Gitlab Repository Biofysica

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Description

The biofysica repository is the main repository written by and used in the Biophysics Department. The code consists mainly of for matlab code for performing experiments and analysing experimental data.

Experiments:

• Sound Localization experiments with TDT System 3 or RZ6
• EEG experiments
• NIRS experiments
• Audiogram (arcMAA) with RZ6

Data analysis:

• Audition
• Bayesian data analysis
• Pupillometry
• Reaction time
• Saccade analysis
• Spike analysis

Other:

• utilities

N.B. The Matlab files beginning with 'pa_' are developed by Marc van Wanrooij and are originally part of the Perception and Action Toolbox (PandA).

How to install the toolbox

• Download the biofysica toolbox from Gitlab and save it in C:\Users\MyName\Documents\MATLAB\biofysica
• Add to your startup.m file:

addpath('C:\Users\MyName\Documents\MATLAB\biofysica'); 
init_biofysica;

When you are not certain how to use Gitlab you can find more info here: Gitlab.

Repository content

The repository has several directories:

TDT

Contains all relevant TDT manuals for ActiveX programming, RZ6, system3 and RPvdsEx programming.

• MF1: contains info about the MF1 speaker kit of tucker davis
• PM2rRBOXRZ6: contains info about connecting the RBOXRZ6 to the PM2r control port (DB25 digital I/O).
• Users/Marc van Wanrooij: contains some *.rcx files used by Marc van Wanrooij

audiogram

Contains matlab and rcx code for the arcMAA experiment. MAA stands for Minimum Audible Angle. The experiments is done in the NIRS-EEG lab with the speaker arc.

audition

Contains basic and advanced functions for manipulating audiological units and spectra.

• HRTF: contains matlab functions for calculating and manipulating head-related transfer functions.
• localization: contains matlab functions for localization of stimuli.
• oldpa: contains older matlab functions from the Panda toolbox.

backwards

Contains only the script loadtdt.m that reads a *.tdt file. It is no longer used.

bayesdataanalysis

Contains matlab scripts for bayesian data analysis based on programs for use with the book:

Kruschke, J. K. (2015). Doing Bayesian Data Analysis

The codebase also includes code from JAGS (Just another Gibbs sampler ), which is a program for simulation from Bayesian hierarchical models using Markov chain Monte Carlo (MCMC), developed by Martyn Plummer

• NHST: contains matlab script bayesfactor.m
• anova: contains matlab scripts for ANalysis Of VAriance (ANOVA)
• binomial: contains matlab scripts for binomial analysis
• correlation: contains a matlab script for Pearson Correlation
• diagnose: contains matlab scripts for Markov Chain Monte Carlo (MCMC) diagnostics
• functions: contains matlab script for several useful functions
• psychophysics: contains matlab scripts for analysing psychometric functions (curves)
• regression: contains matlab scripts for regression analysis
• reparametrization: contains matlab scripts for %todo
• statistics: contains matlab scripts for calculating summary statistics.
• HDI: contains matlab scripts for calculating Highest Density Intervals (HDI)
• utilities: contains matlab scripts for several utility functions used in the bayesian data analysis code.

eeg

Contains two EEG demos (AM tones and Oddball) with matlab code and RZ6 circuits (RPvdsEx files).

experiment

Contains Matlab and other files for experiments and for controlling devices. See Gitlab Repository Biofysica/experiment.

• Experiments: SpherePrime, SphereTTL, SphereMinor, NewSpherePrime, SLIMS, arcMAA, ripple_prt_experiment, Experiment generator (Exp), psychoILD, HRTF, EEG
• Devices: Panasonic PLC Led controller, DCN-LED Led controller, Panasonic Servomotors, Pupillabs
• Other: BIOX toolbox, HDF5 toolbox, Ini-file toolbox, FileIO utilities, IP utilities, Modbus utilities, Mewtocol utilities, LSL utilities

init.d

Contains Matlab initialization code. Maintained by Günter Windau.

liblsl

Contains LSL (LabStreamLayer) code. Maintained by Günter Windau.

nirs

Contains NIRS related Matlab files and a NIRS analyse document.

• basics: contains Matlab files for fnirs hemodynamics
• layout: contains EEG *.lay files and *.xml optode template files.

plot

Contains Matlab code for advanced plotting of figures and graphs

pupillometry

Contains Matlab code for pupillometry measurements.

reactiontime

Contains Matlab files for calculating reciprobit plots of saccadic latencies.

saccade

Contains Matlab code for Saccade analysis. Part of PANDA toolbox.

spike

Contains Matlab code for spike analysis for neuro-physiological experiments. Part of PANDA toolbox.

utilities

Contains general functions:

• Colors: colorcodes from names in English, German, Dutch and Spanisch. See Colors in Matlab.
• Coordinates: coordinate classes and coordinate transformations. See Coordinate systems.
• DSP: Signal processing: filters, power, smooth
• Coordinates: several conversion functions for Azimuth, Elevation, Cartesian, Radial, Degrees, Quaternions etc...
• FileIO: file utilities
• Graphics: graphics utilities
• Python: utilities for python installation and use in Matlab.
• Statistics: utilities for statistics
• Text: function for finding strings in a textcellarray
• Tutorials: How2 examples of all kinds of data analysis