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Institute of Medical Psychology • GRP at Ludwig-Maximilian University München • Dept. of Med. Psychology Univ. Göttingen
(A) Libraries for Psychophysics (B) Public Domain Applications for Psychophysics
- PsychToolbox (Matlab/Octave)
- VideoToolbox (C)
- Stimulus presentation from MatLab, Mathematica, Visual Basic etc.:
ShowTime, MatVis, Cogent 2000, PsychToolbox, Cinematica
- Cogent (Matlab)
- Palamedes (Matlab/Octave)
- MGL (Matlab/Octave)(openGL)
- Psychophysica (Mathematica)
- Vision Egg (Python)(openGL)
- PsychoPy (Python)(openGL)
- PyEPL (Python) (Unix)
- psyphy, MLDS, and MLCM (R)
- PXL ("Pixel"), PXLab (C)
- McLeod's C routines
- Peach (C++)(openGL)
- Adaptive Threshold Measurement,
MLPest, YAAP, Quest, bestPest, Kontsevich & Tyler, Palamedes, FAST, Levitt's up/down (Matlab), Treutwein's review
- Colorlab (Matlab/Octave)
- Image processing (IPRS, Gabor decomposition, QUIP)
- QuIP (Unix)
- GERT (perceptual grouping) (Matlab/Octave)
- Open Perimetry Initiative (OPI) (R)
- Freiburg Visual Acuity Test
- quick CSF
- Irtel's Psychology Applications
- Colour Vision Demo (Educational)
- Additive & Subtractive Colors of Light (Educational)
- Visual World (Visuelle Welt, VIWO) (Educational)
- Project LITE (Educational)
- CU Colour Deficiency Screening
- Motion contrast (Düsseldorf)
- Little Stimulus Maker (LSM)
- Digital Embryo
- nrec - neuronal recording(openGL)
- L-POST for neuropsychological screening
(C) Commercial Systems for Psychophysics (D) Psychophysical data analysis, SDT
Related Domains of Software
(F) Psychological Experimenting Systems
- Ophthalmic Screening
- Umist Eye System
- Thompson Software Solutions
- Lea Hyvärinen
- Precision Vision printed charts
- Macular Mapping Test (MMT)
- Open Perimetry Initiative (OPI) (R)
Cognitive Neuroscience General Experimenting Systems fMRI and EEG analysis tools
- Presentation, VisGen
- PsychoPy (Python)
- Paradigm (Python)
- PyEPL (Unix, Python)
- Experiment Builder
- OpenSesame (Python)
- Wiener Testsystem
- ERTS, ERTSLab
- PEBL (Psychology Experiment Building Language)
How well do we see? How can visual function be described and which mechanisms can be thought to underly? Visual psychophysics tries to give answers to these general questions, and research in this area needs specialised software. This is an overview on what is available.
Since I first compiled the overview in May 1995 there were uncountable revisions. But he general picture has not changed – the three main platforms are still the PC, the Macintosh, and Unix variants. With the increased power of hardware the notion of special Unix workstations has disappeared in the 90s and has been replaced by public-domain Unix derivatives like Linux, Debian, Ubuntu etc. The three communities, still live happily in parallel, mostly unaffected by the boring developments in the other. There are a few signs of true integration, however, as is perhaps evidenced by cross links between the entries below. Many packages have been steadily supported and improved, and find more wide-spread use. Others have stagnated. I left the latter in the overview – by the regularity of updates one can easily assess whether a system has supporters.
The status of 1997 is captured in two special issues of the journal Spatial Vision, Vol. 10(4) and 11(1), named Use of computers and cathode-ray-tube displays in visual psychophysics, Part I & II. The tables of contents are on the web; they contain links to authors and pdf's provided by them. All papers are available online (pdf) through a subscribing library, some are available on authors' personal homepages. – This is now more than a decode ago, and an up-to-date scholarly compilation would be needed. Those were the times when monitors still did what the experimenter wanted them to do. Have you kept a CRT in your storage room? You didn't (like I) because they are just too bulky but might be unpleasantly surprised by the limitations of current technology. Read the papers of Elze & Tanner on LCD monitor timing and misspecifications of stimulus duration, and the CVNet discussions collected in the monitors section below.
When I started this overview, I had a simple question: How should we best do psychophysical experimenting – including simple things like measuring a contrast-sensitivity function or visual acuity? When somebody starts anew, should one recommend a Unix base or a simple PC or Mac? Is there a certain package that is best suited? It turns out there is no simple answer. It also turns out there is a wealth of software and hardware out there to do the experiments.
The story of software development for psychophysics – like any other story of software development – is one of continuously reinventing the wheel. Hundreds of laboratories have set up powerful facilities. When I started out, the software was mostly tied to specific hardware, perhaps custom designed or not easily available. This has changed quite a bit and hardware dependency is less of a problem today. But nowadays operating system dependency can be an equal hindrance, despite all the claims to the contrary. Good software does not catch on when it is simply not polished enough to be spread and used by others. Sometimes good packages get abandoned by their authors when they (have to) switch their field of work; support then becomes a problem. Where ever one looks, different packages represent incompatible solutions to overlapping areas of application. The three platforms for psychophysical experimentation, PC, Macintosh and Unix, still are the focus of often separate user communities. Back in the 90s, however, Denis Pelli has started to turn the wheel by giving an inspiring example of sharing when he made available his VideoToolbox, a highly stable, well supported software basis for visual psychophysics on the Macintosh. The VideoToolbox has paved the way for the use of high-level languages like Matlab and is the basis for the Psychtoolbox which has finally led to convergence of platforms. Today there are systems in many high level languages. My aim with this web page is to contribute to cooperation by bringing together the developers of software and their users.
An important development is the maturation of general purpose psychological experimenting systems (Section F). Due to the inability of earlier versions of Windows to handle real-time applications, professional packages were for the Macintosh only (an early system was PsyScope). Nowadays there is an impressive line of general-purpose systems for Windows. To add flexibility, several can optionally be programmed with Python. Ironically, whilst timing with millisecond accuracy is no longer an obstacle for the current operating systems, it has become a problem with monitor technology.
Scope: The overview covers both public domain material and commercial systems. A number of related fields of software have further been added because it is often not possible to draw a sharp line between areas.
The list is ordered into 15 sections:
(A) program libraries (public domain);
(B) public domain applications, i.e., executable programs or program systems;
(C) commercial systems for psychophysics;
(D) psychophysical data analysis including programs for signal detection theory-based analysis;
(E) programs from Ophthalmology and Optometry;
(F) general-purpose psychological experimenting systems, i.e. systems that are more general in applicability;
(G) Psychological Experimenting Systems that are geared towards cognitive neuroscience;
(H) More general experimenting systems;
(I) Analysis tools for fMRI and EEG;
(J) programs from visual neuropsychology, i.e. geared towards brain-injured patients;
(K) programs from visual neurophysiology, e.g. for single-cell recording;
(L) a pointer to the eye-movement list;
(M) a few pointers to virtual reality software;
(N) a few hints on hardware matters like response boxes
(O) some random examples for auditory psychophysics
(P) Notes on Open Science, and
(Q) a collection of museums and illusions
For easier spotting, I have put platforms in bold
Since the times of Gustav Theodor Fechner, psychophysics was aimed at more than the understanding of (quantitative) relationships between external and internal world (physis and psyche). Fechner intended it to be a means of thereby also learning about the underlying, neural or other, mechanisms of perception. Exemplified is this when Fechner used the Weber fraction from physiology for quantifying the increment in Empfindungsstärke (intensity of sensation). Today we see the same when psychophysical techniques find use in the sciences that study perception in a broader sense, like sensory physiology and anatomy, biopsychology, or indeed the whole of visual and cognitive neuroscience. I therefore hope that the software shown here is seen as a core which will find more widespread use in all these neighboring sciences. Indeed it already does whenever perception is involved.
This Overview is available on the VisionScience page (under Resources/Software and Guides&FAQs) and on my personal homepage in München (direct link). There are numerous links from other software- and methods overviews. It was reviewed in iPerception in 2012 (open access) by Damien Mannion. Note that now all the links have been dusted-off! Entries that are of historical interest only are marked by using past tense. Note also that the ordering in each category tries to group similar items (as far as that goes) and implies no ranking of resource quality. Furthermore, the site is now HTML 4.01 compatible.
A regular source of information on software is the journal
"Behavior Research Methods, Instruments, and Computers".
There are occasional papers in
Journal of Neuroscience Methods and in Computers in Biology and Medicine (CBM).
Monitors and Timing
There are my two special issues in Spatial Vision (10/4 and 11/1):
"Use of computers and cathode-ray-tube displays in visual psychophysics"
An overview of methodological issues in stimulus presentation is found in our paper
Bach M, Meigen T & Strasburger H (1997). Raster-scan cathode ray tubes for vision research–limits of resolution in space, time and intensity, and some solutions. Spatial Vision 10, 403–414.
For monitor calibration I would like to refer to my own paper
Strasburger H, Wüstenberg T & Jäncke L (2002). Calibrated LCD/TFT stimulus presentation for visual psychophysics in fMRI. Journal of Neuroscience Methods 121, 103-110.
Paper of Tobias Elze & Thomas Tanner (2009) on LCD monitor timing
A further paper by Tobias Elze (in PLoS ONE) on mis-specifications of stimulus duration. Check out Fig. 6!
A paper by S. Wiens et al. in Psychological Science, "Keeping It Short. A Comparison of Methods for Brief Picture Presentation"
Short chapter on LED monitors by Watson & Silverstein.
Thread on Visionlist 2009 on timing issues with subject "CRT monitor solutions"
Mail on 120 Hz TFTs by Michael Dorr, 2010
Danko Nikolic wrote a report on a 120 Hz Samsung Monitor. A preprint appeared on his web page. Answers by by Michael Bach and Vincent Ferrera.
Informal comparison of Unix, MacOS and Windows wrt timing by Mario Kleiner
Also check out the VIEWPixx monitor system described below.
Comparisons of Psychophysics Software
This section is at the moment mostly a stub. Comparisons are important but presently I am aware of only one independent paper. I will add more (hopefully) with time.
Rolf Kötter (2009) (based on Peirce, 2007, and Straw, 2008) briefly compares the two Python-based packages Vision Egg and PsychoPy, also touching Psychtoolbox, and Presentation.
Textbooks or Chapters on Psychophysical Methods
Psychophysical measurement, in general
Ehrenstein WH, Ehrenstein A (1999). Psychophysical Methods. In: Windhorst U, Johansson H (Eds): Modern Techniques in Neuroscience Research, pp. 1211-1241, Springer-Verlag, Berlin.
