Debian Med Project
Help us to see Debian used by medical practitioners and biomedical researchers! Join us on the Salsa page.
Summary
Imaging
Debian Med - billedbehandling og visualiseringspakker

Denne metapakke vil installere Debianpakker, som kan være nyttige i medicinsk billedbehandling og visualisering.

På den ene side installeres flere pakker, som understøtter diverse billedfilsformater og billedhåndtering, såsom DICOM (Digital Imaging and Communications in Medicine), der er de facto-standarden i medicinsk billedhåndtering og NIFTI. På den anden side tilbydes en række programpakker, som kan bruges til at visualisere og for billedbehandling - enten fra en grafisk brugerflade, kommandolinjen eller implementeret i arbejdsforløb.

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 Imaging packages

Official Debian packages with high relevance

Aeskulap
Medicinsk billedfremviser og DICOM-netværksklient
Versions of package aeskulap
ReleaseVersionArchitectures
bullseye0.2.2-beta2+git20190406.ef77f01-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.2.2-beta2+git20190406.ef77f01-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
squeeze0.2.2b1-6amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy0.2.2b1-11amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie0.2.2b1-13amd64,armel,armhf,i386
stretch0.2.2b1+git20161206-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.2.2-beta2+git20180219.8787e95-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package aeskulap:
fieldbiology, medicine, medicine:imaging
interfacex11
networkclient
roleprogram
scopeapplication
uitoolkitgtk
useviewing
works-withimage
x11application
Popcon: 68 users (28 upd.)*
Versions and Archs
License: DFSG free
Git

Aeskulap er i stand til at indlæse en serie af specielle billeder gemt i DICOM-formatet, så de kan gennemses. Derudover er programmet i stand til at hente og sætte billeder fra DICOM i kø fra arkivknuder (også kaldt PACS) over netværket. Aeskulap forsøger at blive en fuldt open source-erstatning for kommercielt tilgængelige DICOM-fremvisere.

Screenshots of package aeskulap
Amide
Program til medicinsk billedbehandling
Versions of package amide
ReleaseVersionArchitectures
jessie1.0.5-2amd64,armel,armhf,i386
squeeze0.9.2-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
bullseye1.0.5-15amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
wheezy1.0.1-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
stretch1.0.5-7amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.0.5-12amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.0.5-15amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package amide:
fieldmedicine, medicine:imaging
roleprogram
Popcon: 36 users (65 upd.)*
Versions and Archs
License: DFSG free
Git

AMIDE: (Amide's a Medical Imaging Data Examiner, på dansk: Amides er et dataundersøgelsesværktøj til medicinsk billedbehandling) AMIDE er et værktøj til at fremvise og analysere medicinske billeder af datasæt. Dets egenskaber inkluderer simultan håndtering af adskillige datasæt, importeret fra en vifte af filformater, billedfusion, optegning og analyse for områder af interesse i 3D, optegnelse af volumen, og justering af stive legemer.

Amide importerer de fleste kliniske DICOM-filer (via DCMTK-biblioteket).

Please cite: Andreas Markus Loening and Sanjiv Sam Gambhir: AMIDE: A Free Software Tool for Multimodality Medical Image Analysis. (PubMed) Molecular Imaging 2(3):131-7 (2003)
Other screenshots of package amide
VersionURL
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17673/simage/large-7640f62c8ac17498b7e825bdc3e3be71.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17677/simage/large-8f7aaa9529343865541ebc968e464c74.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17678/simage/large-deeb0fc832965282d8e7bd9a43b6065e.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/16980/simage/large-bad825aa1bf433c09104699fb7be429c.png
0.9.1-2https://screenshots.debian.net/shrine/screenshot/356/simage/large-a3b9d7e99aafc8e159ad1288d6031445.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17676/simage/large-6cc9cfe18a76cd3b247214d8ae0339b6.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17675/simage/large-d5d4f705acb3ff24758ea101b026c05b.png
Screenshots of package amide
Ants
Avancerede normaliseringsværktøjer for hjerne og billedanalyse
Versions of package ants
ReleaseVersionArchitectures
jessie2.1.0~rc2+git3-g9103999-4amd64,i386
stretch2.1.0-5amd64,i386
sid2.1.0-5amd64,i386
experimental2.2.0-1amd64,i386
wheezy1.9.2+svn680.dfsg-4amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,powerpc,s390x,sparc
squeeze1.9+svn532-5amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Debtags of package ants:
fieldmedicine:imaging
interfacecommandline
roleprogram
sciencecalculation
scopeapplication
works-withfile, image, image:raster
Popcon: 7 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

