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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

Physical Resource or Software Tool Software

34 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
SPMResource, software resource, software application, data analysis software, data processing software, image analysis softwareSoftware package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.analysis, brain, imaging, data, sequence, fMRI, PET, SPECT, EEG, MEGSCR_007037(SPM, RRID:SCR_007037)University College London; London; United Kingdom related to: WFU Biological Parametric Mapping Toolbox, vis: SPM Visualized Statistics toolbox, LEAD-DBS, CCHMC Pediatric Brain Templates, IBMA toolbox, ArtRepair for robust fMRI, ASL data processing tool box, BrainVISA / Anatomist, MRIcro Software, xjView: A Viewing Program For SPM, BrainMagix SPM Viewer, MarsBaR region of interest toolbox for SPM, NIRS-SPM, SPM SS - fMRI functional localizers, Wisconsin White Matter Hyperintensities Segmentation Toolbox, Dementia-specific FDG PET Template for SPM analyses, SPM Anatomy Toolbox, MIPAV: Medical Image Processing and Visualization, MATLAB, used by: rsfMRI_fconn calculation, Automatic Analysis, uses: Neuroimaging Data Model, imcalc: SPM batch image calculator, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC), 3DVC, affiliated with: Clinical Toolbox for SPM, Statistical non-Parametric Mapping, provides: TSDiffAna, has plug-in: ICN_Atlas, works_with: UManitoba - JHU Functionally Defined Human White Matter Atlas, NIAG Addiction Data, ICN_Atlas, spm_auto_reorient_coregisterLast checked upnif-0000-00343http://www.nitrc.org/projects/spm, https://www.fil.ion.ucl.ac.uk/spm/software/spm12/
Spatio- Spectro- Temporal Receptive FieldResource, software resourceSTRFPak is a Matlab toolbox for estimating the linear and nonlinear stimulus-response mapping function of sensory systems. This mapping function is commonly called the spatio- or spectro-temporal receptive field (STRF). A quantitative estimate of the STRF can be used in subsequent computational modeling studies or to predict future responses of the system. STRFPak implements several general STRF estimation techniques and can be used with any stimuli (including natural scenes and sounds). The theoretical basis for STRF estimation has been known for some time, but estimation software has not been widely available. This project aims to develop appropriate software and make it available to the wider community of sensory neuroscientists. Although STRFPak is based on established methods it incorporates two important innovations. First, STRFPak can be used to characterize a sensory system from its response to arbitrary stimuli including natural signals (e.g., vocalizations, natural scenes). Second, STRFPak incorporates several methods for estimating nonlinear STRFs. STRFPak also includes tutorial examples and documentation.matlab, neuroscience, nonlinear, receptive field, response, sensory, signal, spatio, spectro, stimulus, sensory system, temporalSCR_007995(Spatio- Spectro- Temporal Receptive Field, RRID:SCR_007995)University of California; Berkeley; USA related to: MATLABLast checked upnif-0000-07191
MultiPhase-SEGResource, software resource, segmentation software, software application, data processing software, image analysis softwareA segmentation software that employs the implementation of the active contours without edges level set based segmentation model. Its features include: segmentation of three-dimensional brain volumes into two or more regions (for example, regions could be WM, GM, and CSF), visualization of surfaces representing boundaries of different brain regions, and being written in Matlab with the ability to run on any platform with Matlab installed.segementation, visualization, 3D, softwareSCR_008275(MultiPhase-SEG, RRID:SCR_008275)University of Southern California; Los Angeles; USA NCRR, NIBIBrelated to: Laboratory of Neuro Imaging, MATLABLast checked downnif-0000-23319http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=16
An Open-Source MATLAB-to-Python CompilerResource, software resource, software application, software development tool, compilerOMPC aims to enable reuse of the huge open and free code base of MATLAB on a free and faster growing Python platform. Running Python and MATLAB in a single interpreter avoids issues with running two separate applications. Python adds general purpose programming libraries to the convenient syntax of the language of technical computing. OMPC is not an interpreter, it lets Python to do the work. This means that if Python gets faster OMPC gets faster too. OMPC translates the m-files preserving the structure of the original programs as much as possible. Although OMPC comes with a library that emulates the features of numerical array of MATLAB there is nothing that will stop you from running the translated code the way you like it. This means that you could run the OMPC generated code on IronPython, Jython, PyPy or whatever else if you write your own numerical class. Sponsors: This resource is supported by RIKEN Brain Science Institute.code, compiler, python, matlab, computng, software, programSCR_008409(An Open-Source MATLAB-to-Python Compiler, RRID:SCR_008409)related to: Python Programming Language, MATLABLast checked upnif-0000-30104
