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updated 1 month ago

AIS quantification by Matthew Grubb

Quantitative measures of the axon initial segment (AIS) (neuroscience, neuron, ais)

ais(cell,chosen)

ais_auto(cell,threshold,smooth)

ais_z3(cell,chosen)

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updated 1 month ago

findInRange by Joseph O'Doherty

Find elements within many ranges. Faster than find() for large N. Useful for PSTHs and rasterplots. (neuroscience, psth, rasterplot)

findInRange.m

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updated 3 months ago

UEA_geometry.zip by Aleksander Bapst

Extract dimensions of Utah array electrodes from .TIF SEM images (utah array, microelectrodes, sem)

calculateEllipse(x, y, a, b, angle, steps)

frustum_analysis(varargin)

main(varargin)

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updated 7 months ago

Flexible and Fast Spike Raster Plotting by Jeffrey Chiou

Plots spike rasters from spike times or binary trains. Faster than most implementations. (biotech, data exploration, neuroscience)

plotSpikeRaster(spikes,varargin)

testSpikeRasterPlotting.m

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updated 7 months ago

Dual quaternion toolbox by Guillaume Leclercq

This toolbox provides dual quaternion methods, focusing on 3D kinematics for points and lines. (quaternion, dual quaternion, geometric algebra)

EXAMPLE_FORWARD_KINEMATICS

AV2dquat(AV)

DQconj(dv,WHICHCONJ)

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updated 1 year ago

MatClust by Mattias Karlsson

Spike sorting program for extracellular recordings. Version 1.4 (spike sorting, neuroscience, clustering)

CSI()

ExcludeOverlappingPoints(clustnum)

ISIfilter()

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updated 1 year ago

spikegauss: continuous firing rate time series from discrete spiketimes by R P

Generate spike vector time series (SPKVEC) from the TIMESTAMPS of the spikes. (neuroscience, convolution, gaussian)

[spkvec,timevec]=spikegauss(timestamps,srate,min_timevec,...

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updated 1 year ago

CellSort by Eran Mukamel

Toolbox for automated sorting of cellular calcium signals from optical imaging data. (neuroscience, image processing, signal processing)

CellsortApplyFilter(fn, ica_segments, flims, movm, subtra...

CellsortChoosePCs(fn, mixedfilters)

CellsortFindspikes(ica_sig, thresh, dt, deconvtau, normal...

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updated 2 years ago

Gabor function by Niru Maheswaranathan

Generates a 2D spatial Gabor function. Useful for generating model simple cell receptive fields. (gabor, function, image processing)

gabor(varargin)

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updated 2 years ago

Import of log files created by Presentation by Tobias Otto

This function imports log files created by Presentation into MATLAB for analysis. (neuroscience, presentation, log file)

importPresentationLog(fileName, extraNames)

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updated almost 3 years ago

Tracking neurons over multiple days by George Fraser

Algorithm from Fraser and Schwartz, "Recording from the same neurons chronically in motor cortex" (neuroscience)

computeAutoScore(auto)

computeBaseScore(base)

computeCorrScore(correlations, survival)

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updated 3 years ago

erp_reject by Luca Citi

Rejection of outlier trials from Event-Related Potential (ERP) studies (signal processing, medical, statistics)

erp_reject(erp, baseline_int, strip_g, out_max)

test_erp_reject.m

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updated 3 years ago

CeItrConnGUI by Gal Haspel

This GUI is used to study the iterativity of connections within the locomotion network of C. elegans (c elegans, neuronal network, connectivity)

CIC_MNtoMN(MuscleBin, NeurConnNames, NeurConnNumbs, MNnam...

CIC_NMJs(MuscleBin, MNnamesSrc, FPNumbs, FPNames, MNnames...

CIC_Open(Method, FileName, PathName)

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updated 3 years ago

Spike Train Regularity Analysis by Matthew Wright

Implements an improved regularity analysis for spike trains obtained from auditory neurons. (neuroscience, spike train, hearing)

VCN_regularity(t,spikes,type,N_min)

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updated 3 years ago

create_mosaic.m by Simon Robinson

create_mosiac.m - Create tiled "mosaic" images from volumes (mri, fmri, nifti)

centre_and_save_nii(image_nii, filename, pixdim)

centre_header(nii_hdr)

load_nii(filename, img_idx, dim5_idx, dim6_idx, dim7_idx,...

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updated 3 years ago

Univariate and bivariate spiking statistics for the dLIF neuron model by Robert

Functions to calculate the statistics for the dLIF neuron model. (neuroscience, integrateandfire, spike train)

A=bivgenerator(re1,ri1,IL1,lb1,th1,re2,ri2,IL2,lb2,th2,ce...