Advanced Normalization Tools (ANTS) er en ITK-baseret programpakke af normaliserings-, segmenterings- og skabelonbygningsværktøjer til kvantitativ morfometrisk analyse. Mange af ANTS-registreringsværktøjerne er diffeomorfiske, men deformationstransformationer (elastiske og med BSpline) er også tilgængelige. Unikke komponenter af ANTS inkluderer similaritetsbestemmelse i flere variable, brug af »landmærker«, mulighed for at bruge etiketbilleder til at vejlede kortlægningen, og både grådige og rumtidsoptimale implementeringer af diffeomorfier. Den symmetriske normaliseringsstrategi (SyN) er en del af ANTS-værktøjssættet sammen med directly manipulated free form deformation (DMFFD).

Denne pakke tilbyder konfiguration af miljømoduler. Brug »module load ants« til at gøre alle værktøjer for kommandolinjen tilgængelige i din skal.

Screenshots of package ants
Bart
Værktøjer for beregnet magnetisk resonansbilledoprettelse
Versions of package bart
ReleaseVersionArchitectures
buster0.4.04-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch0.4.00-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.6.00-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.6.00-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream0.7.00
Popcon: 12 users (10 upd.)*
Newer upstream!
License: DFSG free
Git

The Berkeley Advanced Reconstruction Toolbox (BART) er en fri ramme til billedrekonstruktion for Computational Magnetic Resonance Imaging. Det består af et programmeringsbibliotek og en værktøjskasse for kommandolinjeprogrammer. Biblioteket tilbyder fælles operationer på tabeller med flere dimensioner, Fourier- og wavelet-tranformationer samt generiske implementeringer af iterative optimeringsalgoritmer. Værktøjerne for kommandolinjen tilbyder direkte adgang til grundlæggende operationer på tabeller med flere dimensioner samt effektive implementeringer af mange kalibrerings- og rekonstruktionsalgortimer for parallel billedoprettelse og pakket opfattelse.

Please cite: Martin Uecker, Sebastian Rosenzweig, H. Christian M. Holme, Moritz Blumenthal, Zhengguo Tan, Xiaoqing Wang, Jonathan I. Tamir and Michael Lustig: BART Toolbox for Computational Magnetic Resonance Imaging.
Bart-view
Fremviser for flerdimensionale kompleks-vurderede data
Versions of package bart-view
ReleaseVersionArchitectures
sid0.1.00-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster0.1.00-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.1.00-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 4 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

Berkeley Advanced Reconstruction Toolbox (BART) er en fri ramme til billedrekonstruktion for Computational Magnetic Resonance Imaging.

Denne pakke tilbyder en billedfremviser som en valgfri komponent for BART-rammen. Fremviseren er designet til flerdimensionale kompleks-vurderede data.