Extensible MATLAB Medical image AnalysisResource, software resource, data visualization software, software toolkit, data processing software, software applicationEMMA (Extensible MATLAB Medical image Analysis) is a toolkit designed to ease the use of MATLAB in the analysis of medical imaging data. It provides functions for reading and writing MINC files, viewing images, performing ROI operations, and performing several popular analyses. Also, there are toolkits for performing kinetic analysis of dynamic PET rCBF (regional cerebral blood flow) and FDG data. The goal for this site is to provide a centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools that are of use to the general community.analysis, matlab, medical, neurological, tool, image, toolkitSCR_013499(Extensible MATLAB Medical image Analysis, RRID:SCR_013499)Human Brain Projectrelated to: MATLAB, MINC, listed by: Internet Analysis Tools RegistryLast checked downnif-0000-33081
FieldTripResource, image analysis software, data analysis software, data processing software, image reconstruction software, software application, software resource, software toolkitSoftware tool for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.MEG, EEG, iEEG, analysis, data, time, frequency, source, reconstruction, dipole, beamformers, non parametric, statistical, testingSCR_004849(FieldTrip, RRID:SCR_004849)Radboud University; Nijmegen; The Netherlands Human Connectome project, Netherlands Ministry of Economic Affairs, Netherlands Ministry of Education Culture and Science, NIH Blueprint for Neuroscience Researchrelated to: Human Connectome Coordination Facility, MATLAB, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC), works_with: CoSMoMVPA, SleepTripPMID:21253357Last checked upnlx_143928http://www.nitrc.org/projects/fieldtrip
Libeep EEGLAB pluginResource, software resource, software application, software toolkitSoftware as an EEGLAB tool used for LIBEEP recordings.plugin, library, recording, electrophysiological, data, neuroscienceSCR_016334(Libeep EEGLAB plugin, RRID:SCR_016334)related to: LIBEEP, EEGLAB, MATLAB, submitted by: Resource Identification PortalLast checked up
Reglo ICC control with MatlabResource, software resource, application programming interface, data access protocolA Matlab adapter class and user interface to control the Reglo ICC peristaltic pump provided by Ismatec.adapter, class, user, interfce, control, Reglo ICC, peristaltic, pump, IsmatecSCR_016353(Reglo ICC control with Matlab, RRID:SCR_016353)related to: MATLABLast checked up
Mastrave modelling libraryResource, software resource, software toolkit, software libraryA software library written to perform vectorized scientific computing and oriented to ease complex modelling tasks such as those typically needed within environmental models, even when involving irregular and heterogeneous data series. The Mastrave project attempts to allow a more effective, quick interoperability between GNU Octave and Matlab users by using a well documented wrap around the main incompatibilities between those computing environments and by promoting a general idiom based on their common, stable syntagms.free software, array programming, semantics, mathematics, statistics, semantic array programming, library, environmental modelling, environmental modelingSCR_014399(Mastrave modelling library, RRID:SCR_014399)related to: GNU Octave, MATLABLast checked up
BVA import/export EEGLAB pluginResource, software resource, software toolkit, software applicationSoftware package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software.interfacing, brain, vision, analyser, data, file, load, save, Matlab, routine, compatible, EEGLABSCR_016333(BVA import/export EEGLAB plugin, RRID:SCR_016333)related to: SourceForge, EEGLAB, MATLAB, submitted by: Resource Identification PortalLast checked up
The Bergen fMRI Toolbox Plugin for EEGLabResource, software resource, software toolkit, data analysis software, data processing software, software applicationSoftware package as a set of Matlab tools which allow the correction of fMRI-related gradient artifacts from EEG data. Designed to work within the EEGLAB environment, providing a GUI to remove fMRI gradient artifacts from the EEG. Can also be used from the Matlab command line, providing expert users with the ability to use them in custom scripts.correct, gradient, artifact, data, electrophysiology, functional, magnetic, resonance, imaging, neuroscienceSCR_016335(The Bergen fMRI Toolbox Plugin for EEGLab, RRID:SCR_016335)University of Bergen; Bergen; Norway related to: EEGLAB, MATLAB, submitted by: Resource Identification PortalLast checked up