A=univgenerator(re,ri,IL,lb,th)

A=univgenerator_abs(re,ri,IL,lb,th)

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updated almost 4 years ago

Raster and PETH Simple Version by Sisi Ma

Raster and PETH for neuroscientists and others :) (signal processing, data exploration, biotech)

RSTPTHSMPL(node,spike,pre,pos)

[h1,h2]=PLTRSTPTHSMPL(rst,filename,bin,pre,pos,nodename)

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updated 4 years ago

paramsNeurofit - import parameters from Neurofit by Cengiz Gunay

Extract Hodgkin-Huxley type ion channel parameters from a Neurofit report file. (neurofit, hodgkinhuxley, channel)

paramsNeurofit(file_name, props)

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updated 4 years ago

MATRIS v0.10.10.09sb for Windows by Mingjing Zhang

A Full-Fledged MATLAB Based Tetris Game like none you've ever seen! (tetris, game, psychtoolbox)

GetGlobalValue(globalVar)

addTetradToPlayfield(blkMatrix, TetradX, TetradY, colorIn...

checkTetradOverlapping(blkMatrix, TetradX, TetradY)

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updated 4 years ago

Discrete-time cross-correlogram by Alex Wiltschko

Cures cross-correlograms and headaches!* *note: does not actually cure headaches. (crosscorrelogram, neuroscience, autocorrelogram)

crosscorrelogram(ts1, ts2, window)

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updated 4 years ago

spike_times.m by Rune W Berg

Detection of location of spike times (action potential, spikes, detection)

spike_times(trace,threshold)

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updated 4 years ago

SqueakySpk v0.1 by Jon Newman

SQUEAKYSPK: Matlab class for making extracellular, microelectrode array data squeaky clean. (neuroscience, action potential, electrophysiology)

false) SqueakySpk

SSExample.m

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updated almost 5 years ago

Spiking Neurons simulator by Massimiliano Versace

This GUi implements the Eugene Izhikevich (2003) spiking equation. (spiking neurons, artificial neural net..., demo)

SpikingNeurons(varargin)

SpikingNeurons(varargin)

SpikingNeurons(varargin)

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updated 5 years ago

spikePlot by Kai

Plotting function for waveform data; window discrimination (neuroscience, window discrimination, raster)

spikePlot(data, Fs)

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updated 5 years ago

SDFConv by Matthew Nelson

Given spike times across trials, create smoothed peri-event hist convolved with a PSP or Gaus kernel (neuroscience, histogram, spike)

sdf=SDFConv(spk,AlignEv,bn,ktype,sig)

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updated 5 years ago

Find Optimal Kernel by Matthew Nelson

Find optimal causal filter kernel that convolves with one time series to approximate another (neuroscience, psychology, filter)

k=FindOptKern(InSig,OutSig,MaxnLags)

TestFindOptKern.m

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updated 5 years ago

Align repeated trials of analog data to a variable event by Matthew Nelson

Align matrices of repeated trials of analog data to a variable event without a for loop over trials. (matrices, trial, saccade)

varargout=ADAlignTrials(AlignEv,bn,minTrTime,varargin)

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updated 5 years ago

Find Clipped Trials by Matthew Nelson

Find trial indices in which "clipping" occurred for recorded analog data in a trials format (neuroscience, psychology, trials)

ClipTrs=FindClipTrs(curADMat,nConsecSampCutoff)

getchunks(a, opt)

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updated almost 6 years ago

Minimal Stimulation analysis for pClamp by Chessa Scullin

paired pulse traces from a abf file and make comparisons to an average trace (neuroscience, abf, minimal stimulation)

import_abfminstimfiltered(file, en, dt)

datasum.m

minstimdl2fil.m

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updated 6 years ago

Two-Syringe MED Perfusion System by Matthew A. I. Ua Cruadhlaoich

Instructions and m-files for setting up a remote-controlled multielectrode dish perfusion system. (biotech, pharmaceutical, multielectrode dish)

mediumchanger1.m

mediumchanger2.m

mediumrefresher.m

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updated 6 years ago

MClust Spike sorting toolbox by A David Redish

Spike sorting toolbox (medical, neuroscience, tetrode)

((size(WVD,3) + 2) * (it-1)) + (1:size(WVD,3)); ...

AverageWaveform(WV,varargin)

CalculateFeatures(basename, featureList)

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updated 6 years ago

Postsynaptic Potential Detector by Phil Larimer

Detect postsynaptic currents or potentials (medical, epsp, epsc)

detectPSPs(data, varargin)

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updated 6 years ago

Nodose neuron action potential firing. by Vladislav Snitsarev

Model of action potential firing by an A-type nodose neuron (biotech, pharmaceutical, neuron)

NodoseNeuron

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updated 8 years ago

BrainMaps Analyze by Shawn Mikula

BrainMaps Analyze is a powerful tool for applying image analysis routines to BrainMaps.org high reso (medical, brain, image processing)

bmanalyze( varargin )

bmanalyzeGetPaths( varargin )

bmanalyzeInfo( varargin )

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updated 8 years ago

Rasterplot by Rajiv Narayan

Plotting Routine to display neural spike trains (specialized, plotting, rasterplot)

rasterplot(times,numtrials,triallen, varargin)

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updated 10 years ago

NESim by Chris Eliasmith

General package for large-scale biologically plausible simulations (with GUI). (neural and fuzzy syst..., neural simulation, neural networks)

EnsembleInfo(filename)

RunSimulation(Method,tauSyn)

a=genActivities(NeuronParms,Rvalues,Type)

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