Screenshots of package bart-view
Biosig-tools
Konverteringsværktøjer for biomedicinske dataformater
Versions of package biosig-tools
ReleaseVersionArchitectures
stretch1.3.0-2.2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2.1.2-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2.1.2-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
wheezy1.3.0-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie1.3.0-2amd64,armel,armhf,i386
buster1.9.3-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
upstream2.2.1
Debtags of package biosig-tools:
interfacecommandline
roleprogram
useconverting
Popcon: 7 users (8 upd.)*
Newer upstream!
License: DFSG free
Git

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)
Camitk-imp
Arbejdsbordprogram for CamiTK-biblioteket
Versions of package camitk-imp
ReleaseVersionArchitectures
sid4.1.2-4amd64,i386
jessie3.3.2-2amd64,armel,armhf,i386
stretch4.0.4-2amd64,i386
buster4.1.2-3amd64,i386
bullseye4.1.2-4amd64,i386
Popcon: 4 users (4 upd.)*
Versions and Archs
License: DFSG free
Git

CamiTK hjælper forskere og klinikere med nemt og hurtigt at samarbejde om at udarbejde prototyper for CAMI-programmer, som indeholder medicinske billeder, kirurgisk navigation og biomekaniske simuleringer.

Camitk-imp er CamiTK-arbejdsbordprogrammet, hvor du kan teste alle tilgængelige udvidelser som prototype. Det giver en nem og interaktiv adgang til alle tilgængelige data og algoritmeparametre, herunder dem du selv bygger ved hjælp af CamiTK SDK'en.

For eksempel kan camitk-imp visualisere medicinske billeder fra en masse forskellige (standard)formater, tilbyde billedbehandling og segmenteringsalgoritmer til at rekonstruere en mesh-geometri og køre en biomekanisk simulering.

Please cite: Céline Fouard, Aurélien Deram, Yannick Keraval and Emmanuel Promayon: CamiTK: a Modular Framework Integrating Visualization, Image Processing and Biomechanical Modeling. :323-354 (2012)
Screenshots of package camitk-imp
Caret
Værktøjssæt til computerbaseret anatomisk rekonstruktion og redigering
Versions of package caret
ReleaseVersionArchitectures
jessie5.6.4~dfsg.1-3amd64,armel,armhf,i386
wheezy5.6.4~dfsg.1-3amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze5.6.1.3~dfsg.1-4amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Debtags of package caret:
roleprogram
uitoolkitqt
Popcon: 2 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

Denne software gør det muligt at skabe, vise og manipulere overfladiske rekonstruktioner af storhjernen og hjernebarken, vise volumener, samt til at vise eksperimentelle data fra overflader og volumener. Selv om Caret primært er en applikation med en grafisk brugerflade, så er der også et fleksibelt kommandolinjeværktøj, der tillader adgang til en stor del af Carets egenskaber.

Caret kan hente og anvende stereotaktiske atlasser (menneske, abe, mus og rotte) fra en åben online-database.

Nogle af Carets egenskaber er kun tilgængelig når ekstra datafiler, der tilbydes af pakken caret-data, er tilgængelige. Dette inkluderer:

  • Kortvolumener til overflader via PALS-atlas
  • Morfing i flere opløsninger
  • Projektion af foci via PALS-atlas
  • Overfladebaseret registrering
  • Udjævning af overflade

På nuværende tidspunkt er pakken caret-data kun tilgængelig fra arkivet NeuroDebian. Se venligst http://neuro.debian.net for mere information.

Please cite: David C. Van Essen, Heather A. Drury, James Dickson, John Harwell, Donna Hanlon and Charles H. Anderson: An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex. (PubMed,eprint) Journal of American Medical Informatics Association 8(5):443-459 (2001)
Conquest-common
ConQuest DICOM-server - fælles filer
Versions of package conquest-common
ReleaseVersionArchitectures
jessie1.4.17d-1amd64,armel,armhf,i386
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

En DICOM-server, med alle funktioner, som er blevet udviklet baseret på og har udvidet sig med UCDMC DICOM-kode i offentlig ejendom. Nogle mulige programmer for ConQuest DICOM-programmer er:

  • DICOM-træning og test
  • Arkiver for demonstration og videnskabsbilleder
  • Konvertering af billedformat fra en skanner med DICOM-netværksadgang
  • Visning af DICOM-billede og udarbejdelse af dias
  • Valg af DICOM-billede, (begrænset) redigering samt opdeling og sammenføjning af serier
  • Avanceret billedændring, filtrering, videresendelse og konvertering via skripter
  • DICOM-mellemlager og arkivsammenføjning

Denne pakke indeholder fælles filer. Du skal bruge en pakke, der tilbyder conquest-docm-server (f.eks. conquest-mysql, conquest-postgres, conquest-sqlite eller conquest-dbase).

