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http://www.nitrc.org/projects/neuritetracer

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.

Proper citation: NeuriteTracer (RRID:SCR_014146) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/bvqxtools

A Matlab-based toolbox initially created for reading, writing, and processing of BrainVoyager (QX) files in Matlab.

Proper citation: NeuroElf (RRID:SCR_014147) Copy   

•   Source: SciCrunch Registry

http://copasi.org/

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.

Proper citation: COPASI (RRID:SCR_014260) Copy   

•   Source: SciCrunch Registry

http://www.cyana.org/wiki/index.php/Main_Page

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.

Proper citation: CYANA (RRID:SCR_014229) Copy   

•   Source: SciCrunch Registry

https://www.bruker.com/products/mr/nmr/nmr-software/software/topspin/overview.html

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.

Proper citation: TopSpin (RRID:SCR_014227) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/exposition/

An R package for descriptive (i.e., fixed-effects) multivariate analysis with singular value decomposition.

Proper citation: ExPosition Packages (RRID:SCR_014107) Copy   

•   Source: SciCrunch Registry

https://www.cgl.ucsf.edu/home/sparky/

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.

Proper citation: Sparky (RRID:SCR_014228) Copy   

•   Source: SciCrunch Registry

http://www.scilifelab.se

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.

Proper citation: SciLifeLab (RRID:SCR_014078) Copy   

•   Source: SciCrunch Registry

https://svi.nl/HuygensSoftware

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.

Proper citation: Huygens Software (RRID:SCR_014237) Copy   

•   Source: SciCrunch Registry

http://www.creative-peptides.com/Peptide-synthesis.html

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.

Proper citation: Peptide Synthesis (RRID:SCR_014070) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/aca_rc

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.

Proper citation: Advanced Connectivity Analysis (ACA) (RRID:SCR_014195) Copy   

•   Source: SciCrunch Registry

http://dbm.neuro.uni-jena.de/vbm/

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.

Proper citation: VBM toolbox (RRID:SCR_014196) Copy   

•   Source: SciCrunch Registry

http://www.malvern.com/en/products/technology/nanoparticle-tracking-analysis/

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.

Proper citation: Nanoparticle Tracking Analysis (RRID:SCR_014239) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/biomag_group/

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).

Proper citation: Biomag Discussion Group on Yahoo (RRID:SCR_014089) Copy   

•   Source: SciCrunch Registry

http://www.icpsr.umich.edu/CrimeStat/about.html

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.

Proper citation: CrimeStat (RRID:SCR_014243) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/image_synthesis/

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.

Proper citation: Image Synthesis Tools (RRID:SCR_014123) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/hdbig/

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.

Proper citation: HDBIG (RRID:SCR_014120) Copy   

•   Source: SciCrunch Registry

http://www.jmp.com/en_us/software/jmp.html

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.

Proper citation: JMP (RRID:SCR_014242) Copy   

•   Source: SciCrunch Registry

http://www.perkinelmer.com/catalog/category/id/living%20image%20software

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.

Proper citation: Living Image software (RRID:SCR_014247) Copy   

•   Source: SciCrunch Registry

https://usa.healthcare.siemens.com/magnetic-resonance-imaging/options-and-upgrades/clinical-applications/autoalign-head-ls

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.

Proper citation: AutoAlign Head (RRID:SCR_014245) Copy   

•   Source: SciCrunch Registry