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STRFPak 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.
Proper citation: Spatio- Spectro- Temporal Receptive Field (RRID:SCR_007995) Copy
http://www.nitrc.org/projects/gazereader/
A toolbox for a point-process derived GLM analysis of eye tracking data in Matlab. Data loading, model specification, fitting and review are organized into a sequence of events, each of which is handled by a separate module in the toolbox. The graphical interface was created using the Matlab graphical user interface development environment.
Proper citation: GazeReader (RRID:SCR_014112) Copy
https://github.com/EIN-lab/CHIPS
Image processing software designed to analyse functional images of cells and blood vessels, primarily from two-photon microscopy. CHIPS is a set of classes and functions for MATLAB that integrates a number of algorithms, both novel and existing, into a complete image processing pipeline.
Proper citation: CHIPS (RRID:SCR_015741) Copy
Software for detection and reporting of spindle or slow oscillation events, simple automatic EMG artifacts, and their co-occurance or respective matching non-events. SpiSOP was designed to process large data quanta at once and multiple datasets in parallel.
Proper citation: SpiSOP (RRID:SCR_015673) Copy
http://fmatoolbox.sourceforge.net
Matlab toolbox used to help analyze electrophysiological and behavioral data recorded from freely moving animals.
Proper citation: FMAToolbox (RRID:SCR_015533) Copy
Software for birdsong analysis that performs automated recording and analysis of animal vocalization. It can record, analyze and manage sound data over prolonged periods.
Proper citation: Sound Analysis Pro (RRID:SCR_016003) Copy
http://www.cma.mgh.harvard.edu/iatr/display.php?spec=id&ids=107
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. 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.
Proper citation: Extensible MATLAB Medical image Analysis (RRID:SCR_013499) Copy
https://github.com/ICB-DCM/PESTO
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.
Proper citation: PESTO (RRID:SCR_016891) Copy
http://www.nitrc.org/projects/mricros
A Matlab-based tool for computational neuroscience-based analysis and data visualization. Its features include: surface mesh visualization in PLY, PIAL, NV, STL,VTK, and GIFTI formats; conversion of NIfTI voxel images to surface meshes and saving as PLY or VTK; track (TRK files) visualization; connectome data (BrainNet Viewer .node and .edge files) visualization; intuitive GUI; that availability of all functions available in the GUI through scripting (automated scripts can be created); and exporting of rendered image as bitmap.
Proper citation: MRIcroS (RRID:SCR_014142) Copy
http://mariannebezaire.com/simtracker/
MATLAB-based tool for use with NEURON network models. It supports the modeler with model design, organization, execution (including on supercomputers), analysis, and reproducibility.
Proper citation: SimTracker (RRID:SCR_014735) Copy
https://sourceforge.net/projects/bva-io/
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.
Proper citation: BVA import/export EEGLAB plugin (RRID:SCR_016333) Copy
https://github.com/csitron/Microscopy_tif_Channel_Quant_MATLAB
Software application for quantification of fluorescence channel area in TIFF images using MATLAB.
Proper citation: Microscopy_tif_Channel_Quant_MATLAB (RRID:SCR_026999) Copy
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.
Proper citation: An Open-Source MATLAB-to-Python Compiler (RRID:SCR_008409) Copy
http://www.nitrc.org/projects/aperture/
A MATLAB-based toolbox for analysis of EEG, MEG, and ECoG data. APERTURE allows flexible multivariate analysis of ERPs and oscillatory activity and supports mass-univariate analysis with advanced statistical tests. Computations are accelerated using parallel computing supported through the MATLAB distributed computing toolbox. Examination of large, high-dimensional datasets is made simple through data visualization tools, including advanced plotting routines and generation of PDF reports with many figures.
Proper citation: APERTURE (RRID:SCR_014082) Copy
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
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
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
https://www.mathworks.com/products/computer-vision.html
Software tool to provide algorithms, functions, and apps for designing and testing computer vision, 3D vision, and video processing systems for MATLAB. You can perform object detection and tracking, as well as feature detection, extraction, and matching. For 3D vision, toolbox supports single, stereo, and fisheye camera calibration; stereo vision; 3D reconstruction; and lidar and 3D point cloud processing. Computer vision apps automate ground truth labeling and camera calibration workflows.
Proper citation: Computer Vision System Toolbox (RRID:SCR_017581) Copy
https://github.com/zburkett/VoICE
Software that groups vocal elements of birdsong by creating a high dimensionality dataset through scoring spectral similarity between vocalizations.
Proper citation: Vocal Inventory Clustering Engine (VoICE) (RRID:SCR_016004) Copy
https://github.com/keepersecond/Soma-Segmentation
Source code for a soma segmentation method suitable for datasets with touching soma distributions. The method contains three main parts: soma detection based on DT and local maximum searching and refining; an improved Rayburst sampling algorithm for isolated and touching soma surface detection; and ellipsoid fitting to generate the segmentation results.
Proper citation: Soma-Segmentation (RRID:SCR_015649) Copy
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