Ctn
Central Test Node - en DICOM-implementering for medicinske billeder
Versions of package ctn
ReleaseVersionArchitectures
bullseye3.2.0~dfsg-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
squeeze3.0.6-13amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
stretch3.2.0~dfsg-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster3.2.0~dfsg-6amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie3.2.0~dfsg-2amd64,armel,armhf,i386
sid3.2.0~dfsg-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package ctn:
fieldmedicine:imaging
interfacecommandline, web, x11
roleprogram
scopeapplication
uitoolkitathena, motif
useconverting
works-withdb, image, image:raster
x11application
Popcon: 14 users (5 upd.)*
Versions and Archs
License: DFSG free
Git

DICOM er standarden for billedlagring, annotation og netværk. Det er vidt udbredt for medicinske billeder. Central Test Node-programmet (CTN) tilbyder en implementering af denne standard.

Denne pakke inkluderer de binære filer og kørselstids konfigurationsfiler for CTN.

Please cite: S.M. Moore, S.A. Hoffman and D.E. Beecher: DICOM Shareware: A Public Implementation of the DICOM Standard 2165:772–781 (1994)
Ctsim
Beregnet tomografisimulator
Versions of package ctsim
ReleaseVersionArchitectures
bullseye6.0.2-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid6.0.2-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
squeeze5.1.4-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
jessie5.2.0-2amd64,armel,armhf,i386
stretch5.2.0-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster6.0.2-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package ctsim:
fieldbiology
interface3d, commandline
roleprogram
scopeapplication
uitoolkitwxwidgets
useviewing
works-with3dmodel
x11application
Popcon: 9 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

CTSim tilbyder en interaktiv beregnet tomografisimulator. Beregnet tomografi er en teknik til stimering af interiøret for et objekt ved at måle x-strålingabsorbering igennem objektet.

CTSim har både kommandolinjeværktøjer og en grafisk brugerflade. CTSim har meget undervisende sporingstilstande for visning af dataindsamlingssimuleringen samt rekonstruktionen.

Screenshots of package ctsim
Dcm2niix
Næste generation DICOM- til NIfTI-konverteringsprogram
Versions of package dcm2niix
ReleaseVersionArchitectures
bullseye1.0.20201102-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch1.0.20161101-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.0.20201102-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster1.0.20181125-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
upstream1.0.20210317
Popcon: 20 users (37 upd.)*
Newer upstream!
License: DFSG free
Git

Dcm2niix er efterfølgeren til dcm2nii, et populært værktøj for konvertering af billeder fra de kompilerede formater brugt af skannerproducenter (DICOM, PAR/REC) til det simplere NIfTI-format brugt af mange videnskabelige værktøjer. Den fungerer for alle modaliteter (T, MRI, PET, SPECT) og sekvenstyper.

Dcmtk
OFFIS DICOM-værktøjssættets kommandolinjeredskaber
Versions of package dcmtk
ReleaseVersionArchitectures
stretch3.6.1~20160216-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid3.6.5-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.6.5-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster3.6.4-2.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie-security3.6.0-15+deb8u1amd64,armel,armhf,i386
jessie3.6.0-15+deb8u1amd64,armel,armhf,i386
wheezy-security3.6.0-12+deb7u1amd64,armel,armhf,i386
wheezy3.6.0-12amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze3.5.4-4amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
upstream3.6.6
Debtags of package dcmtk:
interfacecommandline
roleprogram
scopeutility
useconverting, downloading
works-withimage, image:raster
Popcon: 190 users (33 upd.)*
Newer upstream!
License: DFSG free
Git

DCMTK inkluderer en samling af biblioteker og applikationer til at undersøge, konstruere og konvertere DICOM-billedfiler, håndtere medier uden forbindelse, sende og modtage billeder over en netværksforbindelse, såvel som demonstrative servere til billedlagring og arbejdslister (»worklist«).