Gescheider GA & Gescheider. Psychophysics: The Fundamentals. Lawrence Erlbaum Ass., 1997
Norton, Corliss, & Bailey (2002/2007). The psychophysical measurement of visual function. Previously published by Butterworth-Heinemann - now available from Richmond Products (direct link).
Rose D (2006). Psychophysical methods. In Breakwell GM, Hammond S, Fife-Schaw C and Smith JA (eds.) Research Methods in Psychology, Third Edition, Sage, London, pp. 160-181. (mentions psychometric functions and 2AFC – without any of those tedious boring details)
Schwartz (2004). Visual Perception: A clinical orientation. 3rd ed. McGraw-Hill. The book has a chapter on "Psychophysical Methodology".
Kingdom, F.A.A. & Prins, N. (2010). Psychophysics: A Practical Introduction. Academic Press, an imprint of Elsevier, London. It's (currently) the most recent treatise on psychophysics, and provides details about the Palamedes toolbox.
Signal Detection Theory
Macmillan & Creelman (2004). Detection Theory: A User's Guide. 2nd ed. Lawrence Erlbaum Associates. Also available as an electronic version.
Wickens (2001). Elementary signal detection. Oxford University Press. (Best introductory text to my opinion)
McNicol: A primer of signal detection theory. Lawrence Erlbaum Assoc, 2004 (Nice little book)
Classroom Materials for Psychophysical Methods and Perception
These are just a few that I came across. If somebody points me to a survey I can post it here.
Scott Steinman makes available his classroom material. To quote him, these are "70 demo programs for eye exams and vision science. Nothing fancy, but they work for the classroom. They're available to vision science instructors for both Mac OS X and Windows (although the Mac versions work a little better).
"Precision and Accuracy with Three Psychophysical Methods" is an interactive web-site for students developed by Hiroshi Ono, Kenzo Sakurai and others. It covers the method of adjustment, method of constant stimuli, and method of limits. Remarkably, it is available in Englisch, French, Japanese, and Chinese.
Explaining what simple cells do: A Matlab script by Daisuke Kato & Izumi Ohzawa performing a 2D Gabor Wavelet Transform on an arbitrary image, and back. Slowly and sequentially you can visualize how the original image is reconstructed by summing many Gabor wavelets.
Three classical illusions with adjustable parameters modified from Java applets of Tony Azevedo:
Ponzo Illusion; Poggendorf Illusion; Müller-Lyer Illusion.
On a different topic, Robert Jacobs from Rochester made available his lab's "Computational Cognition Cheat Sheets". These (currently 22) notes provide brief introductions to several computational methods, mostly stemming from multivariate analysis (like Bayesian estimation, Factor analysis etc).
A few further materials were already mentioned in Section B:
Colour Vision Demo
Additive & Subtractive Colors of Light
Visual World (Visuelle Welt, VIWO)
Project Lite, a collection of free visual illusion and experimenting apps.
Discussion Lists, Archives
PsychToolbox Discussion List: The discussion list for the PsychToolbox
Encyclopedia of Psychology: A comprehensive portal to psychology software
Visiome is an impressive Japanese vision archive with many original contributions
The Colour & Vision Research Laboratory, London, maintains a large, very well organized repertory of vision related materials.
NeuroDebian is a platform and software archive (see below)
AVA Vision research
and its applications
The International Society for
When I was young and pretty I learned about public domain software and believed it was a great idea to give your software away for free. I wrote a package for the measurement of visual evoked potentials on the PDP-11 — in Fortran. My next package was for visual psychophysics (R_Contrast), also for the PDP-11 and also in Fortran. There were what was called Special Interest Groups of people who shared their software. That spirit was what got me started doing this Overview. But the fascinating thing is how it has caught on! At some point there came Open Source, then Open Access publishing, and now Open Science. So for me it's really coming full circle with OpenVisionScience. What can I say! Join and enjoy! Here is a photo of me playing Zork on my home-built CP/M Z80 machine (it had a RAM disk and was fast).
Perception Museums (in Europe)
When you come to Europe (with your kids), don't miss the little perception museums:
"Turm der Sinne" in Nürnberg!
Explora (Erlebnismuseum, Frankfurt)
Perception Museums (elsewhere)
I wanted to limit the fun part to Europe. Oh well — what the heck; here are more — elsewhere. It probably all started with the Exploratorium in San Francisco, which you all know. Here are some that you don't know:
PuzzlingWorld is in New Zealand. It has the largest Ames room of all and a great suite of tilted rooms, according to Robert O'Shea.
Art connected to Vision Science
Arts exhibition at the Torre di Sulis during ECVP 2012 in Alghero
(>> back to table of contents)
For maintaining this site, I need coffee. Here is your chance to buy me some:
(A) Libraries, public domainGeneral purpose psychophysics libraries for Mac, PC, and X-Windows platforms.
The PsychToolbox (PTB) (previously Psychophysics Toolbox) is a (free) package of interface routines to do visual psychophysics from within MatLab under Mac OSX, Linux and Windows. It evolved out of the desire to create a high-level environment for Denis Pelli's VideoToolbox on the (pre-OSX) Macintosh (by David Brainard) and now probably is the most comprehensive and has the largest followership of all psychophysics packages. Main developer since around 2006 is Mario Kleiner.
To become independent of commercial Matlab, PTB supports GNU/Octave, a free and open-source replacement for Matlab. The PTB further ships with MOGL (Matlab OpenGL), a thin wrapper around every OpenGL function as known from C. This makes developing pure OpenGL in Matlab easy. One can switch between this lower level functionality and the PTB functionality to compose a screen. Full-3D scenes are easy to do. The PTB supports the Bits++ box. There is an integrated PsychToolbox forum and also a PsychToolbox discussion list on Yahoo.
The most general one for a long time was Denis Pelli's (formerly Syracuse U., now New York U.) VideoToolbox for the Mac. It is a collection of 200 subroutines written in C, using Apple's Macintosh (pre-OSX) Toolbox, compatible with Metrowerks and THINK C, 68k and PowerPC. Things which were not hardware specific, like threshold estimation, are in standard C and can be used on other machines. (Also see Psychophysics Toolbox and Cinematica, to use the VideoToolbox from within MatLab or Mathematica.) The VideoToolbox is free (and may not be sold without permission) and is still available on the web site (click here). There is a mailing list for users and prospective users (email). Higher than 8 bit grayscale resolution on the Mac can be achieved by using Denis Pelli's Video attenuator. It works by combining colour channels to achieve 12 bit on a black-and-white monitor. (Is it discontinued?) (Another way is to use the Bits++ box, and still another way is Tyler's color bit stealing technique).
While we're at it: Check out Denis' tips on scientific writing!
2a) VideoToolbox & MatLab:
The Psychophysics Toolbox, written by David Brainard in collaboration with Denis Pelli, is a package of interface routines to use the VideoToolbox from within MatLab on the Macintosh. It is superseded by the PsychToolbox.
2b) VideoToolbox & Mathematica:
Joshua Solomon and Beau Watson of NASA have developed a Mathematica front-end to Video Toolbox and the Pelli-Zhang Video Attenuator, called Cinematica, for producing calibrated grayscale movies on a Mac. It is part of Psychophysica (see below).
2c) Advice for the Macintosh
Denis Pelli provided a general advice page, centered around the VideoToolbox, on how to set up psychophysical experiments on the Macintosh. Is seems to be discontinued?
3) Stimulus presentation from
MatLab, Mathematica, Visual Basic etc.
As computers got faster, interpretative high level languages like Mathematica and MatLab became particularly attractive. A number of packages bridge the gap between these "slow" languages and the time-critical task of stimulus presentation.
3a) Psychophysics Toolbox
3b) ShowTimeShowTime, developed by Andrew Watson, James Hu, Cesar Ramirez, and Denis Pelli, is a package for presenting calibrated dynamic stimuli from high-level languages (Mathematica, MatLab, Visual Basic), using Apple's QuickTime technology. As such it should run on both the Macintosh and the PC.
3c) MatVis / WinVisMatVis by Thom Carney of Berkeley was a package for presenting precisely-timed stimuli from within MatLab for the PC. It was extended considerably into WinVis (see below). Both are no longer available.
3d) CinematicaCinematica is part of Psychophysica(see below). It runs on the Power Macintosh.
Cogent is a (now) freeware MatLab Toolbox for stimulus generation and presentation, and response recording on the PC, in an fMRI environment, initially (1995) written to allow a novice in the Functional Imaging Laboratory (University College London) to do brain imaging and psychophysical studies. It consists of Cogent 2000 for the precisely timed interaction with peripherals, and Cogent Graphics for the graphics.
Cogent 2000, besides presenting stimuli and recording responses with precise timing provides additional utilities for the manipulation of sound, keyboard, mouse, joystick, serial port, parallel port, subject responses and physiological monitoring hardware. For fMRI experiments, Cogent 2000 can be configured to receive synchronization pulses from a scanner allowing experimental timing to be tightly coupled with image acquisition.
Cogent Graphics, written by John Romaya (in Zeki's Lab) is a graphics toolbox for MatLab on the PC. It can generate realtime graphical animations for use as stimuli in visual experiments. Cogent Graphics provides commands for generating animations with millisecond accuracy at refresh rates up to 160 Hz as well as mouse and keyboard support for user input.
The project is funded by the Wellcome Trust, groups involved in the development are the Laboratory of Neurobiology, the Functional Imaging Laboratory (the place where SPM was developed), and the Institute of Cognitive Neuroscience
Palamedes, written by Nick Prins (Mississippi University) and Fred Kingdom (McGill Univ.) is a free toolbox of Matlab or GNU Octave routines for the analysis of psychophysical data. It allows
- Psychometric Function fitting (ML and Bayesian, with an option of simultaneous PF fitting where certain parameters are kept constant across the fit),
- Max.-Likelihood Difference Scaling,
- Bootstrapping (parametric and non-parametric),
- Signal Detection measures,
- Goodness-of-fit tests,
- Statistical Model Comparisons (e.g., "do thresholds differ significantly between experimental conditions?" or even: "do thresholds vary as a linear function of, say, adaptation duration or is that accelerating/decelerating trend in the data 'real'?"), and
- various adaptive methods (up/down, best PEST, QUEST, Psi Method, Kontsevich & Tyler).
All user-end routines include elaborate help comments, including example code that will execute when typed into command window. Also provided is a set of heavily commented demonstration scripts which guide the user through all of the major analyses. Palamedes requires either basic Matlab (with no additional toolboxes; it is compatible with older versions of Matlab, going back to at least release 14  and likely much further), or GNU Octave, making it available to folks who do not have Matlab. Kingdom & Prins' textbook on psychophysics makes use of Palamedes.
MGL is a library for Matlab and Octave that allows easy programming of visual (and some auditory) stimuli using OpenGL. Current versions run on Mac OS X and Linux; a Windows port is underway. MGL was developed jointly by Justin Gardner and Jonas Larsson at New York University, and others. A mirror of the documentation and a Linux version can be found here.
