Gitlab Repository Biofysica
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:
- Bayesian data analysis
- Saccade analysis
- Spike analysis
- Pupillometry
- Reaction time
- Audition
Other:
- Plot utilities
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 making an audiogram.
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.
https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/eeg?ref_type=heads 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.
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 Matlab utilities:
- Signal processing: filters, power, smooth
- Tutorials: How2 examples of all kinds of data analysis
- Coördinates: 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