Denne pakke indeholder DCMTK-redskabsprogrammerne.

Bemærk: Denne version blev kompileret med libssl-understøttelse.

Dicom3tools
DICOM-medicinske billedfiler - manipulerings- og konverteringsværktøjer
Versions of package dicom3tools
ReleaseVersionArchitectures
stretch1.00~20170109062447-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie1.00~20140902075059-1amd64,armel,armhf,i386
buster1.00~20180803063840-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye1.00~20190724083540-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.00~20190724083540-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
wheezy1.0~20120505-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze1.0~20100510-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Debtags of package dicom3tools:
fieldmedicine, medicine:imaging
roleprogram
useconverting
works-withimage
Popcon: 28 users (13 upd.)*
Versions and Archs
License: DFSG free
Git

Redskaber til kommandolinjen for oprettelse, ændring, dumpning og validering af filer for DICOM-attributter. Understøtter konvertering af nogle proprietære medicinske billedformater til DICOM. Kan håndtere ældre ACR/NEMA-formatdata og nogle proprietære versioner såsom SPI.

Dicomnifti
konverterer DICOM-filer til NIfTI-formatet
Versions of package dicomnifti
ReleaseVersionArchitectures
bullseye2.33.1-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2.33.1-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
squeeze2.28.14-2amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
jessie2.32.1-1amd64,armel,armhf,i386
stretch2.32.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.33.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package dicomnifti:
interfacecommandline
roleprogram
scopeutility
useconverting
Popcon: 12 users (11 upd.)*
Versions and Archs
License: DFSG free
Git

dinifti-programmet konverterer MRI-billeder gemt i DICOM-formatet til NIfTI-formatet. NIfTI-formatet er tænkt som det nye standardbilledformat for medicinske billeder og kan bruges for eksempel med FSL, AFNI, SPM, Caret eller Freesurfer.

dinifti konverterer enkeltfiler, men understøter også fulde batchkonverteringer af fulde dicom-mapper. Derudover kan konverterede NIfTI- filer navngives korrekt, med brug af billedserieinformation fra DICOM- filerne.

Dicomscope
OFFIS DICOM-fremviser
Versions of package dicomscope
ReleaseVersionArchitectures
buster3.6.0-20all
stretch3.6.0-15all
squeeze3.6.0-2amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
bullseye3.6.0-22all
jessie3.6.0-11amd64,armel,armhf,i386
wheezy3.6.0-10amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
sid3.6.0-22all
Debtags of package dicomscope:
fieldmedicine, medicine:imaging
roleprogram
useviewing
Popcon: 26 users (12 upd.)*
Versions and Archs
License: DFSG free
Git

DICOMscope er en fri DICOM-fremviser som kan vise ukomprimerede monochrome DICOM-billeder fra alle modaliteter og som understøtter kalibrering af skærm jævnfør DICOM part 14 samt præsentationstilstande.

DICOMscope tilbyder en udskrivningsklient (DICOM Basic Grayscale Print Management) som også implementerer den valgfrie Presentation LUT SOP- klasse.

Udviklingen af denne prototype blev igangsat af »Committee for the Advancement of DICOM« og fremvist på European Congress of Radiology ECR 1999. En forbedret udgave blev udviklet for »DICOM Display Consistency Demonstration« på RSNA InfoRAD 1999.

Den aktuelle version 3.5.1 er blevet demonstreret på ECR 2001 og indeholder mange udvidelser, inklusiv en udskrivningsserver, understøttelse af krypteret DICOM-kommunikation, digitale underskriftere og struktureret rapportering.