7) PsychophysicaPsychophysica is a collection of Mathematica 'Notebooks' containing functions for collecting and analyzing data and presenting stimuli in psychophysical experiments. The components at this time are Quest.ma, Psychometrica.ma, and Cinematica.
Psychometrica.ma contains functions for fitting and plotting psychometric data, as well as definitions of Weibull, Logistic, and Normal psychometric functions.
Quest.ma contains functions that implement the QUEST adaptive psychometric procedure for use in psychophysical experiments.
Cinematica is a software package for producing calibrated grayscale displays from within Mathematica, written by Josh Solomon and Andrew Watson.
The three components - Psychometrica, Quest, and Cinematica - are designed to work together, though each may be used on its own. Each includes a brief tutorial. The package is described in detail in the mentioned special issue of Spatial Vision (Part I).
8) Vision Egg
The Vision Egg aims at addressing many of the points raised in my introduction above. It is a cross-platform programming library under Windows/Linux +SGI Irix/Mac OS X, to produce visual stimuli for vision research experiments on standard graphics cards. The primary author is Andrew Straw. Citing from the web page, "The Vision Egg allows the vision scientist (or anyone else) to program these cards using OpenGL, the standard in computer graphics programming. Potentially difficult tasks, such as initializing graphics, getting precise timing information, controlling stimulus parameters in real-time, and synchronizing with data acquisition are greatly eased by routines within the Vision Egg." A popular and fast supported graphics card on the PC is from nVidia. The 10 bit DACs/LUTs available on most recent video cards are supported. (The advantage of using an SGI is that it has true 10-bit grayscale resolution, i.e. 10-bit framebuffers. Other video cards which support 10-bit framebuffers in OpenGL will work similarly once available). The Vision Egg comes with demo applications. Because it is an open-source project (GNU LGPL), it is free to download and use.
See below under Psychological Experimenting Systems
See below under Psychological Experimenting Systems
11) psyphy, MLDS, and MLCM
Ken Knoblauch from Lyon, France has written three libraries for R that are aimed at psychophysics and scaling, psyphy, MLDS, and MLCM
(See also the section on psychophysical data analysis below; statistics, psychometric function fitting, SDT), and the new book on modeling psychophysical data in R.
psyphy is an assortment of functions useful in analyzing data from pyschophysical experiments. It includes functions for calculating d' from several different experimental designs, routines for fitting the (m-afc) psychometric function using the generalized linear model, and selfStart functions for estimating gamma values for CRT (and possibly other RGB) screen calibration data (a selfStart function is a special kind of function in R that includes a nonlinear model specification as well as a function to estimate initial values for the fitting process directly from the data). See their paper in Behav. Res. Meth. Instr. Comp. mentioned below
MLDS implements analyses for Maximum Likelihood Difference Scaling. Difference scaling is a method for scaling perceived super-threshold differences. The package contains functions that allow the user to fit the resulting data by maximum likelihood and to test the internal validity of the estimated scale. There are also example functions that might be used to design and run a difference scaling experiment.
MLCM provides tools for analyzing conjoint measurement experiments. Conjoint measurement is a psychophysical procedure in which stimulus pairs are presented that vary along two or more dimensions and the observer is required to compare the stimuli along one of them. The package contains functions to estimate the contribution of the n scales to the judgment by a maximum likelihood method under several hypotheses of how the perceptual dimensions interact. It is described here, here, and here.
Once you have loaded R from CRAN, you can get any of the packages from within R using the function install.packages() (provided that you are connected to the internet). A direct link is above. Any suggestions, criticisms, bug-reports, etc. are always welcome.
12) PXL ("Pixel")Hans Irtel's PXL is superseded by his web-based PXLab, which is developed as part of a Virtual University. The experiments in Irtel's book (Stroop effect, Sternberg paradigm etc.) are already available.
PXL: For visual perception, including visual psychophysics, on the PC and on Unix machines, there is Hans Irtel's (formerly Regensburg, now Mannheim) library PXL. It is written in C and runs on PCs under MsDos (including the DOS in Windows95/98) and on Unix machines under X-Windows. The library supports 8 bit per color channel on many SuperVGA Boards and there are special compiled versions for Texas Instruments TIGA boards and for miro SuperVGA boards based on S3 graphics accelerator chips. It also has support for 8-bit monochrome gray-scale (important for contrast-sensitivity measurement) on some SVGA boards including the popular Matrox Mystique and later Matrox boards. There is further an interface to the Cambridge Research Systems VSG2/x boards, see below), so applications developed for standard VGA can use a high-quality back end. About 100 well-known psychology experiments have been developed as applications running on top of the library, some of which are described in a book (see below). Some might know Irtel's demonstration program CVD (see below) which has been written with this library. The library, documentation, and demos are available from the web page. The complete PXL manual is on the web. The main disadvantage of PXL is the dependence on specific graphics boards (stemming from the DOS architecture) and this is the reason why it is not further developed. The succesor is the Java based PXLab.
There is further an interface package to Fortran, FORPXL written by Martin Jüttner (now Aston University), that provides access to PXL from applications written in the Fortran language, thus allowing to use these older applications on current systems without the need for a rewrite. FORPXL is described in the special issue of Spatial Vision (Part I).
13) McLeod's C Routines
A further set of C routines for psychophysical experimentation under DOS is the library exp by Don McLeod, developed out of earlier work by Jeff Mulligan, John Krauskopf, and Walter Kropfl. The documentation of how to use is contained in the program sources. Interaction with the user is by parameter files. The library contains a 'staircase with "conservatism" to limit excursions from previously presented values'. There is further a set of MatLab scripts for the analysis of data acquired with exp.
Peach, written by Yury Petrov of Northeastern University, is a new large C++ library for visual psychophysics, running under Linux or Mac OS X. It contains an extensive collection of visual primitives (Gabors, Disks, Bars, Text, Images, etc.) as well as a set of experimental functions, which are said to allow coding a complicated experiment in a few dozen lines. It features subpixel resolution, gamma correction, 10-bit pixel depth (by dithering) and 13-bit pixel depth (via CRS Bits++ box), stereoscopic presentation (anaglyphic, mirrors, or shutters), Method of Constant Stimuli and the Kontsevich & Tyler (1999) adaptive thresholding algorithm, graphical user interface, OpenGL support, command line scripting (Pearl), and more. Only basic knowledge of C is required.
15) Adaptive Threshold MeasurementFor software concerning the underlying psychometric principles see Section D below, and a special issue of Perception & Psychophysics (Vol. 63) on the topic.
15a) MLPestFor the more specific purpose of presentation strategy, there is Lew Harvey's (Boulder, CO) library MLPest (previously called ML-TEST) which implements a maximum likelihood staircase procedure. It is avaliable in standard C and C++ and should be mostly machine independent. For the Mac and the PC you can download executable files from Harvey's web page. There is a good treatment in Harvey (1986), Behav. Res. Meth. Instr. Comp. 18, 623-632, and in Spatial Vision 11, 121-128. Harvey's documentation is especially thorough and helpful.
Bernhard Treutwein has a package YAAP for adaptive staircasing, based on Bayesian statistics, which has certain refinements over the maximum-likelihood approach. The package is written in Component Pascal but if requested can be provided machine-translated to C.
For a comprehensive overview of adaptive procedures see his review: Treutwein, B. (1995). Minireview: Adaptive psychophysical procedures. Vision Research 35, 2503-2522.
15c) QuestQuest (Watson, A.B. & Pelli, D.G., 1983, Perception & Psychophysics 33, 113-120) is available, (probably: also), as Mathematica Notebook. See Psychophysica, above.
15d) bestPestPentland's (1980) best PEST has been implemented by Hans-Jörg Zuberbühler as a " web-based application for non-expert users" which allows easy calculation of individual thresholds. It can be downloaded from the ETH Zürich.
15e) Kontsevich & Tyler (1999)
Kontsevich & Tyler's thresholding algorithm (Vision Res. 39:2729-37, 1999) is implemented e.g. in Yury Petrov's Peach C++ package, in PsychToolbox, and in Palamedes.
Palamedes (see the entry above) contains several adaptive thresholding algorithms: up/down, bestPEST, QUEST, Psi Method
15g) Functional Adaptive Sequential Testing (FAST) (Matlab)
FAST, written by Ed Vul, is a Matlab toolbox for running advanced staircases. "Functional" refers to the fact that FAST operates over two-dimensional functions: (e.g., the contrast sensitivity function), where the probability of response depends on stimulus strength (e.g., contrast) and another variable (e.g., spatial frequency). You might use it when estimating thresholds as a function of another variable, rather than running multiple independent staircases (a la the method of 1000 staircases).
Here are the manual (Vul & MacLeod) and the toolbox files.
15h) Lugtigheid's Up-Down toolbox (Matlab)
Arthur Lugtigheid (Birmingham) has written a relished Matlab toolbox implementing the Transformed Up-Down method as specified by Levitt (1971). It allows for interleaving of multiple staircases and "is (hopefully) developed to be as versatile as possible."
15i) Treutwein's review on adaptive methods
Treutwein's (1995) Minireview: Adaptive Psychophysical Procedures. Vision Res. Vol. 35. No. 17, pp. 2503-2522, is in my opinion still the best scholarly review on adaptive procedures.
16) ColorlabColorlab is a MatLab toolbox for color computation and visualization in general-purpose quantitative colorimetric applications like color image processing or psychophysical experimentation. It uses colorimetrically meaningful representations of color and color images (tristimulus values, chromatic coordinates and luminance, or, dominant wavelength, purity and luminance), in any system of primaries. Colorlab relates these colorimetric representations to the usual device-dependent discrete-color representation, i.e. it solves the problem of displaying a colorimetrically specified scene in the monitor within the accuracy of the VGA.
A number of interesting color representations are further provided, as CIE uniform color spaces (as L*a*b* and L*u*v*), opponent color representations, and color appearance representations (RLab, LLab, SVF, ATD and CIECAMs). All these representations are invertible.
Colorlab includes visualization routines to represent colors in the tristimulus space or in the chromatic diagram of any color basis, as well as an advanced vector quantization scheme for color palette design. An extensive color data base is further included, with the CIE 1931 color matching functions, reflectance data of 1250 chips from the Munsell Book of Color, McAdam ellipses, normalized spectra of a number of standard CIE illuminants, matrices to change to a number of tristimulus representations, and calibration data of an ordinary CRT monitor.
The program is developed by Jesús Malo and José Luque at the University of València. It can be downloaded and tested for free from the VISTA web site. A comprehensive user guide (220 pages) is included.
