Debian Science Project
Summary
Psychophysics
Debian Science packages for Psychophysics

This metapackage will install Debian packages which might be useful for carrying out any experiment relating physical stimuli and their psychological effects.

The selection of packages is targeting software for stimuli delivery. For additional software related to the analysis of the acquired data refer to science-neuroscience-cognitive, med-imaging depending on the domain of application. Additionally look into science-bci since those often provide a complete loop frameworks including stimuli delivery.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Science to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Science mailing list

Links to other tasks

Debian Science Psychophysics packages

Official Debian packages with high relevance

Libfreenect-dev
library for accessing Kinect device -- development files
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libfreenect is a cross-platform library that provides the necessary interfaces to activate, initialize, and communicate data with the Kinect hardware. Currently, the library supports access to RGB and depth video streams, motors, accelerometer and LED and provide binding in different languages (C++, Python...)

This library is the low level component of the OpenKinect project which is an open community of people interested in making use of the Xbox Kinect hardware with PCs and other devices.

This is the development package containing the libraries and header for software development with libfreenect.

Octave-psychtoolbox-3
toolbox for vision research -- Octave bindings
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Psychophysics Toolbox Version 3 (PTB-3) is a free set of Matlab and GNU/Octave functions for vision research. It makes it easy to synthesize and show accurately controlled visual and auditory stimuli and interact with the observer.

The Psychophysics Toolbox interfaces between Matlab or Octave and the computer hardware. The Psychtoolbox's core routines provide access to the display frame buffer and color lookup table, allow synchronization with the vertical retrace, support millisecond timing, allow access to OpenGL commands, and facilitate the collection of observer responses. Ancillary routines support common needs like color space transformations and the QUEST threshold seeking algorithm.

See also http://www.psychtoolbox.org/UsingPsychtoolboxOnUbuntu for additional information about systems tune-up and initial configuration.

This package contains bindings for Octave.

Psychopy
environment for creating psychology stimuli in Python
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PsychoPy provides an environment for creating psychology stimuli using Python scripting language. It combines the graphical strengths of OpenGL with easy Python syntax to give psychophysics a free and simple stimulus presentation and control package.

The goal is to provide, for the busy scientist, tools to control timing and windowing and a simple set of pre-packaged stimuli and methods. PsychoPy features

  • IDE GUI for coding in a powerful scripting language (Python)
  • Builder GUI for rapid development of stimulation sequences
  • Use of hardware-accelerated graphics (OpenGL)
  • Integration with Spectrascan PR650 for easy monitor calibration
  • Simple routines for staircase and constant stimuli experimental methods as well as curve-fitting and bootstrapping
  • Simple (or complex) GUIs via wxPython
  • Easy interfaces to joysticks, mice, sound cards etc. via PyGame
  • Video playback (MPG, DivX, AVI, QuickTime, etc.) as stimuli
The package is enhanced by the following packages: python-pyoptical
Please cite: J. W. Peirce: PsychoPy - Psychophysics software in Python. (2007)
Screenshots of package psychopy
Python-pyepl
module for coding psychology experiments in Python
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PyEPL is a stimuli delivery and response registration toolkit to be used for generating psychology (as well as neuroscience, marketing research, and other) experiments.

It provides

  • presentation: both visual and auditory stimuli
  • responses registration: both manual (keyboard/joystick) and sound (microphone) time-stamped
  • sync-pulsing: synchronizing your behavioral task with external acquisition hardware
  • flexibility of encoding various experiments due to the use of Python as a description language
  • fast execution of critical points due to the calls to linked compiled libraries

This toolbox is here to be an alternative for a widely used commercial product E'(E-Prime)

This package provides PyEPL for supported versions of Python.

The package is enhanced by the following packages: python-pyoptical
Python-pyoptical
python interface to the CRS 'OptiCAL' photometer
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The 'OptiCAL' is a photometer that is produced by Cambridge Research Systems (CRS). This device is a standard tool for gamma-calibration of display devices in vision research. This package provides a free-software replacement for the Windows-software distributed by the manufacturer that allows querying an OptiCAL via a serial connection. pyoptical can be used as a library for third-party applications or as a standalone command line tool.

Official Debian packages with lower relevance

Opensesame
graphical experiment builder for the social sciences
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This graphical environment 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.