Electrographic Seizure AnalyzerResource, software resource, software application, data analysis software, data processing softwareSoftware to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting.automate, analysis, electrographic, seizure, EEG, LFP, data, event, detection, parameter, settingSCR_016344(Electrographic Seizure Analyzer, RRID:SCR_016344)related to: MATLABLast checked up
ROIs selection with a non-graphical user interfaceResource, software resource, application programming interface, data access protocolIt is non-graphical user interface in MATLAB which relies on keyboard callback functions.\\nUsed for analyzing big data sets.non graphical, user, interface, keyboard, callback, function, analysis, big, data, setSCR_016352(ROIs selection with a non-graphical user interface, RRID:SCR_016352)related to: MATLABLast checked uphttps://ptrrupprecht.wordpress.com/2015/06/24/a-simple-non-graphical-user-interface-in-matlab-keyboard-callback-functions/
QModelingResource, image analysis software, data analysis software, data processing software, software application, software resource, software toolkitSoftware toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences.statistical, parametric, mapping, reference, region, kinetic, model, dynamic, analysis, brain, data, imaging, sequenceSCR_016358(QModeling, RRID:SCR_016358)related to: University of Malaga, Andalusia, Spain, MATLAB, submitted by: Resource Identification PortalDOI:10.1007/s12021-018-9384-yLast checked up
MicroFilament AnalyzerResource, software resource, image analysis software, software toolkit, data processing software, software applicationSoftware package for image analysis to determine the orientation of filamentous structures on digital images. Used as an image?processing tool for analyzing cytoskeleton and cellulose fiber orientation in pant imagesk.image, analysis, determine, orientation, filamentous, structure, digital, cytoskeleton, cellulose, fiberSCR_016411(MicroFilament Analyzer, RRID:SCR_016411)related to: MATLABPMID:23489480Last checked uphttp://www.ua.ac.be/bimef/MFA
LetswaveResource, software resource, software toolkit, data visualization software, data processing software, software applicationOpen source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals.process, visualise, EEG, MEG, data, neurophysiological, signal, brain, neuroscienceSCR_016414(Letswave, RRID:SCR_016414)related to: MATLABLast checked uphttps://www.letswave.org/
KiloSortResource, software resource, software application, algorithm resource, data processing softwareSoftware tool that implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings.implement, integrated, template, matching, framework, detect, cluster, spike, multi, channel, electrophysiology, recording, dataSCR_016422(KiloSort, RRID:SCR_016422)related to: MATLABLast checked up
kCSD-MatlabResource, software resource, software application, data analysis software, data processing softwareSoftware tool for analyzing recordings from multielectrodes. Source code for the Matlab implementation of the Kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes.analyzing, recording, data, multielectrode, transmembrane, current, source, estimate, kernel, source, density, methodSCR_016424(kCSD-Matlab, RRID:SCR_016424)related to: MATLABLast checked up
Suite2PResource, data analysis software, data processing software, software application, software resource, software toolkit, image processing softwareSoftware package for processing two-photon recordings. Available together with a graphical user interface that allows manual curation of the results. Used in two-photon microscopy for the analysis of data from two-photon imaging. Registers raw movies, detects active cells, extracts their calcium traces and infers their spike times.two, photon, microscopy, processing, image, data, recordSCR_016434(Suite2P, RRID:SCR_016434)University College London; London; United Kingdom related to: MATLAB, submitted by: Neuroscience Information FrameworkLast checked up
nonparametricGGC_toolboxResource, software resource, software application, data analysis software, data processing softwareSoftware package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions.nonparametric, Granger, causality, simulation, framework, code, estimate, brain, functionSCR_016539(nonparametricGGC_toolbox, RRID:SCR_016539)the Swiss National Science Foundationrelated to: MATLABLast checked up
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