17) Image Processing
17a) IPRSFor a different purpose, but closely related to psychophysical interests, are libraries for image processing. Of them, the IPRS system was particularly interesting because it had been developed by people who also worked in psychophysics. IPRS stood for "Image processing and recognition system"; the primary responsible was Terry Caelli (previously in Edmonton/Alberta and Melbourne/Australia) but quite a number of people had contributed. It was a collection of 500+ routines, covering a wide range. It was written in C and ran on a range of platforms including Suns, SGIs, (under X-Windows) and PCs (under Linux). There came a 450 page user manual with it, written in LaTeX. Although the system was user friendly once you had it up and running, the installation was non-trivial. The system is described in the 1997 special isue of Spatial Vision; it was public domain.
17b) Gabor/wavelet decomposition
Fiser & King have a more specialised image-processing software for Gabor-wavelet decomposition-based filtering of images. The package is described in the special issue of Spatial Vision (Part I). and is available from the authors.
A large package for image processing is QuIP. Since it does more than that it is listed as separate entry below.
QuIP (QUick Image Processing) is a complete environment for image processing, pschophysical experimentation, and data analysis written by Jeff Mulligan from NASA. Since QuIP is interpretative it can be used interactively, line-by-line. Large programs are typically written directly in the scripting language. Graphical user interfaces may be constructed in the scripting language, and linkage is provided to a number of external libraries such as OpenCV, GSL, etc. Scripts can be executed with very little modification on nVidia GPU's on systems where CUDA is installed. The system has recently been ported to Apple's iOS for iPad and iPhone (released soon). The system builds on UNIX systems such as Linux and Mac OSX using standard tools. Here is the online manual.
The Grouping Elements Rendering Toolbox (GERT) developed by GestaltReVision of Leuven, Belgium, is a Matlab and Octave Toolbox for constructing perceptual grouping stimuli. It is open source and free and comes with a manual and demo files. A paper on it has been published by Demeyer & Machilsen (2011) in Behavior Research Methods. On the right are some example stimuli.
20) Open Perimetry Initiative (OPI)
This R package from the Open Perimetry Initiative is a free-to-use, exciting Open Source library for psychophysical research in peripheral vision and clinical neuro-ophthalmology and neuropsychology. It allows external control of commercial visual-field testing machines (perimeters) such as the Octopus 900 (Haag-Streit) and Heidelberg Edge Perimeter (Heidelberg Engineering), using the R language. These commercial machines have built in gaze tracking, calibration, and allow wide fields of view, so are useful for vision tasks that require peripheral vision. The project was recently described in a Methods paper in Journal of Vision.
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1) Freiburg Visual Acuity Test
The Freiburg Visual Acuity Test FrACT (Freiburger Visustest) is a "shrink-wrap" application developed for the Macintosh by Michael Bach in Freiburg. The new version, however, is platform independent and runs on Linux, Mac and Windows (based on FlashPlayer). Its basic purpose is to measure Landolt acuity but it has been extended to include contrast sensitivity to Landolt-Cs. It uses some tricky programming to overcome pixel and grey-value resolution limits and thus runs on any standard Mac without requiring hardware modifications. The methods used for obtaining the required precision on a standard Mac are explained in the special issue of Spatial Vision (Part II). The program is available without cost from Bach's web site.
3) MorphonomeMORPHONOME is a stand-alone Mac application for the generation and presentation of 2-D grayscale, motion and color images for psychophysical testing of perceptual limits, developed by Tyler, McBride and Miller. It is written in Code-Warrior C and requires a color monitor including latptop machines. No additional hardware is required. The program allows the input of any set of user-defined static grayscale images of any size for randomized sequential presentation. Paradigms include psychophysical detection threshold, contrast masking, contrast discrimination, contrast matching, adaptation, lateral interactions, etc. Psychophysical techniques include rapid Y/N or 2AFC staircases and constant stimulus methods. Output contrast can be varied in increments as low as 0.2%! (by use of their software "bitstealing" technique). A variety of temporal presentation profiles is available. Initial cost is $300 including email support but the software may be distributed within the lab. See Tyler's web site (www.ski.org/cwt) and Part I of the special issue of Spatial Vision.
3) quick CSF
qCSF developed by Luis Lesmes at Salk and Zhong-Lin Lu at USC is a member is a member of a newly developed set of "quick" thresholding procedures, where adaptive threshold measurement is combined with heuristic, timesaving assumptions. The 2afc Matlab version for measuring the spatial contrast sensitivity function is free to use for non-commercial purposes. Since only four key CSF parameters are measured, a full CSF is obtained in ~ 100 trials. The qCSF is described in a 2009 paper in Journal of Vision. Commercial versions for the iPad are underway.
4) Irtel's Psychology Applications
Over 100 different experiments from all areas of Experimental Psychology ran on top of Irtels PXL library, each representing a whole class of experiments since controlling parameters were read from a file. Six of these constituted a course in experimental psychology and were described in a nice (German) book:
Hans Irtel: Experimentalpsychologisches Praktikum. Springer 1993. ISBN 3-540-56330-X.
See the PXL manual and the entry on PXL above.
PXL was replaced by PXLab. Since Hans Irtel has left us 2008, and commercial packages exist, I'm afraid nobody will take over the maintenance
5) FlashDotFlashDot is a stand-alone program for generating and presenting visual perceptual experiments that require high temporal precision. Developed by Tobias Elze, it "aims to be an alternative to such popular libraries or packages as the Psychophysics Toolbox, VisionEgg, or PsychoPy". It runs on many platforms (Linux, Mac OSX, Windows). Experiments are controlled either by a specific scripting language or by XML; it includes a large number of mathematical and statistical functions.
6) ActiveSTIMActiveSTIM is a commercial system but there is a fully functional free test version available. For more information on the package see the entry below.
7) PsyScope, XA powerful and easy-to-use general purpose program for psychological experiments on the Macintosh, that can be used for research in visual perception, is PsyScope. Even though development of the original PsyScope had ceased (around 1998) it works smoothly on all Macs running OS7 to OS9. Development of an OS-X version started around 2009 – the PsyScope X project – and it is now available.
PsyScope and PsyScope X are available free of charge, without support, from the web page on which you also find the manual, a tutorial and more. For support, there is an email list and an email archive. The program's general purpose and function are described in detail in Cohen, J., MacWhinney, B., Flatt, M. & Provost, J. (1993). PsyScope: An interactive graphical system for designing and controlling experiments in the Psychology laboratory using Macintosh computers. Behav. Res. Meth. Instr. Comp. 25, 257-271. There is a short description in Part II of the special issue of Spatial Vision.
Citing from the abstract in Behav. Res. Methods, "PsyScope is an integrated environment for designing and running psychology experiments on Macintosh computers. The primary goal of PsyScope is to give both psychology students and trained researchers a tool that allows them to design experiments without the need for programming. PsyScope relies on the interactive graphic environment provided by Macintosh computers to accomplish this goal. The standard components of a psychology experiment – groups, blocks, trials, and factors – are all represented graphically, and experiments are constructed by working with these elements in interactive windows and dialogs. In this article, we describe the overall organization of the program, provide an example of how a simple experiment can be constructed within its graphic environment, and discuss some of its technical features (such as its underlying scripting language, timing characteristics, etc.). PsyScope is available for noncommercial purposes free of charge and unsupported to the general community."
Support for a commercial version was discontinued, probably because programs for the PC took a large market but, as the authors say, until some of these become available for the Macintosh PsyScope remains as possibly the best way to build experiments on the Macintosh.
For further integrated systems for psychological experimenting see the section below.
8) Colour Vision Demo
Hans Irtel had also developed a PC program called CVD for demonstrating colour illusions. It is especially useful for didactic purposes.
Colour Vision Demo
9) Spotlights and Filters: Additive and Subtractive Colors
There was another little colour program (for colour mixing), "Spotlights and Filters". It was low cost and had a free demo. It was intended "for beginning physics, art education, computer and TV screen design, photography, theatre lighting, color printing, and general interest". The authors were Judy Kaul and Chris Leavitt.
10) Visual World (Visuelle Welt), a demonstration program for visual illusions
Ronald Hübner, Konstanz (formerly Braunschweig), developed a similar program, VIWO, also for the PC. It covers a range of well-known visual illusions and allows user interaction. Its main use is for didactic purposes but it can serve as a starting point for experiments.
Both these programs are *VERY COLOURFUL!*
11) Project LITE
Project LITE: Light Inquiry Through Experiments by Kenneth Brecher, Boston University, is a project for software, curriculum and materials development. You get free applets, colorful high-quality images, surface patterns for spinning tops, and other materials which are fun to use at home or in the classroom. Here is an example, Nick Wade's "Chrysanthemum".
12) City University Colour Deficiency Screening
There is a web-based test for screening for severe colour deficiency. The test is freely available and works on most colour monitors balanced at ~9000K.
13) Düsseldorf Test of Dynamic Vision (DTDV)
Eugene Wist, Walter Ehrenstein (†), and Michael Schrauf from Düsseldorf developed a test measuring the sensitivity to motion contrast: "The Düsseldorf Test of Dynamic Vision (DTDV) allows the assessment of visual function solely based on motion contrast. In a computer-generated random-dot display, completely camouflaged Landolt rings become visible only when dots within the target area are moved briefly, while those of the background remain stationary. Detection of gap location relies on motion contrast (form-from-motion) instead of luminance contrast. Task difficulty is graded by changing the percentage of moving dots within the target. The standard version of the computer program easily allows for various modifications. These include the option of a synchronizing trigger signal to allow for recording of time-locked motion-onset visual-evoked responses, the reversal of target and background motion, and the displacement of random-dot targets across stationary backgrounds."
WIST ER, EHRENSTEIN WH, SCHRAUF M (1998)
A computer-assisted test for the electrophysiological and psychophysical measurement of dynamic visual function.
Journal of Neuroscience Methods 80: 41-47
Here is a paper on an application (age dependency).
14) Little Stimulus Maker (LSM)Little Stimulus Maker by John P. Kelly (Washington) is a freeware DOS program for stimulus generation and presentation on standard graphics cards (Windows 98 and lower). You see features and sample stimuli on the web page (circular gratings, gabor gratings, random dot patterns...).
15) PixxPixx, coded by Peter April in conjunction with Michael von Grünau and Rick Gurnsey is for motion experiments on the PowerMac and is – I assume – a precursor to VPixx described below. It is available for free from Rick Gurnsey.
16) Digital Embryos
Digital Embryo Workshop written by Mark Brady from NDSU in North Dakota creates strange looking, novel objects.
Here is a list of what it can do:
- Generate novel objects singly or in batches.
- Control embryo shape by using either random seeds or pre-selected seeds.
- Control embryo shapes by selecting 6 different types of growth and programmed cell death (PCD) episodes.