Screenshots of package dicomscope
Fslview
fremviser for (f)MRI- og DTI-data
Versions of package fslview
ReleaseVersionArchitectures
squeeze3.1.8+4.1.6-2amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
jessie4.0.1-4amd64,armel,armhf,i386
Debtags of package fslview:
interfacex11
made-ofhtml
roledocumentation, program
scopeutility
suitedebian
uitoolkitqt
useviewing
x11application
Popcon: 9 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

Denne pakke tilbyder en fremviser for 3D- og 4D-MRI-data samt DTI- billeder. FSLView kan vise ANALYZE- og NIFTI-filer. Fremviseren understøtter flere 2D-fremvisningstilstande (ortogonal, letboks eller enkelte skiver), men også 3D-lydstyrkeoptegning. Derudover er FSLView i stand til at visualisere tidsserier og kan lave overlag på metriske og stereotaktiske atlasdata.

FSLView er en del af FSL.

Please cite: S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady and P.M. Matthews: Advances in functional and structural MR image analysis and implementation as FSL. (PubMed) NeuroImage 23:208-219 (2004)
Remark of Debian Med team: fslview was removed from Debian (see #647810)

The bug log (http://bugs.debian.org/647810) explains the reasons for the removal. The maintainers did never respond whether they plan to bring back a more recent version of this package

Gdf-tools
IO-bibliotek for GDF'en - hjælpeværktøjer
Versions of package gdf-tools
ReleaseVersionArchitectures
bullseye0.1.3-8amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.1.3-8amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster0.1.2-2.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch0.1.2-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie0.1.2-2amd64,armel,armhf,i386
wheezy0.1.2-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package gdf-tools:
roleprogram
Popcon: 5 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

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)
Ginkgocadx
Medicinsk billedsoftware og en komplet DICOM-fremviser
Versions of package ginkgocadx
ReleaseVersionArchitectures
jessie3.7.0.1465.37+dfsg-1amd64,armel,armhf,i386
buster3.8.8-1amd64,i386
bullseye3.8.8-5amd64,i386
sid3.8.8-5amd64,i386
stretch3.8.4-1amd64,i386
wheezy2.12.0.4889-1amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package ginkgocadx:
fieldmedicine, medicine:imaging
roleprogram
uitoolkitgtk, wxwidgets
useviewing
Popcon: 37 users (8 upd.)*
Versions and Archs
License: DFSG free
Git

Ginkgo CADx tilbyder en komplet løsning til DICOM-fremvisning, der har avancerede egenskaber og understøtter udvidelsesmoduler.

  • Nem grænseflade som kan tilpasses gennem profiler.
  • Visualisering af DICOM-billeder med fuld funktionalitet.
  • Komplet værktøjssæt (måling, markører, tekst, ...).
  • Understøttelse af flere modaliteter (neurologisk, radiologisk, dermatologisk, oftalmologisk, ultralyd, endoskopi, ...).
  • Understøttelse af dikomisering fra JPEG, PNG, GIF og TIFF.
  • Understøttelse af fuld EMH-integration: HL7-standardiserede og IHE-kompatible arbejdsgange.
  • PACS-arbejdsstation (C-FIND, C-MOVE, C-STORE, ...).
  • Kan udvides gennem tilpassede udvidelsesmoduler.
  • Mosaik-komposition af retina-billeder.
  • Automatisk diagnostik af retina-analyse.
  • Automatisk psoriasis-diagnostik.
Gwyddion
Værktøj til visualisering og analyse via Skanning Probe Mikroskopi
Versions of package gwyddion
ReleaseVersionArchitectures
jessie2.38-2amd64,armel,armhf,i386
wheezy2.28-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze2.20-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
sid2.57-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye2.57-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.52-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch2.47-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
upstream2.58
Debtags of package gwyddion:
fieldphysics
interfacex11
roleprogram
sciencevisualisation
scopeapplication
uitoolkitgtk
useanalysing, viewing
works-withimage, image:raster
x11application
Popcon: 41 users (16 upd.)*
Newer upstream!
License: DFSG free
Git

