Tools   Select Another Resource Report Type

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

http://www.moleculardevices.com/systems/microplate-readers/softmax-pro-data-acquisition-and-analysis-software

A software package for microplate reader control and microplate data analysis. It includes analysis templates for a variety of assays run on Molecular Devices microplate readers.

Proper citation: SoftMax Pro Data Acquisition and Analysis Software (RRID:SCR_014240) Copy   

•   Source: SciCrunch Registry

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

A Matlab tool for simulating extracellular potential recordings in spiking neural network (SNN) models. VERTEX is designed to facilitate the simulation of extracellular potentials generated by activity in SNNs; in particular, spatially-organised networks containing thousands or hundreds of thousands of neurons. It has a limited scope but has a simpler user interface so that a simulation can be specified simply by setting some parameters and run using a few function calls.

Proper citation: Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) (RRID:SCR_014178) Copy   

•   Source: SciCrunch Registry

http://www.photonics.com/Product.aspx?PRID=47380

Image processing software used to modify and clarify sample images for FluoView FV1000 range of confocal laser scanning microscopes and Fluoview FV1000MPE multiphoton excitation systems. The software incorporates high-dynamic-range imaging, minimized signal-to-noise ratios, partial stitching with multiarea time-lapse imaging, and channel unmixing. The software also allows users to select specific areas of the whole sample, which can stitched together.

Proper citation: FluoView FV10-ASW software (RRID:SCR_014215) Copy   

•   Source: SciCrunch Registry

https://www.phenix-online.org/documentation/reference/phaser.html

Crystallographic software which solves structures using algorithms and automated rapid search calculations to perform molecular replacement and experimental phasing methods.

Proper citation: Phaser (RRID:SCR_014219) Copy   

•   Source: SciCrunch Registry

http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver721/introduction.html

Software which processes diffraction data/images and produces an MTZ file of reflection indices with their intensities, standard deviations, and other parameters. The MTZ file is passed onto other programs of the CCP4 program suite for further data reduction. iMosflm processes data from CCD and pixel detectors. It is available for Windows, Mac OSX and Linux platforms. Tutorials are available at the website.

Proper citation: iMosflm (RRID:SCR_014217) Copy   

•   Source: SciCrunch Registry

http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available.

Proper citation: Coot (RRID:SCR_014222) Copy   

•   Source: SciCrunch Registry

http://shelx.uni-ac.gwdg.de/SHELX/

A set of software programs that utilizes dual spaces algorithms for the determination of small and macromolecular crystal structures by single crystal X-ray and neutron diffraction. Libraries, extra files and environment variables are not required for the executables. SHELX is intended to be run on a command prompt but may be called from GUIs such as shelXle, Olex2, Oscail or WinGX, or hkl2map., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SHELX (RRID:SCR_014220) Copy   

•   Source: SciCrunch Registry

http://molprobity.biochem.duke.edu

A structure-validation web application which provides an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. MolProbity works best as an active validation tool (used as soon as a model is available and during each rebuild/refine loop) and when used for protein and RNA crystal structures, but it may also work well for DNA, ligands and NMR ensembles. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot.

Proper citation: MolProbity (RRID:SCR_014226) Copy   

•   Source: SciCrunch Registry

http://cns-online.org/v1.2/

Software designed to provide a multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Features include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data. Modules, libraries, utility programs, tutorials, and a syntax manual are available on the website.

Proper citation: Crystallography and NMR System (CNS) (RRID:SCR_014223) Copy   

•   Source: SciCrunch Registry

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

A Matlab tool to perform statistical analysis on cortical thickness signals on brain surfaces obtained from Freesurfer. It is used for multi-resolutional analysis of such cortical thickness signals and detecting group differences. It is based on the Spectral Graph Wavelet Transform (SGWT) toolbox and provides plug and play methods for deriving Wavelet Multiscale Descriptor (WMD), cortical thickness smoothing using SGWT, Multivariate General Linear Model (MGLM), and False Discovery Rate (FDR).

Proper citation: Wisconsin Cortical Thickness Analysis (CTA) Toolbox (RRID:SCR_014180) Copy   

•   Source: SciCrunch Registry

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

Segmentation software for multimodal image analysis of brain tumor studies. It performs volumetric segmentation of healthy and tumor tissues by employing multispectral MRI sequences. Segmented tissues include Gray Matter, White Matter, Cerebrospinal Fluid, necrotic core, edema, non-enhancing tumor and enhancing tumor.

Proper citation: BraTumIA (Brain Tumor Image Analysis) (RRID:SCR_014184) Copy   

•   Source: SciCrunch Registry

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

A multi-platform software dedicated to designing, testing and using brain-computer interfaces (BCI). OpenViBE is a software for real-time neurosciences that can be used to acquire, filter, process, classify and visualize brain signals in real time.

Proper citation: OpenViBE (RRID:SCR_014156) Copy   

•   Source: SciCrunch Registry

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

A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data.

Proper citation: Northwestern University Schizophrenia Data and Software Tool (NUSDAST) (RRID:SCR_014153) Copy   

•   Source: SciCrunch Registry

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

Open source tool for multi-modal medical and brain data visualization. It is a tool for the scientific user and a powerful framework for the visualization researcher. It is written in Standard C++ and uses a number of portable libraries (e.g. Qt, Boost and OpenSceneGraph). It runs on common GNU/Linux operating systems, Mac OSX and Windows.

Proper citation: OpenWalnut (RRID:SCR_014157) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/csa-odf

A Matlab toolbox that computes the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) for diffusion-weighted MRI.

Proper citation: Orientation Distribution Function in Constant Solid Angle (CSA-ODF) (RRID:SCR_014158) Copy   

•   Source: SciCrunch Registry

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

A set of Matlab scripts for analyzing neuroimaging data from clinical populations. The NiiStat tools are designed to correlate behavioral data (task performance) with brain imaging data.

Proper citation: NiiStat (RRID:SCR_014152) Copy   

•   Source: SciCrunch Registry

http://www.waters.com/waters/en_US/MassLynx-MS-Software/nav.htm?cid=513662&locale=en_US

Software which can acquire, analyze, manage, and share mass spectrometry data. MassLynx controls any Waters mass spectrometry system, from sample and solvent management components to mass spectrometer and auxiliary detectors. The software can acquire nominal mass, exact mass, MS/MS and exact mass MS/MS data. The software system also maintains and consolidates all user sample data. Optional Application Manager programs provide additional information for specific MS analyses and data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MassLynx (RRID:SCR_014271) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ruby-nifti/

A library for handling NIfTI data in the Ruby programming language. Ruby NIfTI supports basic read and write access to NIfTI files, including basic and extended header information and image information. It doesn't attempt to touch the image data but it does provide access to qform and sform orientation matrices. It also provides a nice interface to get at NIfTI info from within Ruby.

Proper citation: Ruby NIfTI (RRID:SCR_014164) Copy   

•   Source: SciCrunch Registry