Debian Med Project
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Summary
Physics
Debian Med-pakker for medicinske fysikere

Denne metapakke indeholder afhængigheder for en samling af programmer og dokumentation, som er nyttige for medicinske fysikere indenfor strålingsonkologi, diagnostik billedbehandling og relaterede felter.

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
Konverteringsværktøjer for biomedicinske dataformater
Versions of package biosig-tools
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bookworm2.5.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky3.9.0-1amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bullseye2.1.2-4amd64,arm64,armhf,i386
upstream3.9.1
Debtags of package biosig-tools:
interfacecommandline
roleprogram
useconverting
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Baseret på BioSig-biblioteket tilbyder denne pakke værktøjer for kommandolinjen, såsom:

  • save2gdf: konverteringsprogram mellem forskellige filformater, inklusive men ikke begrænset til CP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF, BDF, CWFB
  • biosig2gdf: konverterer biosig-datafiler til GDF, for at forenkle fortolkning og indlæsning af skriptsprog (f.eks. loadgdf.{py,r})
  • rec2bin, bin2rec, heka2itx, save2aecg, save2scp: flere konverteringsværktøjer baseret på save2gdf
  • biosig_fhir: pakker biosignal-data til HL7/FHIR-binær skabelonfil
  • physicalunits: konverteringsprogram til at kode og afkode fysiske enheder jævnfør ISO 11073-10101
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-bibliotek for GDF'en - hjælpeværktøjer
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sid0.1.3-12amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye0.1.3-8amd64,arm64,armhf,i386
bookworm0.1.3-11amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
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GDF (General Dataformat for Biosignals) er lavet for at tilbyde et generisk lager for biosignaler, såsom EEG, ECG, MEG etc.

Denne pakke tilbyder værktøjet leveret med biblioteket (gdf_merger).

Please cite: Alois Schlögl: GDF – A general dataformat for BIOSIGNALS. The Computing Research Repository abs/cs/0608052 (2006)
octave
GNU Octave-sprog til talberegninger
Versions of package octave
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experimental10.2.0-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
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trixie9.4.0-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
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sid9.4.0-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
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Octave er et (for det meste Matlab®-kompatibelt) sprog på højt niveau, primært beregnet til numeriske beregninger. Programmet tilbyder en nem brugerflade fra kommandolinjen til løsning af lineære og ikkelineære problemer numerisk.

Octave kan udvides dynamisk med filer i C++ som leveres af brugeren.

The package is enhanced by the following packages: liboctave-dev octave-dev octave-doc texmacs-bin
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)
Registry entries: SciCrunch 
r-base
GNU R statistisk beregning og grafiksystem
Maintainer: Dirk Eddelbuettel
Versions of package r-base
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R er et system til statistisk beregning og grafik. Det består af et sprog plus et afviklingsmiljø med grafik, et aflusningsredskab, adgang til særlige systemfunktioner, samt evnen til at køre programmer som er gemt som skriptfiler.

Designet af R er tungt påvirket af to eksisterende sprog: Becker, Chambers & Wilks' S og Sussman's Scheme. Hvor sprogudformningen i sin fremtræden i høj grad ligner S, så er den underliggende implementering og semantik afledt fra Scheme.

Kernen i R er et fortolket programmeringssprog som tillader forgrening og løkker, så vel som modulær programmering med brug af funktioner. De fleste funktioner som er synlige for brugeren i R er skrevet i R. Det er muligt for brugeren at tilgå procedurer skrevet i C, C++ eller FORTRAN sprogene for effektivitet, og mange af R's kernefunktioner gør dette. Distributionen R indeholder funktionalitet til et stort antal statistiske procedurer og underliggende anvendte matematiske beregninger. Der er også et stort sæt af funktioner, der tilbyder et grafisk miljø til oprettelse af adskillige slags datarepræsentationer.

Derudover er flere tusinde udvidelsespakker tilgængelige fra CRAN (Comprehensive R Archive Network), mange også som Debianpakker, der er navngivet »r-cran-«.

Disse pakker er en metapakke, som letter overgangen fra pre-1.5.0-pakkestrukturen med dennes store r-base-pakke. Så snart den er installeret, kan den uden videre fjernes og apt-get vil automatisk opgradere dens komponenter under fremtidige opgraderinger. Denne pakke gør det muligt for brugerne kun at installere r-base-core, hvis de ønsker det.

The package is enhanced by the following packages: texmacs-bin
Screenshots of package r-base

Official Debian packages with lower relevance

libbiosig-dev
I/O-bibliotek for biomedicinske data - udviklingsfiler
Versions of package libbiosig-dev
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bookworm2.5.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
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forky3.9.0-1amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie3.9.0-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye2.1.2-4amd64,arm64,armhf,i386
upstream3.9.1
Debtags of package libbiosig-dev:
develexamples, library
roledevel-lib
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BioSig er et bibliotek for adgang til filer i flere forskellige biomedicinske dataformater (inklusive EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro, TMS32). Den fulde liste over understøttede filformater er tilgængelig på http://pub.ist.ac.at/~schloegl/biosig/TESTED .

Denne pakke tilbyder hovedfiler og det statiske bibliotek.

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
Octavebindinger for BioSig-biblioteket
Versions of package octave-biosig
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bookworm2.5.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
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bullseye2.1.2-4amd64,arm64,armhf,i386
trixie3.9.0-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky3.9.0-1amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
upstream3.9.1
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Denne pakke tilbyder Octavebindinger for BioSig-biblioteket. Primært formål er en I/O-grænseflade til en række biomedicinske filformater, inklusive men ikke begrænset til 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)
python3-biosig
Python 3-bindinger for BioSig-biblioteket
Versions of package python3-biosig
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trixie3.9.0-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
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bookworm2.5.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye2.1.2-4amd64,arm64,armhf,i386
upstream3.9.1
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Denne pakke tilbyder Python 3-bindinger for BioSig-biblioteket. Primære formål - I/O-grænseflade til en række biomedicinske filformater, inklusive men ikke begrænset til 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)
python3-multipletau
multiple-tau algorithm for Python3/NumPy
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Multiple-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

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

paw
Physics Analysis Workstation - a graphical analysis program
Versions of package paw
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VCS1:2.14.04.dfsg.2-10all
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License: free
Debian package not available
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Version: 1:2.14.04.dfsg.2-10

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)
Versions of package paw++
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License: free
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Version: 1:2.14.04.dfsg.2-10

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.

paw-demos
Physics Analysis Workstation examples and tests
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Version: 1:2.14.04.dfsg.2-10

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.

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.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 267670