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on page 1 showing 20 out of 31 results

Cite this (An Open-Source MATLAB-to-Python Compiler, RRID:SCR_008409)

URL: http://ompc.juricap.com

Resource Type: Resource, software resource, software application, software development tool, compiler

OMPC 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.

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Cite this (BVA import/export EEGLAB plugin, RRID:SCR_016333)

URL: https://sourceforge.net/projects/bva-io/

Resource Type: Resource, software resource, software toolkit, software application

Software 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.

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Cite this (Colour maps for brain imaging, RRID:SCR_016715)

URL: https://github.com/CPernet/brain_colours

Resource Type: Resource, data visualization software, software application, data processing software, image analysis software, software resource

Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging.

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Cite this (Electrographic Seizure Analyzer, RRID:SCR_016344)

URL: https://github.com/KM-Lab/Electrographic-Seizure-Analyzer

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting.

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Cite this (Extensible MATLAB Medical image Analysis, RRID:SCR_013499)

URL: http://www.cma.mgh.harvard.edu/iatr/display.php?spec=id&ids=107

Resource Type: Resource, software resource, data visualization software, software toolkit, data processing software, software application

EMMA (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.

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Cite this (FieldTrip, RRID:SCR_004849)

URL: http://www.fieldtriptoolbox.org

Resource Type: Resource, image analysis software, data analysis software, data processing software, image reconstruction software, software application, software resource, software toolkit

Software tool for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.

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Cite this (Frozen Noise, RRID:SCR_016558)

URL: https://github.com/DepartmentofNeurophysiology/Analysis-tools-for-electrophysiological-somatosensory-cortex-databank/tree/master/Frozen%20Noise

Resource Type: Resource, software resource, software toolkit, data analysis software, data processing software, software application

Software analysis tools for electrophysiological somatosensory cortex databank.
Allows to estimate the information content of spiking in single neuron resolution. It accompanies the open source intracellular recording database by Lantyer and colleagues.

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Cite this (kCSD-Matlab, RRID:SCR_016424)

URL: https://github.molgen.mpg.de/MPIBR-coattia/MatlabMain/tree/master/behaviorAnalysis/code/NSKtoolbox/externalToolboxes/kCSDv1

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software 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.

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    KiloSort

Cite this (KiloSort, RRID:SCR_016422)

URL: https://github.com/cortex-lab/Kilosort

Resource Type: Resource, software resource, software application, algorithm resource, data processing software

Software tool that implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings.

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    Letswave

Cite this (Letswave, RRID:SCR_016414)

URL: https://github.com/NOCIONS/letswave6/wiki/Download-and-setup

Resource Type: Resource, software resource, software toolkit, data visualization software, data processing software, software application

Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals.

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Cite this (Libeep EEGLAB plugin, RRID:SCR_016334)

URL: http://download.ant-neuro.com/matlab/

Resource Type: Resource, software resource, software application, software toolkit

Software as an EEGLAB tool used for LIBEEP recordings.

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Cite this (Mastrave modelling library, RRID:SCR_014399)

URL: http://mastrave.org

Resource Type: Resource, software resource, software toolkit, software library

A 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.

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Cite this (MicroFilament Analyzer, RRID:SCR_016411)

URL: https://www.ncbi.nlm.nih.gov/pubmed/23489480

Resource Type: Resource, software resource, image analysis software, software toolkit, data processing software, software application

Software 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.

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Cite this (Microscopy Image Browser, RRID:SCR_016560)

URL: http://mib.helsinki.fi/

Resource Type: Resource, data analysis software, data processing software, software application, data visualization software, standalone software, software resource, image processing software

Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets.

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Cite this (MrDiffusion, RRID:SCR_016567)

URL: http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/MrDiffusion

Resource Type: Resource, image analysis software, data analysis software, data processing software, software application, data visualization software, software resource

Software package for diffusion imaging analysis and visualization. Module of Vistasoft for processing diffusion weighted data and measuring and visualizing fractional anisotropy, mean diffusivity, axial and radial diffusivity, RGB fiber direction maps and analysis of MRI data.

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Cite this (MultiPhase-SEG, RRID:SCR_008275)

URL: http://www.loni.usc.edu/Software/MultiPhase-SEG

Resource Type: Resource, software resource, segmentation software, software application, data processing software, image analysis software

A 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.

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Cite this (NMF Toolbox, RRID:SCR_017069)

URL: https://github.com/colinvaz/nmf-toolbox

Resource Type: Resource, software resource, software application, data processing software

Software package for performing non negative matrix factorization and several variants. Used to factorize one non negative matrix into two non negative factors. Applied in bioinformatics as data mining approach.

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Cite this (nonparametricGGC_toolbox, RRID:SCR_016539)

URL: https://doi.org/10.1016/j.neuroimage.2018.07.046

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions.

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    PESTO

Cite this (PESTO, RRID:SCR_016891)

URL: https://github.com/ICB-DCM/PESTO

Resource Type: Resource, software resource, software application, data analysis software, data processing software, software toolkit

Software customizable toolbox for parameter estimation in MathWorks MATLAB. Offers scalable algorithms for optimization, uncertainty and identifiability analysis which do not depend on any problem-specific assumptions.

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    PPR-Meta

Cite this (PPR-Meta, RRID:SCR_016915)

URL: http://cqb.pku.edu.cn/ZhuLab/PPR_Meta

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software tool to identify metagenomic sequences of phages, chromosomes or plasmids. Used for identifying phages and plasmids from metagenomic fragments using deep learning.

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