Debian Med Project
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Summary
Physics
Debian Med packages for medical physicists

This metapackage contains dependencies for a collection of software and documentation which is useful for medical physicists in radiation oncology, diagnostics imaging and related fields.

The list to the right includes various software projects which are of some interest to the Debian Med Project. Currently, only a few of them are available as Debian packages. It is our goal, however, to include all software in Debian Med which can sensibly add to a high quality Debian Pure Blend.

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 Med 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 Med mailing list

Links to other tasks

Debian Med Physics packages

Official Debian packages with high relevance

Biosig-tools
format conversion tools for biomedical data formats
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Based on BioSig library, this package provides command line tools, such as

  • save2gdf: converter between different file formats, including but not limited to SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF, BDF, CWFB. save2gdf can be also used to upload or retrieve data from a bscs server.
Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
Gdf-tools
IO library for the GDF -- helper tools
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GDF (General Dataformat for Biosignals) is intended to provide a generic storage for biosignals, such as EEG, ECG, MEG etc.

This package provides the tool shipped with the library (gdf_merger).

Octave
GNU Octave language for numerical computations
Maintainer: Debian Octave Group
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Octave is a (mostly Matlab (R) compatible) high-level language, primarily intended for numerical computations. It provides a convenient command-line interface for solving linear and nonlinear problems numerically.

Octave can be dynamically extended with user-supplied C++ files.

The package is enhanced by the following packages: texmacs
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Paw
Physics Analysis Workstation - a graphical analysis program
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CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

PAW is an interactive program providing interactive graphical presentation and statistical and mathematical analysis tools. It is designed to work on objects familiar to physicists such as histograms, event files (Ntuples), vectors, etc.

The program is linked statically against the CERN libraries on 64-bit architectures in order to function properly, as its design is not very 64-bit clean.

Paw++
Physics Analysis Workstation (Lesstif-enhanced version)
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CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This package includes Paw++, an interactive program for use in analysis and graphical presentation. Paw++ is the same program as PAW (in the "paw" package), but with a more user-friendly Motif-based GUI, compiled against Lesstif in Debian.

The program is linked statically against the CERN libraries on 64-bit architectures in order to function properly, as its design is not very 64-bit clean.

R-base
GNU R statistical computation and graphics system
Maintainer: Dirk Eddelbuettel
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R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files.

The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme.

The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations.

Additionally, several thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-'.

This package is a metapackage which eases the transition from the pre-1.5.0 package setup with its larger r-base package. Once installed, it can be safely removed and apt-get will automatically upgrade its components during future upgrades. Providing this package gives a way to users to then only install r-base-core if they so desire.

The package is enhanced by the following packages: texmacs
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Official Debian packages with lower relevance

Libbiosig-dev
I/O library for biomedical data - development files
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BioSig is a library for accessing files in several biomedical data formats (including EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro, TMS32). The complete list of supported file formats is available at http://pub.ist.ac.at/~schloegl/biosig/TESTED .

This package provides header files and static library.

Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
Octave-biosig
Octave bindings for BioSig library
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This package provides Octave bindings for BioSig library. Primary goal -- I/O interface to variety of biomedical file formats, including but not limited to SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF.

Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
Paw-demos
Physics Analysis Workstation examples and tests
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CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.

This package includes example scripts for use by PAW or Paw++, and test scripts to make sure that the PAW or Paw++ programs behave correctly. You may run the examples and tests with the included paw-demos program.

Python-biosig
Python bindings for BioSig library
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This package provides Python bindings for BioSig library. Primary goal -- I/O interface to variety of biomedical file formats, including but not limited to SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF.

Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
Python-multipletau
multiple-tau algorithm for Python/NumPy
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Multipe-tau correlation is computed on a logarithmic scale (less data points are computed) and is thus much faster than conventional correlation on a linear scale such as numpy.correlate

An online reference is available at http://paulmueller.github.io/multipletau

This is the Python 2 version of the package

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

Gate - wnpp
Geant4 Application for Emission Tomography
Responsible: Nicolas Spalinger
License: LGPL
Debian package not available

GATE incorporates the Geant4 libraries in a modular, versatile, and scripted simulation toolkit which is adapted to the field of nuclear medicine both in PET (Positron Emission Tomography) and SPECT (Single Photon Emission Computer Tomography). It allows the accurate description of time-dependent phenomena such as source or detector movement and source decay kinetics. The ability to synchronize all time-dependent components allows a coherent description of the acquisition process. It makes it possible to perform realistic simulations of data acquisitions in time.

Openvibe - wnpp
platform for the design, test and use of BCI
License: LGPL
Debian package not available
Language: C++

OpenViBE enables to design, test and use Brain-Computer Interfaces (BCI). OpenViBE is a software for real-time neurosciences (that is, for real-time processing of brain signals). It can be used to acquire, filter, process, classify and visualize brain signals in real time.

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