- Multiple episode types can contribute to the shape of a single embryo.
- Specify the length of episodes, thus controlling differences in shape parametrically.
- Simulate evolution by growing 2 or more embryos from a single ancestor.
- Apply textures using 6 different algorithms.
- Create scenes.
- Automatically generate camouflage.
- Output movies of embryo growth.
- Open existing files for viewing.
- Output scene and object images.
- Output embryos in .obj format for latter input to Maya or other packages.
For more detail see the Digital Embryos website
17) nrec – neuronal recording / neurological recording
nrec, developed by Friedemann Bunjes and Jan Gukelberger at the Neurology of Tübingen University, is a package for stimulation, data acquisition and experiment control in the flavour of cognitive fMRI research, which has been expanded to include flexible biosignal acquisition and sensory stimulation. It runs under Linux on PCs with standard graphics cards, produces Matlab-readable files and generally puts an emphasis on standards like using the comedi Linux data acquisition library, OpenGL, XML parameter file format and hdf5 data storage files format. See the screenshots and sample setups, and the YouTube video for a quick impression.
NeuroDebian provides a free turnkey software platform and repository of maintained, free and open-source software for Cognitive Neuroscience and Experimental-Psychology/Psychophysics, for Debian GNU/Linux and Ubuntu. The NeuroDebian virtual appliance makes it easy to start using this powerful Linux system under other operatins systems (Windows, Mac OS, etc.). Here is a list of psychophysics packages that are currently included, and here is a list with more details.
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(C) Commercial Systems
1) Cambridge Research Systems (ViSaGe, VSG 2/5)Cambridge Research Systems builds excellent and affordable PC-based systems for visual psychophysics. For years it had been the well known VSG 2/5 (which itself had superseded earlier models like the 2/3) which is now followed by the ViSaGe visual stimulus generator. The ViSaGe hardware is a sleek external box, that of the VSG 2/5 a graphics board (informally called the "Robson board"). Both support high frame rates (ViSaGe up to 200 Hz, VSG 2/5 up to 500 Hz; unfortunately there are no monitors that go that fast; CRS no longer officially offers the 250 Hz model they once had) and high and colour/gray-scale resolution (14-15 bit!). There is a range of support software: A library of 250 routines (probably more now) that can be linked to MatLab, C, C++, Pascal (i.e. Delphi), Visual Basic, and Windows DLL; use of a script language. There is now also a MatLab toolbox. There are further complete applications like PsychoWin contrast sensitivity software, stereo stimuli, the Optima visual evoked potential recording system and more. Full library source code is provided; the library is expanded continuously. The price was in the range of 5000 English pounds for the board including Optical gamma correction system and the library sources. Contact information is at their home page which has been newly designed.
Among their many products they also have "a little box" containing an external signal processor (Bits#) (the successor to the Bit++ box) to get much improved grey scale resolution on a standard monitor (>14 bit) and other nice things. Apart from CRS's own software, the box works together with other software systems listed in this overview (Psychophysics Toolbox and PsychoPy). CRS also offer calibration systems and response boxes.
Irtel's PXL (see above) and VisionWorks are alternative libraries to drive this board.
2) quick Methods for the iPad
Michael Dorr at Schepens and L. Lesmes at Salk developed a set of fast Bayesian thresholding procedures for psychophysical measurement on the iPad (see also above). Viewing distance is automatically detected by the iPad's camera after a simple calibration. Contrast resolution is improved to 0.1% Michelson contrast (11.5 bits) through efficiently implemented spatio-temporal dithering. Reliable CSF estimates are obtained by qCSF after ~ 7 min. A further member of the set is quick Surface for spatio-temporal CSF measurements (i.e., simultaneously vs. spatial and temporal frequency). Other members are in the works. Pricing is not decided upon yet, but there will be academic options. Here is the ECVP 2012 poster.
Another high-end system is Vision Research Graphics' (Durham, NH, USA) PC-based VisionWorks. It supports Cambridge Research System's VSG system and provides a large range of sophisticated stimulus generation and psychophysical testing procedures. There is further support for display calibration, and they have products for stereo vision. An older version of the system is described in Part II of the special issue of Spatial Vision. For information, contact firstname.lastname@example.org, Tel.: (603) 868-2090, Fax (603) 868-1352.
4) WinVis for MatLab
WinVis for MatLab, written by Tom Carney of Berkeley, was a nice package for stimulus generation and presentation on the PC, running as an extension to Matlab. There was a web-based stimulus data base where users could donate their stimuli. It was marketed by Neurometrics and it superseded (the pubic domain) MatVis.
From the announcement, "Psykinematix for Mac OSX (by William Beaudot at KyberVision) is a new OpenGL-based Software Package dedicated to Visual Psychophysics running on Mac OSX for both PowerPC- and Intel-based Macintosh computers. It consists in a stand-alone application that does not require any programming skill to create and run complex experiments. Easy to use, subject-friendly, powerful and reliable, Psykinematix runs standard psychophysical protocols, presents complex stimuli, collects subject's responses, and analyzes results on the fly. Psykinematix is also a great learning tool to introduce visual perception in classroom and to illustrate psychophysical concepts to students.Psykinematix features:
- Easy experimental design (no programming required, use of a hierarchical structure, design wizard)
- Standard methods (constant stimuli, staircase, bayesian)
- Standard procedures (nAFC, yes/no, discrimination, adjustment)
- A large variety of visual stimuli (shapes, carrier modulated by envelope, checkerboard type, expression-based)
- Stimuli composing (static, dynamic, timeline, conditional)
- Support for multimedia stimuli (text, image, movie, sound)
- Display calibration (geometry, Gamma correction, color)
- Precise control of time-varying properties
- Data plotting and fitting with psychometric functions
- Subjects, groups and sessions management
- Communication with external devices (USB, serial, network)
- Easy export of stimuli (clipboard, image and movie files)
- Built-in documentation, demos and examples, tutorials
Here are some tutorials (orientation-discrimination staircase etc.).
A single-user license costs 600$ (Canadian dollars); a student version is $300. Several licensing schemes and support packages are available. A 15-day trial version & free educational demo of Psykinematix is available. For more information, visit Psykinematix homepage (http://psykinematix.kybervision.net)."
ActiveSTIM, by Danko Nikolic at the MPI in Frankfurt, is a new Windows software for building experiments in vision, behavioral and cognitive sciences. It provides management of bitmap files in memory, their accurate presentation of the screen, digital I/O and measurement of response times (10 µs accuracy). ActiveSTIM uses ActiveX for communication with client applications; the latter can be written in any programming language that supports ActiveX. There is a feature list on the web site from where you can download the package, including example client applications written in different languages.
7) VPixx Technologies
VPixx Technologies, founded by Peter April , makes a high-grade monitor (VIEWPixx), the DATAPixx video processing and data acquisition system, precise button boxes, and psychophysics software
VIEWPixx is a piece of hardware: a monitor with toolbox, conceived to replace CRTs in vision science labs. It features high-performance industrial LCD glass, and a panel controller which has been custom designed to support vision research. The innovative scanning LED backlight design features superior display uniformity, and a wide color gamut exceeding that of CRTs. It further includes an array of peripherals which often need to be synchronized to video during an experiment, including a stereo audio stimulator, a button box port for precise reaction-time measurement, triggers for electrophysiology equipment, and a complete analog I/O subsystem.
- -120 Hz refresh rate
- -12-bit RGB intensity
- -1920 x 1200 display resolution
- -Deterministic timing between reception of video signal and update of display pixels
- -22 inch display size
- -Response box interface
- -Electrophysiology trigger outputs
- -Fast 16-bit data ADCs/DACs
- -Stereo audio input/outputs
- -All analog and digital inputs/outputs feature microsecond synchronization to video refresh
DATAPixx is a hardware toolbox for the vision community. Some features, provided by the manufacturer, include:
- Analog video outputs with custom 16-bit video DACs on each of the RGB components
- Dual VGA outputs for simple implementation of perfectly synchronized dual displays like haploscopes
- Accepts dual-link DVI input, for generating high resolutions and high refresh rates
- Mini-DIN-3 port for direct connection to stereo shutter goggles
- 4 channels of 16-bit DACs generating +-10V arbitrary waveforms at up to 1 MHz, synchronized to video.
- 16 channels of 16-bit ADCs simultaneous sampling +-10V inputs at up to 200 kHz, synchronized to video.
- stereo audio input/output channels sampling up to 96 kSPS, synchronized to video.
- 24 TTL inputs, can timetag standard or MRI-compatible button box transitions.
- 24 TTL outputs, can generate triggers and other digital waveforms, synchronized to video.
- All of the I/O types can be hardware synchronized to video vertical sync pulse with sub-microsecond precision.
- Supported by PsychToolbox with Matlab/Octave, under OS X, Windows, Linux
"The DATAPixx (http://www.vpixx.com/datasheets/ds_datapixx.pdf) is field upgradable to add new features requested by the vision science community. A new low-latency gaze-contingent display mode to the DATAPixx Toolbox was recently implemented. Eyelink Toolbox users can now pass forground/inset images to the DATAPixx as left/right halves of a single OpenGL texture. The DATAPixx dynamically combines the forground/inset images as defined by the Region Of Interest programmed into the DATAPixx registers. This reduces the gaze-contingent latency from 1-2 video frames to 2-3 milliseconds. The DATAPixx Toolbox will continue to evolve through input from the vision community."
VPixx (direct link) is a commercial package for the Intel Mac for stimulus preparation and presentation and psychophysical paradigms. It has an Excel interface and in particular has direct support for the EyeLink eyetracker.
Here are features, provided by the author:
"Stimulus Presentation: Frame-synchronized rectangle, oval, arc, text, and imported PICT shapes containing static or dynamic gratings, windmills, concentric circles, looming circles, uniform fields, gaussian blobs, checkerboards, binary/uniform/gaussian noise, drifting/rotating/loomingdots, and custom patterns defined by general "C" expressions or imported from PICT files. Multiple patterns can be combined additively or multiplicitively generating plaids, gabors, second-order stimuli etc. Stimulus metrics can be specified in pixels, cm, inches, or degrees of visual angle. Stimulus chromaticities can be specified in RGB, LMS (cone contrast), or CIE XYZ, Lxy, Lu'v', L*u*v* and L*a*b*. Can also present most sound files."
"Interface: Graphical Interface, Drag-and-Drop. Complex animations can be sequenced using a high-level graphical scripting language. Also has an interactive receptive-field mapping mode."
"Testing: Method of adjustments, method-of-constant-stimuli, subject events, reaction-times and event durations. Classical staircase with up/down or 2/3/4AFC, or VPEST adaptive staircase w 2/3/4AFC. All data stored to MicroSoft Excel files for easy graphing or further analysis. Also can export dynamic stimuli as QuickTime movies for teaching or web publishing."
