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,ma...

CellSort by Eran Mukamel

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

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

CellsortChoosePCs(fn, mixedfilters)

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

MatClust by Mattias Karlsson

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

CSI()

ExcludeOverlappingPoints(clustnum)

ISIfilter()

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)

Gabor function by Niru Maheswaranathan

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

gabor(varargin)

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)

Whisker Tracker WT by Per Magne Knutsen

Whisker Tracker is an application for tracking rodent head/whisker movements from high-speed movies. (image processing, whisker tracking, whiskers)

CheckFilename(sFilename)

D=rad2deg(R)

ExportToExcel(cHeaders, cData)

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)

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

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, MNnames...

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

CIC_Open(Method, FileName, PathName)

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)

create_mosaic.m by Simon Robinson

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

centre_and_save_nii(image_nii, filename, pixdim)

centre_header(nii_hdr)

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

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

Functions to calculate the statistics for the dLIF neuron model. (integrate and fire, integrateandfire, statistics)

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

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

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

AIS quantification by Matthew Grubb

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

ais(cell,chosen)

ais_z3(cell,chosen) %%% for cell-by-cell analysis

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)

paramsNeurofit - import parameters from Neurofit by Cengiz Gunay

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

paramsNeurofit(file_name, props)

MATRIS v0.10.10.09sb for Windows by Mingjing Zhang

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

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)

spike_times.m by Rune W Berg

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

spike_times(trace,threshold)

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

Spiking Neurons simulator by Massimiliano Versace

This GUi implements the Eugene Izhikevich (2003) spiking equation. (spiking neurons, demo, simulation)

SpikingNeurons(varargin)

SpikingNeurons(varargin)

SpikingNeurons(varargin)

spikePlot by Kai

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

spikePlot(data, Fs)

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)

Find Optimal Kernel by Matthew Nelson

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

k=FindOptKern(InSig,OutSig,MaxnLags)

TestFindOptKern.m

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)

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)

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

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

MClust Spike sorting toolbox by A David Redish

Spike sorting toolbox (medical, neuroscience, tetrode)

Postsynaptic Potential Detector by Phil Larimer

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

detectPSPs(data, varargin)

Nodose neuron action potential firing. by Vladislav Snitsarev

Model of action potential firing by an A-type nodose neuron (action potential, hodgkinhuxley model, neuron)

NodoseNeuron

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 )

Rasterplot by Rajiv Narayan

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

rasterplot(times,numtrials,triallen, varargin)

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)