Neuron Resource Report Resource Website 1+ mentions |
L-Neuron (RRID:SCR_014132) | simulation software, software application, software resource | A program which creates anatomically realistic virtual neurons using the formalism of the Lyndenmayer systems to implement sets of neuroanatomical rules discovered by several research groups. The program algorithms read in experimental data - in the form of statistical distributions - to generate virtual structures. L-Neuron samples the values of the parameters within these statistical distributions in a stochastic (random) fashion during dendritic growth. | simulation softare, virtual neuron, neuronal modeling |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: George Mason University; Virginia; USA |
Available to the research community | http://krasnow1.gmu.edu/cn3/L-Neuron/home.htm | SCR_014132 | SciCrunch Registry | L Neuron | 2026-11-07 11:58:17 | 5 | ||||||||
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Lightweight Data Pipeline Resource Report Resource Website |
Lightweight Data Pipeline (RRID:SCR_014135) | data processing software, software application, software resource, workflow software | 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 | SciCrunch Registry | 2026-11-07 11:57:56 | 0 | |||||||||
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CSIM Resource Report Resource Website 10+ mentions |
CSIM (RRID:SCR_014256) | simulation software, software application, software resource | Software tool for simulating heterogeneous networks composed of different model neurons and synapses. CSIM simulates networks containing up to a few thousand neurons and up to the order of 1.000.000 synapses. It is capable of supporting different levels of modeling and has an object oriented design. A user manual is available on the site. | simulation software, circuit simulator, heterogeneous network, object oriented design | is related to: PCSIM | Available for download | SCR_014256 | SciCrunch Registry | Circuit SIMulator, CSIM: A neural Circuit SIMulator | 2026-11-07 11:57:48 | 11 | |||||||||
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NeoCortical Simulator Resource Report Resource Website |
NeoCortical Simulator (RRID:SCR_014257) | NCS | simulation software, software application, software resource | A neural simulator which models integrate-and-fire neurons with conductance-based synapses. NCS supports simulations for larger models and also supports real-time neurorobotics applications. Two versions of NCS are available: NCS 5, which is based on CPU cluster; and NCS 6, a multi-box, multi-GPU version. NCS 5 models integrate-and-fire neurons with conductance-based synapses using two clusters: four SUN 4600 machines and 208 Opteron cores. NCS 6 is a neural simulator for heterogeneous clusters of both CPUs and GPUS. | simulation software, neural simulator, conductance based synapse, neurobiotics | has parent organization: University of Nevada at Reno; Nevada; USA | Source code is available | SCR_014257 | SciCrunch Registry | 2026-11-07 11:57:57 | 0 | |||||||||
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NeuriteTracer Resource Report Resource Website 10+ mentions |
NeuriteTracer (RRID:SCR_014146) | data acquisition software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 11:58:04 | 39 | ||||||||
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NeuroElf Resource Report Resource Website 100+ mentions |
NeuroElf (RRID:SCR_014147) | data processing software, software application, software resource, software toolkit, workflow software | 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 | SciCrunch Registry | 2026-11-07 11:57:47 | 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, software resource, standalone software | 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 | SciCrunch Registry | COPASI: Biochemical System Simulator | 2026-11-07 11:58:18 | 445 | |||||
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CYANA Resource Report Resource Website 100+ mentions |
CYANA (RRID:SCR_014229) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 11:57:57 | 428 | |||||||
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TopSpin Resource Report Resource Website 5000+ mentions |
TopSpin (RRID:SCR_014227) | data acquisition software, data analysis software, data processing software, software application, 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 | SciCrunch Registry | 2026-11-07 11:58:06 | 6242 | |||||||||||
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Sparky Resource Report Resource Website 100+ mentions |
Sparky (RRID:SCR_014228) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 11:57:48 | 488 | ||||||||||
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Huygens Software Resource Report Resource Website 100+ mentions |
Huygens Software (RRID:SCR_014237) | data processing software, image analysis software, image reconstruction software, software application, 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 | SciCrunch Registry | 2026-11-07 11:58:06 | 468 | |||||||||||
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Generation R Pediatric MRI Resources Resource Report Resource Website 10+ mentions |
Generation R Pediatric MRI Resources (RRID:SCR_014114) | data or information resource, image collection | An MRI resource which provides age-appropriate images of children. It includes an average, age-appropriate T1-weighted image, constructed from 130 typically developing children ages 6-to-10 and a set of 32 resting-state ICA components. These components were generated from 494 typically developing children, ages 6-to-10 years old, using the MELODIC ICA tool, bootstrapped with 1000 resamples. Both of these resources are described in detail in a manuscript submitted for publication. | image collection, mri, children, ti weighted | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | SCR_014114 | SciCrunch Registry | 2026-11-07 11:58:03 | 15 | |||||||||||
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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 application, software resource | 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 | SciCrunch Registry | Advanced Connectivity Analysis (ACA): a large scale functional connectivity data mining environment, Advanced Connectivity Analysis | 2026-11-07 11:58:05 | 1 | ||||||||
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VBM toolbox Resource Report Resource Website 100+ mentions |
VBM toolbox (RRID:SCR_014196) | data processing software, image analysis software, segmentation software, software application, software resource, software toolkit | 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 | SciCrunch Registry | Voxel Based Morphometry Toolbox | 2026-11-07 11:57:47 | 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 application, software resource | 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 | SciCrunch Registry | Nanoparticle Tracking Analysis (NTA) | 2026-11-07 11:57:48 | 29 | ||||||||
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CrimeStat Resource Report Resource Website 10+ mentions |
CrimeStat (RRID:SCR_014243) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 11:58:06 | 14 | ||||||||
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Image Synthesis Tools Resource Report Resource Website |
Image Synthesis Tools (RRID:SCR_014123) | data processing software, image processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 11:57:46 | 0 | ||||||||||
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HDBIG Resource Report Resource Website |
HDBIG (RRID:SCR_014120) | data processing software, image analysis software, software application, software resource, software toolkit | 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 | SciCrunch Registry | High Dimensional Brain Imaging Genomics Toolkit | 2026-11-07 11:58:16 | 0 | ||||||||
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JMP Resource Report Resource Website 100+ mentions |
JMP (RRID:SCR_014242) | data management software, data processing software, data visualization software, software application, 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 | SciCrunch Registry | 2026-11-07 11:58:17 | 207 | ||||||||||
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Living Image software Resource Report Resource Website 1000+ mentions |
Living Image software (RRID:SCR_014247) | data processing software, software application, software resource, workflow software | 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 | SciCrunch Registry | 2026-11-07 11:58:18 | 3021 |
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