"Intended Users: Researchers and teachers in the fields of psychophysics, electrophysiology, cognition, and fMRI. Free demo, VPixx User Guide, and sample stimuli available at VPixx Technologies. Custom programming and hardware design/interfacing services are also available."
8) Shell & Mac Glib, Vision ShellVision Shell 3.0, formerly Shell & Mac Glib, was a commercial "visual psychophysics and neurophysiology experimentation environment for the Macintosh computer," made by Micro-ML, St-Hyacinthe, Quebec, Canada. The full package price was $425. The web page which also had a list of users is discontinued.
9) HIPSAn image processing package written by visual psychophysicists is HIPS. It was originally developed at New York University and is now commercial "but relatively inexpensive for academics" ($800). It runs under Unix on a range of platforms. It contains around 200 image processing routines and can also handle movies. It is described in Computer Vision, Graphics, and Image Processing (Vol. 25, 1984, pp. 331-347), and in Behav. Res. Meth. Instr. Comp. (Vol. 16, 1984, 199-216). Contact Michael Landy of SharpImage Software at email@example.com.
10) VenusAnother high-end system was Neuroscientific Corporation's VENUS (Farmingdale, NY, USA). Their colour configuration once sold for $28,000. The company went out of business about 1998 as an owner of the system (John Kelly) told me.
11) Psyscope, E-Prime, SuperLab, OpenSesame, etc.
General-purpose psychological experimentation systems have become quite powerful and in many ways are direct competitors to more specialised psychophysical systems. Psychophysicists should be aware of these tools. See the accordant section on these program systems below.
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(D) Psychophysical data analysis, SDT
1) General Statistics, R
General-purpose statistical packages (like SPSS, SAS, Statistica, SysStat, WinStat, Origin, MatLab libraries, etc.) are not the focus here; the section concentrates on specialised statistical packages that are useful in psychophsics.
However, given the emphasis on freely available software, the – freely available – general purpose statistical package R must be mentioned here. Ken Knoblauch from Lyon, France has written three libraries for R that are aimed at psychophysics, psyphy, MLDS, and MLCM, explained above and below. In particular there is now a comprehensive book on modeling psychophysical data by Knoblauch and Maloney. (Here is a preview and Chapter 1)
To cite from the web page, R – a GNU project – is a language and environment for statistical computing and graphics, providing a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible.
2) Fitting the psychometric function, threshold reliability
I currently know of eight packages/approaches for fitting the psychometric function (i.e., the sigmoid function that relates performance to a physical stimulus variable, introduced by Urban, 1910). Three maximum-likelihood based procedures are
- PsychoFit by L. Harvey (for Mac and PC, C++),
- Watson & Solomon's Psychometrica, contained in Psychophysica (Mathematica), and
- Hill's Psignifit which is a MatLab toolbox.
Hill's program in particular includes bootstrap reliability estimates of the psychometric function parameters and seems particularly versatile (see also Hill's thesis and a paper by Wichmann & Hill in the P&P Vol. 63 special issue on psychometric functions).
Two programs which implement constraints on the parameters (i.e. use a Bayesian approach, thus allowing more parameters to be assessed simultaneously), are by Treutwein and by Kuss:
- Treutwein (Perception & Psychophysics 61, 87-106) (Pascal).
- PsychoFun for R by Malte Kuss (MPI Tübingen) is a new package with a Bayesian approach (Linux, MacOsX, Windows). It is described in a paper by Kuss et al. in JOV and a technical report.
Zychaluk and Foster developed a model-free approach of psychometric-function estimation based on local linear fitting. Except for smoothness, no assumption is made about the shape of the true function underlying the experimental data. It is described in a paper in AP&P (pdf for personal use only). The package is implemented in R and Matlab. An earlier program for assessing the reliability of threshold estimates by a bootstrap approach is available from Foster & Bischof; it is described in the Special Issue of Spatial Vision (Part II).
Yssaad-Fesselier & Knoblauch (2006) Behav. Res. Meth. Instr. Comp. 38 show how to use the language R for psychometric function fitting. It is implemented as part of their package psyphy. Ken Knoblauch and Laurence Maloney have now also written a comprehensive book on modeling psychophysical data, again using the language R. Here is a preview.
Palamedes described above is a new extensive Matlab psychometric analysis package also comprising Psychometric Function fitting.
Empirical comparison of psychometric function slopes is a little tricky since slope parameters have different meaning in different analytic representations of the PF. In a paper in P&P (Strasburger, Percept Psychophys 63, 1348-1355) I advocate a slope measure (%corr/log-unit) that can be used somewhat more generally, and I provide conversion equations between the measures.
3) Signal detection theory
A program for obtaining accuracy and bias estimates of psychophysical data, from signal detection theory, is d' (d-prime) by Macmillan & Creelman. The theory is explained in their book "Detection Theory, A User's Guide" (there is a new edition out, ISBN 0805842306), and the program is described in the special issue of Spatial Vision (Part II).
3b) RScore+RScore+, developed by L. Harvey (Boulder, CO), is a well-documented and improved version of the original RScore by Dorfman & Alf. It allows the typical analysis of the receiver operating characteristic (ROC) in a number of useful ways. It is available for the Mac and the PC from Harvey's homepage.
3c) d' in R
d' can be calculated in the statistical software package R as part of Ken Knoblauch's psyphy.
Palamedes described above also does Signal Detection analyses.
3e) ROC Analysis Made Simple
Web-based Calculator for ROC Curves by John Eng from Johns Hopkins University.
Excel spreadsheet for ROC analysis by Ignacio Serrano-Pedraza from Newcastle University (alternate link).
Web page on ROC-analysis software. A web page by Elizabeth Krupinski (radiology/Arizona) listing a number of programs for analysis of the receiver operating characteristic (ROC) (thanks to Neil Macmillan for the hint).
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(E) Ophthalmology / Optometry
1) Ophthalmic Screening
Another group of vision software is constituted by systems for ophthalmic screening of visual well-functioning. Such systems usually measure acuity or other visual functions that are of interest to optometrists and ophthalmologists. Here are a few examples:
- VUTEST marketed from 1993 by Keeler Ltd.;
- VDU Eye Screening developed at City University London;
- the Cambridge Colour Test developed by John Mollon which runs on CRS's ViSaGe system;
- a simple web page with eye chart from Milford Eye Care.
2) Umist Eye System
The UMIST Eye System developed by Chris French at Manchester was a software system on the PC under DOS for general optometry. It had a comprehensive range of acuity tests including upper and lower case letter sets, digits, symbols, pictograms, gratings, and vernier. Presentation was from single-character to multiple-line, with variable contrast, duochrome and stereogram modes, and full format control. A variety of optometric displays was included along with an 18-bit colour vision test and single static, multiple static and kinetic field testing procedures. The system was described in Part II of the special issue of Spatial Vision. The price was 250 Pounds/single user, 500 Pounds/site licence.
There was further the Computer Book of Colour by the same author which simulated the Munsell Book of Colour on the PC under DOS and allowed doing colour experiments with geometrical illusions.
3) Thompson Software Solutions
In the late 90s, David Thomson at City University London developed vision tests for the PC under Windows. Test Chart 2000 already included a wide range of test charts including LogMAR, Snellen and Single Letter. Various optotypes including letters, Landolt Cs, Tumbling Es and Pictures could be displayed in each format and with varying contrast. It also included a Contrast Sensitivity test and a range of other optometric tests. He founded Thompson Software Solutions which markets this chart and its successors, as well as a wide range of other products for ophthalmic use.
4) Lea Hyvärinen
Lea Hyvärinen from Helsinki concentrated on child vision early on and created the well-known Lea symbols: Go to her homepage or to Lea-Test for more. Lea Symbols charts are available from Good-Lite.
5) Precision Vision
Precision Vision markets a wide range of printed charts for vision testing, including the Low Vision Chart by A. Colenbrander.
6) Macular Mapping Test
The Macular Mapping Test (MMT) by Manfred MacKeben and August Colenbrander (The Smith-Kettlewell Eye Research Institute, San Francisco) serves to map residual vision in patients with macular vision loss (maculopathies). The goal is to find intact areas of the retina that can be used for eccentric viewing as a means of visual rehabilitation. Using diminished contrast, the test can also be used for screening purposes to detect the earliest signs of function loss, while visual acuity and morphology do not show those signs yet.
The MMT runs under Windows on standard PCs and can be conducted by anyone with only basic computer skills. It is available in English and German. It has been used on hundreds of subjects, many of them patients with central field loss. The test duration was, on average, just above 3 minutes. The cost is under $1000. For more information see MacKeben's web page or send inquiries to firstname.lastname@example.org. In the German speaking countries the test is described and distributed by .
20) Open Perimetry Initiative (OPI)
The R package from the Open Perimetry Initiative is a free-to-use, exciting package for research in (neuro-) opthalmology. It is described under the psychophysical packages here.
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(F) Psychological Experimenting Systems
Besides the more specialised psychophysical experimenting systems there are also a number of excellent general-purpose psychology experimenting systems. For many applications they are direct competitors to the psychophysical systems: PsyScope, Presentation, E-prime, SuperLab, Inquisit, OpenSesame. Most of these systems also lend themselves to fMRI control, and some to EEG control.
With the earlier versions of Windows, precise temporal control of events or synchronization was not possible and professional packages on the PC (like MEL) had to run under DOS. The only mouse/windows based system in the beginning was PsyScope on the Mac. Newer developments allow precise temporal control, however. Obviously, the mouse/windows-based systems are much more powerful than their DOS counterparts were such that the days of the latter are over.
Listed below are: one system for the Mac: PsyScope, five systems for Windows: Presentation, E-Prime, SuperLab, Inquisit, and ERTSLab, two platform-independent, icon-driven systems: Experiment Builder and OpenSesame, and two systems for DOS: MEL and ERTS. For applied, professional psychological diagnostics, the Wiener Testsystem is a popular and robust tool.1) PsyScope X for the Mac is free of charge. See above.
2) Presentation, VisGen
Presentation is a major stimulus delivery program for psychological and neurophysiological experimentation for Windows 95/98/2000/XP/Win7 on any standard PC. It is powerful and flexible enough to handle almost any behavioral, psychological or physiological experiment using fMRI, ERP, MEG, psychophysics, eye movements, single neuron recording, reaction time measures, etc. It is well supported, with web based user forum, manual, and regular updates with email alert. It was free until fall 2004; the last free version I am aware of is 0.71 which might still be around. Since then it has been expanded continuously and is available under a yearly (moderate) pricing policy. They now have a huge user community and a large library of scripts.
