Debian Med Project
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Summary
Physics
Pakiet medyczny Debiana dla fizyków medycznych

Ten metapakiet zawiera zależności dla zbioru oprogramowania oraz dokumentacji, które są pomocne fizykom medycznym w radioterapii, obrazowaniu diagnostycznym oraz w pokrewnych dziedzinach.

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 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
Narzędzia do konwertowania formatów danych biomedycznych
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Pakiet oparty jest na bibliotece BioSig i zawiera narzędzia wiersza poleceń, takie jak:

  • save2gdf: konwerter pomiędzy różnymi formatami plików, takimi jak: (lecz nie ograniczający się do nich) SCP-ECG (EN 1064), HL7 aECG (FDA-XML), GDF, EDF, BDF, CWFB. Save2gdf może być również używany do przesyłania i pobierania danych z serwera BSCS.
Gdf-tools
Biblioteka wejścia/wyjścia do GDF - narzędzia pomocnicze
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GDF (General Dataformat for Biosignals - powszechny format danych do biosygnałów) służy do uniwersalnego przechowywania biosygnałów, takich jak EEG, EKG, MEG itd.

Pakiet zawiera narzędzie dostarczane z biblioteką (gdf_merger).

Octave
Język GNU Octave do obliczeń numerycznych
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Octave jest (w większości kompatybilnym z Matlab (R)) wysokopoziomowym językiem, początkowo stworzonym do obliczeń numerycznych. Dostarcza wygodny interfejs wiersza poleceń do rozwiązywania liniowych oraz nieliniowych zadań metodami numerycznymi.

Octave może być dynamicznie rozszerzony o dostarczone przez użytkownika pliki C++.

The package is enhanced by the following packages: liboctave-dev octave-doc texmacs
Please cite: John W. Eaton, David Bateman, Søren Hauberg and Rik Wehbring: GNU Octave version 4.2.0 manual: a high-level interactive language for numerical computations. (2016)
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VersionURL
4.0.3-2+b1https://screenshots.debian.net/screenshots/000/015/189/large.png
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Paw
Physics Analysis Workstation (ang. Stacja robocza do analizy dla fizyków) - program do analizy graficznej
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CERNLIB to zestaw narzędzi do analizy danych oraz biblioteka stworzona na potrzeby fizyki doświadczalnej, zawiera jednak również aplikacje pomocne w innych dziedzinach, takich jak nauki biologiczne.

PAW jest interaktywnym programem zawierającym narzędzia do graficznej prezentacji oraz do analizy statystycznej i matematycznej. Jest przeznaczony do pracy na obiektach bliskich fizykom takich jak histogramy, pliki zdarzeń (Ntuples), wektory itp.

W celu poprawnego funkcjonowania, na architekturach 64-bitowych, program jest łączony statycznie z biblioteką CERN, gdyż nie był projektowany na taką architekturę.

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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.

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.

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.

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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