Please cite: Mathôt, S., & Theeuwes, J.: OpenSesame (Version 0.22) [Computer software and manual] (Retrieved December 18, 2010)
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Python-pyxid
interface for Cedrus XID and StimTracker devices
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pyxid is a Python library for interfacing with Cedrus XID (eXperiment Interface Device) and StimTracker devices. XID devices are used in software such as SuperLab, Presentation, and ePrime for receiving input as part of stimulus/response testing experiments.

pyxid handles all of the low level device handling for XID devices in Python projects.

Science-neuroscience-cognitive
Debian Science packages for Cognitive Neuroscience
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This metapackage will install Debian packages which might be useful for scientists doing cognitive neuroscience research. This comprises the full research process from conducting psychophysical experiments, over data acquisition and analysis, to visualization and typesetting of scientific results.

The selection of packages is targeting the application of analysis techniques. Methods developers are referred to the science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, and med-imaging-dev metapackages for a variety of additional software that might be useful in the context of cognitive neuroscience.

Packaging has started and developers might try the packaging code in VCS

Debruijn
De Bruijn cycle generator
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License: BSD-4-clause
Debian package not available
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Version: 1.6-2

Stimulus counter-balance is important for many experimental designs. This command-line software creates De Bruijn cycles, which are pseudo-random sequences with arbitrary levels of counterbalance. "Path-guided" de Bruijn cycles may also be created. These sequences encode a hypothesized neural modulation at specified temporal frequencies, and have enhanced detection power for BOLD fMRI experiments.

Please cite: Geoffrey Karl Aguirre, Marcelo Gomes Mattar and Lucía Magis-Weinberg: de Bruijn cycles for neural decoding. (PubMed,eprint) NeuroImage 56(3):1293-1300 (2011)

Unofficial packages built by somebody else

Psytoolkit
programming and running psychological experiments
License: GPL-3+
Language: Ruby

Psytoolkit offers

  • Scripting language designed for psychological experiments:
  • Structure designed for experiments (tasks/trials/trial lists/random selection/blocks).
  • Use of bitmaps (png,jpeg,tiff,and many more).
  • Use of MPEG videos.
  • Read from keyboard, mouse, and external devices.
  • Voicekey support via IoLab device
  • Easy programming of parallel port and advanced IO cards.
  • Use of variables.
  • Conditional expressions (if/then/while).
  • Easy interfacing with statistical software R for online feedback to participants.
  • Easy interfacing with C language.
  • It is easy to use.
  • Easy functions for visual and auditory stimulus presentation.
  • Precise timing of stimulus presentation and data collection.
  • Can be used as scripting language, but also comes with a C-library.
  • Comes with a questionnaire presenter psyquest
  • Online Documentation.
Remark of Debian Science team: Depends on libhid removed from Debian due to needed TLC

No known packages available but some record of interest (WNPP bug)

Pebl - wnpp
platform for psychology experiments
License: GPL
Debian package not available
Language: C++

PEBL (Psychology Experiment Building Language) is a system designed for creating psychology and neuroscience experiments and tests. It offers a simple programming language tailor-made for creating and conducting many standard experiments.

Please cite: Mueller, S. T.: The PEBL Manual (2011)
Visionegg - wnpp
Python library for 2D/3D visual stimulus generation
License: LGPL
Debian package not available

The Vision Egg is a programming library that uses standard, inexpensive computer graphics cards to produce visual stimuli for vision research experiments.

No known packages available

Nrec
neurological stimulation, data acquisition and experiment control
License: GPL
Debian package not available
Language: C++

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 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.

Psychlops
License: GPL
Debian package not available
Language: C++

Psychlops is a free C++ library to offer the easy way to develop a demonstration of various types of visual stimulus used in the Vision science.

Binary builds are available only for OS X and Windows. Sources available from sf's SVN: http://sourceforge.jp/projects/psychlops/svn/view/cpp/

Tscope
C/C++ experiment programming library for cognitive scientists
License: GPL
Debian package not available
Language: C

Tscope is a C/C++ experiment programming library for cognitive scientists. It provides functions for graphics, sound, timing, randomization and response registration.

Please cite: Stevens, M., Lammertyn, J., Verbruggen, F., & Vandierendonk, A.: Tscope: A C library for programming cognitive experiments on the MS Windows platform (2006)
Remark of Debian Science team: Primarily targeting Windows platform, provides some functionality on Linux
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