Mid 2008 NBS offered the VisGen Toolkit for use with Presentation, for easy generation of a large variety of visual stimuli (sine wave gratings, Gabor patches, checkerboards, radial checkerboards etc.). As of version 14.4 the toolkit is included in Presentation.
PsychoPy, written by Jon Peirce, is an easy-to-use open-source package for psychological experimenting running on all standard platforms (Windows, Mac OS X and Linux) and using Python (a free alternative to Matlab) as the scripting language. It aims to be flexible enough for neuroscience, precise enough for psychophysics, and intuitive enough for undergraduate teaching.
PsychoPy offers two user interfaces, one for non-programmers who want their study up and running, and one for experienced programmers who need precise control of everything. Programmers can write code in the editor of their choice or with the integrated development environment ("Coder"). Those not proficient in Python can use the intuitive graphical "Builder" interface.
OpenGL is used to generate and render stimuli in real time and can be accessed directly, as can a variety of hardware via serial and parallel ports. PsychoPy supports the Bits++ box. As seen from the above it is fully free. It is now used by several labs for a variety of experiments ranging from cognitive psychology to visual psychophysics and neuroimaging.
Paradigm is a new psychology experimenting system for the PC which focuses on ease-of-use and simplicity – "to make building experiments a less daunting task for researchers and students." It has millisecond accuracy, scripting facility in Python, supports button boxes from PST (E-Prime) and Cedrus, and has detailed help files and video tutorials. The single user licence costs around $700 with tiered discounts based on the number of licenses. There is a free trial version.
PyEPL (Python Experiment-Programming Library) is a Unix-based open source library for coding psychology experiments (including virtual reality) in Python. It supports presentation of visual and auditory stimuli, and supports both manual (keyboard/joystick) and sound (microphone) input as responses. It runs on Unix variants (Mac OSX, Linux, Ubuntu, Debian); there is a user forum. The system is also described in a paper in Behavior Research Methods 2007, 39 (4), 950-958
E-Prime is the successor to MEL, running under Windows Like MEL, it is made by Psychology Software Tools Inc. The single user licence for educational institutions was ~ $700; discounts were given to MEL and PsyScope (consortium) users. A disadvantage of E-Prime is that it uses a hardware dongle for copy protection. The dongle is - to our experience - also required for the development of an experiment. They have a newsletter which contains hints on how to use E-prime. Here is an example.
There is also a European E-Prime 2.0 website
7) SuperLabSuperLab (Pro, LT), for Mac and Windows, is an experiment generator for psychology for Macintosh and Windows. It is made by Cedrus Corporation. The version 1.0 that I had used many years ago had a nice user interface and enjoyable booklet but was not useful for well-calibrated stimulus display. It seems to have thoroughly improved, however, or anyway the web page has an impressive list of publications that used it. They also offer response boxes including an fMRI-capable version - supported by the major software packages (E-Prime, Inquisit, SuperLab, MEDx, MEL), shutters, a video splitter, and other hardware. The single-user educational price is ~$600, student version $125 (as of 2012).
Inquisit, to cite from the web page, "is a flexible, open-ended, high performance psychological experiment generation tool for Windows (95, 98, Millenium Edition, NT 4.0, 2000, XP, Vista, and 7). Inquisit supports a wide variety of psychological data collection methods, ranging from simple questionnaires to reaction time tasks where every millisecond counts. ... it also makes it easy to selectively demo tasks, trials, and blocks for presentations and lectures." Like the other major Windows packages is uses DirectX to achieve temporal precision. There is a scripting language. It supports the Cedrus response box. The educational price is $345.
9) Experiment Builder (SR Research)
Experiment Builder by SR Research is an icon-driven programming environment for psychological experimenting under Windows and MacOS X. It offers complex yet precise visual and auditory stimulus delivery, thorough support of the EyeLink series of eye trackers, support of button boxes, touchscreens, etc., and for advanced users Python scripting. There is a free demo version including sample projects (change blindness, smooth pursuit, a pro-saccade task, Stroop, programming demos); further paradigms and updates are available through SR Research's support website. Experiment Builder is simple enough for a novice but rich enough to serve advanced experiment paradigms.
There is also DataViewer which provides visualization (scanpaths, heatmaps, movie playback and 2D graphs) of EyeLink eye movements data, and allows extracting a large number of dependent measures for all areas of eye movement research.
OpenSesame is a platform-independent, free, graphical experiment builder. OpenSesame provides an easy to use, point-and-click interface for creating psychological experiments. In addition to a powerful sketchpad for creating visual stimuli, OpenSesame features a sampler and synthesizer for sound playback. For more complex tasks, OpenSesame supports Python scripting using the built-in editor with syntax highlighting. OpenSesame is freely available under the General Public Licence. There are download packages for Windows, Mac, and Linux. Here is more.
11) Wiener Testsystem
The Wiener Testsystem is a versatile, comprehensive system for professional psychological diagnostics including some of visual function testing, for application in driving fitness, aviation, personality, selection of personell, etc.
12) NeuroScanNeuroScan is mostly dedicated to EEG software but they do have visual stimulation software for EEG and fMRI.
13) MELMEL (Micro Experimental Laboratory) was the precursor to E-Prime, a general-purpose psychology experimenting system for DOS developed by Walter Schneider, Pittsburgh and marketed by Psychology Software Tools Inc. (511 Bevington Rd., Pittsburgh PA 15221, phone 412-244-1908). It is described in Behav. Res. Meth. Instr. Comp. 20 (1988), 206-217. MEL came in a classroom and professional version; the latter had similarities with the Pascal language. Since MEL was a DOS program, it ran on Win 95/98 but not on NT/2000 systems. I know happy users of it but support has ceased as of Dec. 1999, last version 2.01). (The price of MEL 2.01 was $199).
14) ERTS, ERTSLab
ERTS (Experimental Runtime System) by J. Beringer (BeriSoft, Frankfurt, Germany) is a further general-purpose psychology experimenting system for DOS (i.e. Win 95/98/NT/XP). It uses a script language and, like other DOS applications, has millisecond accuracy. It allows synchronisation with external devices both by sending and receiving sync signals. There is a large library of cognitive paradigms. For a description see for example Beringer, J. (1994), Behav. Res. Meth. Instr. Comp. 55(4), 1-1. A demo and trial version are available from the website. The licence fee was $490 for the teaching version several years ago but the web page is silent about current conditions.
The succesor to ERTS is ERTSLab for Windows (9x and NT) which is upward compatible,
i.e. can run the scripts written for ERTS.
15) Psychology Experiment Building Language (PEBL)
The Psychology Experiment Building Language (PEBL), developed by Shane Mueller (Ohio) and others, is a free cross-platform system for computer-based experiments (Gnu: free to use, free to change, free to give). It runs under Windows, Linux, and Macintosh. Experiments are created by a simple scripting language for creating displays (graphics, shapes, text, etc.), collecting responses (mouse and keyboard), experimental design (randomization and counterbalancing), and data recording.
It already includes about 50 ready-to-use standard experiments from cognitive psychology. There's a WIKI, a user manual, a blog, technical reports, etc. Here are some screenshots.
PEBL achieves its cross-platform compatibility by using the open source cross-platform multimedia library SDL (Simple DirectMedia Layer) as its base.
It seems particularly easy to use, as a user wrote me.
Experimental Psychology Software
Experimental Psychology Software is a European distributor for several of the experimental psychology systems, including E-Prime, SuperLab and Presentation. They also resell button boxes (see there). They are part of the SciencePlus commercial reseller group who carry scientific software like EndNote etc., or the Wiener Testsystem (Vienna Test System).
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(G) Cognitive Neuroscience
Most general purpose psychological experimenting systems nowadays allow acquisition of fMRI and/or EEG data and are thus suitable for cognitive neuroscience. So it's hard to draw a distinction (and will become harder with time). The systems listed here are perhaps more streamlined for cognitive neuroscience. There is further overlap with the section on fMRI and EEG analysis tools below.
MonkeyLogic is (to cite from its webpage) a MATLAB toolbox for psychophysical tasks with high temporal precision. It allows construction of sensory, motor, or cognitive tasks, based upon the interaction of a subject with visual stimuli (static and movies) through the use of eye-position, joystick, button, lever, and/or keyboard responses. An experiment is constructed using by a conditions file and a timing script. The conditions file is a tab-delimited text file which enumerates each possible sequence of stimulus presentations that can occur within any given trial of the experiment. The timing script is a MATLAB program that determines when and under what conditions those stimuli are presented. Have a look at the main menu.
Designed by Wael Asaad at Brown and David Freedman & coworkers at U Chicago, it is in some ways a successor to CORTEX, developed by Thomas White at NIH (now Columbia U). It has already been used in quite a number of published studies in the area of cognitive neuroscience.
2) PLDAPS ("Platypus")
PLDAPS (pronounced "Platypus") is a system for cognitive neuroscience with high temporal precision. It integrates Psychtoolbox and the DATAPixx input/output control system with Plexon's recording apparatus. "Despite its capabilities, it is simple enough for someone with basic MATLAB programming skills to design their own experiments". It is described in an abstract. Here is the download link.
3) Topographica et al.: Cortical modeling
Topographica, Param/ParamTk, and ImaGen are a set of free-to-use software packages for neural-systems modeling released by James Bednar from U. Edinburgh that has been applied to modeling the primary visual cortex. A review paper "shows how these separate projects add up into what is hoped to be the most complete model of the development of functional properties of V1 neurons to date." Here are links to 31 publications using this software so far. The packages are written in Python and run under Linux, Mac, and Windows.
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(H) General Experimenting Systems
IGOR, by WaveMetrics, is a powerful interactive software environment for experimentation with scientific and engineering data and for the production of publication-quality graphs and page layouts (Mac and Windows).
LabVIEW (short for Laboratory Virtual Instrumentation Engineering Workbench) is a platform and development environment for a visual programming language from National Instruments. The graphical language is named "G". Originally released for the Apple Macintosh in 1986, LabVIEW is commonly used for data acquisition, instrument control, and industrial automation on a variety of platforms including Microsoft Windows, various flavors of UNIX, Linux, and Mac OS. Wikipedia entry.
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(I) fMRI and EEG Analysis Tools
Web sites with EEG and fMRI analysis links
Psycware (A. Beer, Germany) has put together a comprehensive site listing analysis packages for EEG, fMRI and MEG. Another comprehensive page from the viewpoint of imaging has been collected by Michael Rotte, Univ. Magdeburg.
General Purpose EEG Analysis Packages
Here are pointers to a few well-known EEG analysis packages. For more see the above-mentioned two websites 1, 2.
EEGLAB (by Arnaud Delorme & Scott Makeig) is a Matlab toolbox from UCSD's Swartz Center for Computational Neuroscience. Amongst others it contains the Neuroelectromagnetic Forward-Modeling Toolbox (NFT) which includes the Boundary Element Method (BEM)
Harvard MNE Suite (Minimum Norm Estimates software); created at the Athinoula Martinos Center for Biomedical Imaging
(BrainVision) Analyzer 2 by BrainProducts
CarTool software from U. of Geneva's Functional Brain Mapping Lab
Multifocal Analysis Tool
Simo Vanni of Helsinki has written a multifocal fMRI stimulus generation toolbox, described in Vanni et al. (2005), Neuroimage 27, 95-105. He writes "The utility works without modifications with MatLab 7 (tested with 7.3), and contains also a function for automated estimation of data with SPM2. You can freely modify the tool for your needs." It can also be accessed from the SPM website. Vanni continues "I personally find multifocal fMRI good for V1 mapping and region-of-interest localization, especially when you do not have surface analysis tools. We continue working with this tool to develop it further for versatile purposes. All feedback is welcome, or if you want to have data from the study above for comparison, contact me.
Event Related Potentials Analysis
Steve Luck's lab – in conjunction with others – put together a package of freely available, open source Matlab routines for basic and advanced ERP analyses called ERPLAB Toolbox. It is tightly integrated with EEGLAB.
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(J) Visual NeuropsychologyVisual Neuropsychology, i.e., the area of diagnosing and treating patients with neurological disorders of the visual system, is a field of application for visual psychophysics. Since patients can be severly handicapped, the visual tasks tend to be simple and to cover a wide range of function. I have only started this section, so I expect to find more in this area.
PeriMat by Erich Kasten (his homepage) was a program for qualitative perimetry that offered particularly fine resolution (1 deg) in the center visual field (~ +-25 deg). It was intended for precise circumscribing of visual field loss from brain injuries that might be amenable to functional recovery and therefore specifically offered a perceptual training. The program was for the PC under DOS, to run on simply equipped systems. It was described, together with two further perimetry DOS programs, in the special issue of Spatial Vision, Part I. There was a successor for Windows (copyright owned by NovaVision) but this program seems to be no longer available (cf. e.g. Poggel et al., 2012). So currently there is no program for high-resolution perimetry available that I am aware of ... but it could be done using OPI.
Open Perimetry Initiative: The open source R package OPI is a free-to-use, exciting package for clinical and basic psychophysics research in the visual field. It is described under the psychophysical packages (here).
VS by G. Kerkhoff & C. Marquardt was a DOS based program for the analysis of visuo-spatial perception in brain injured patients (e.g. parietal lesions). It offered the assessment of the subjective vertical and horizontal, a number of spatial discrimination and bisection tasks, the assessment of the influence of optokinetic background stimulation, visuospatial short-term memory and certain simple visuomotor tasks by use of a touch screen input. For more information contact the authors.
L-POST: The Leuven Perceptual Organization Screening Test is a newly developed test of mid-level vision for stroke patients, examining higher stages of visual perception (Torfs, Vancleef, Lafosse, Wagemans & de-Wit, 2012). To cite from the GestaltReVision web site, "in 20 minutes you will be able to test whether you can organize moving dots into coherent objects, detect patterns of oriented lines that form objects, and more. At the end of the test, you will see your score, which you can compare with our previous participants". L-POST consists of 15 subtests, e.g. figure-ground segregation, contour integration, embedded figure detection, biological motion, perceptual grouping, local and global processing, scene segmentation and texture segmentation. To reduce cognitive load, a matching-to-sample task is used throughout where participants indicate the alternative that is the most similar to the target. The online test can be administered in 20-30 minutes, and a neglect-friendly version is available.
L-POST is non-commercial and free to use. It is available in English, Dutch, and Italian (with more to come).
There are further the two commercial packages Birmingham Object Recognition Battery (BORB) and the classical Visual Object and Space Perception Battery (English, German) (VOSP).
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(K) Visual NeurophysiologyVisual neurophysiology is, of course, a whole area in itself. I just list a few packages I have come across. There is also heavy overlap with Section G on cognitive neuroscience.
VSApc was a C++ package for quantitative extracellular single-cell electrophysiology, designed by David L Bohnsack and John B Troy from Northwestern U., IL. It was a suite of DOS programs for measuring spatiotemporal frequency responses and collecting maintained discharge from retinal ganglion cells. The package is described in the special issue of Spatial Vision (Part II, p. 95ff).
"Pep++ is a system for visual neurophysiology experiments. It is available for free to anyone that wants to give it a try..." A brief description can be found on the Web. Contact Dario Ringach (Center for Neural Science, New York Univ.)
RFspotter, developed by Nicolas P. Cottaris from U Pennsylvania, is an app for the iPad 2 to quickly and interactively find receptive fields and explore their tuning properties in single cell recordings.
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(L) Eye Movement Software
Part of psychophysics is the problem of recording and controlling eye movements. The solutions are sufficiently non-overlapping with the foregoing so that for ease of maintenance it is useful to survey them separately.
There is the
EYE-MOVEMENT email discussion list at JISCMail with archives going back to 1998, the
Eye Movement Equipment Database (EMED), both set up originally by late David Wooding at Derby. There is further the
Eye Movement Research Portal set up by Carol Walthew.
Nonetheless, here are a few random links:
OpenEyes is a freely available Matlab and C toolkit. Citing from their web site, "openEyes provides hardware designs and software useful for the tracking of human eye movements.
The development of openEyes stems from the recognition that while the cost of hardware used in eye tracking systems has precipitously dropped, there is lack of freely available software that implements even long-established eye-tracking algorithms.
The openEyes toolkit includes algorithms to measure eye movements from digital videos, techniques to calibrate the eye-tracking systems, and example software to facilitate real-time eye-tracking application development.
Contributions to the openEyes Toolkit have been made by (alphabetically) Jason Babcock, Dongeng Li, Derrick Parkhurst, David Winfield. Questions should be directed to Derrick Parkhurst (derrick dot parkhurst - at - gmail dot com)."
SPIC (Saccadic latency measurement and analysis), developed by Roger Carpenter at U. Cambridge (email), allows acquisition, analysis, display and printing of saccadic latency data. The acquisition part requires the ViSaGe system. Files from an Ober Saccadometer can be imported, however. The latter process can be highly automated. The software is very useful for measuring saccadic latencies to a broad array of stimuli and modelling the responses using the LATER model.
SR Research's Experiment Builder
Experiment Builder by SR Research is a commercial psychological experimenting system supporting the EyeLink series of eye trackers. A companion program is DataViewer for eye-movement data analysis and visualization. See the entry above.
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(M) Virtual Reality
Vision Research had always had close links to virtual reality and robotics. This is not the place to give even a rough overview on what is available in these areas, but I will include a few pointers to packages that could be of interest to vision researchers.
VizardVizard by WorldViz is an impressive, powerful generator of virtual reality which I first saw at VSS 2003. See their website for colourful demonstrations.
Seeing Machines is an Australian-based company developing vision-based human-computer interfaces and tracking systems. One product called faceLAB provides head, pose, gaze tracking and eyelid closure tracking. See their website for more information.
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(N) Hardware hints
Psychophysics software is often tied to specific hardware, and one point where this becomes particularly obvious is when it comes to acquiring subject responses with high temporal accuracy. Given the nowadays exclusive use of non-real-time operating systems, the once straight forward approach of just using a sturdy switch no longer suffices. Quite a number of software/hardware systems now promise millisecond accuracy. Here is a rather sketchy list as a starter into the secret world of "button boxes". Please feel free to point to other boxes you have seen.
- SuperLab / Cedrus
- Psychology Software Tools
- Cambridge Research Systems
- Neuroscan response pad
- fORP (Fiber Optic Response Pad)
- VPixx Technologies
SciencePlus is a European reseller for psychological experimenting systems who also distributes some of the response boxes mentioned here.
James, He & Liu (Neuroimage, 2005) reviewed two plastic keyboards (GrandTec's "Virtually Indestructible Keyboard" and Adesso's "Foldable Keyboard") and reported that GrandTec's keyboard appeared suitable for use in MRI.
Standard graphics hardware offers only 8 bits of gray-scale resolution which is not enough for psychophysics. There are software and hardware solutions to the problem (Bach, Meigen, Strasburger, 1997). By software, gray-scale resolution can be improved in trade-off to spatial resolution, by dithering. On the hardware side the trade-off is against color.
Pelli-Zhang Video Attenuator
Pelli's video attenuator is the popular solution for the Macintosh and is supported by lots of software (see also elsewhere here)
Bits++ BoxSee the entry on Cambridge Research Systems above, or go here
A similar device is the Video Switcher from LOBES which bases on the same principle as Pelli-Zhang video attenuator but can drive both monochrome and color monitors (analog). A trigger can be used to measure reaction time or synchronize response recording accurately. The design and test results are described in Journal of Neuroscience Methods, 2003, 130(1): 9-18. In new versions the switch between grayscale and color displays can be controlled by software (so it works as if it did not exist). Price as of 2012 was $280.
Phosphor properties of the stimulus presentation monitors (luminance, contrast, and decay times) are no longer an issue now that CRTs are mostly obsolete. The new generation of flat screens poses different problems for vision research which are addressed in a section on monitors above.
Fast CRTs, Timing
In cases visual psychophysics research is compromised by technology going backwards. In the 80s, timing could be controlled on a CRT down to sub-microsecond accuracy (!!) using what was called the "point-plot technique" feeding graphical data to a so-called "x-y-z display" or to an oscilloscope where the horizontal deflection had no raster generator (see e.g. Treutwein's work). A few labs still have a modern variant of that. Nowadays even the standard CRTs (not to mention the 250-Hz CRTs) are quickly dying out and LCD displays unnerve the time-conscious experimenter by uncontrollable buffering.
Here are two threads from CVNet, one on fast CRTs and one on timing. There is a paper on timing in LCD displays which shows things are becoming even worse.
Neutral Density Filters
There was a nice little discussion on CVNet on how to obtain low-price neutral density filters.
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(O) Auditory Psychophysics
The title of this psychophysics software overview limits it to visual stuff. However, I couldn't resist to include a few pointers to other psychophysics software when it was pointed out to me.
Staircase, developed by Massimo Grassi of Padua, is a Matlab toolbox for auditory testing like pitch discrimination. It implements the method of limits (Fechner, 1889), the simple up-down (von Békésy, 1947; Dixon & Mood, 1948) and the transformed up-down method (Wetherill & Levitt, 1965; Levitt, 1971). The toolbox comes with more than twenty built-in experiments that can be run with any of the three procedures. For each experiment, the parameters of the staircase can be set through a graphical interface. The toolbox comes with several signal generators and modifiers, and does not require programming skill. There is a paper on the precursor of the toolbox (MLP) by Grassi & Soranzo (2009) in Behavior Research Methods 41, 20-28.
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End of review