Gwyddion er et modulopbygget program for skanning (Skanning Probe Mikroskopi, SPM), samt visualisering og analyse af data. Det er primært beregnet til analyse af højdefeltdata indhentet via mikroskopiteknikker som

  • Atomar Force Mikroskopi (AFM),
  • Magnetisk Force Mikroskopi (MFM),
  • Skanning Tunneling Mikroskopi (STM),
  • Nær-felt Skanning Optisk Mikroskopi (SNOM eller NSOM) og andet. Det kan dog bruges til vilkårlige højdefelter og til billedanalyse.

Denne pakke indeholder det primære program og dets moduler. Den indeholder også en GNOME (og Xfce) miniaturefremstiller som opretter forhåndsvisninger af alle kendte filtyper til Gwyddion.

Please cite: David Nečas and Petr Klapetek: Gwyddion: an open-source software for SPM data analysis. (eprint) Central European Journal of Physics 10(1):181-188 (2012)
Registry entries: SciCrunch  OMICtools 
Screenshots of package gwyddion
Imagej
Billedbehandlingsprogram med fokus på mikroskopbilleder
Versions of package imagej
ReleaseVersionArchitectures
sid1.53g-2all
experimental1.53i-1~0exp0all
buster1.52j-1all
bullseye1.53g-2all
stretch1.51i+dfsg-2all
jessie1.49i+dfsg-1all
wheezy-security1.46a-1+deb7u1all
wheezy1.46a-1all
squeeze1.44c-3all
upstream1.53i
Debtags of package imagej:
roleprogram
useanalysing, editing, viewing
works-withimage, image:raster
works-with-formatgif, jpg, tiff
Popcon: 102 users (82 upd.)*
Newer upstream!
License: DFSG free
Git

Det kan vise, redigere, analysere, behandle, gemme og udskrive 8-bit, 16- bit og 32-bit billeder. Det kan læse mange billedformater inklusive TIFF, GIF, JPEG, BMP, DICOM, FITS og »raw«. Det understøtter »stakke«, en serie af billeder som deler et enkelt vinude.

Den kan udarbejde værdistatistikker for områder og billedepunkter fra brugerdefinerede markeringer. Det kan måle afstande og vinkler. Det kan oprette histogrammer over tæthed og plotte linjeprofiler. Det understøtter standardfunktioner til billedbehandling såsom manipulation af kontrast, øget skarphed, udjævning, kantdetektering og median-filtrering.

Rumlig kalibrering er tilgængelig for at tilbyde målinger af dimensioner fra den virkelige verden i enheder som milimeter. Tætheds- eller gråskala- kalibrering er også tilgængelig.

ImageJ er udviklet af Wayne Rasband (wayne@codon.nih.gov), der er ved: the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.

Please cite: Caroline A Schneider, Wayne S Rasband and Kevin W Eliceiri: NIH Image to ImageJ: 25 years of image analysis. (PubMed,eprint) Nature methods 9:671-675 (2012)
Registry entries: SciCrunch 
Screenshots of package imagej
Imagevis3d
Optegningsprogram for skrivebordsvolumener og store datasæt
Versions of package imagevis3d
ReleaseVersionArchitectures
jessie3.1.0-4amd64,armel,armhf,i386
stretch3.1.0-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster3.1.0-7amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy2.0.1-5amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package imagevis3d:
uitoolkitqt
Popcon: 9 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

ImageVis3D er et optegningsprogram for volumener specifikt designet til at optegne store datasæt. Dette opnås ved at opdele datasættene i flere detaljeniveauer (LoD), hvor hvert niveau i sig selv er opdelt i flere sten (atomisk optegningsprimitiver). Interaktion opstår på den groveste LoD, som kan gengives øjeblikkeligt på næsten alle moderne systemer. Efter en forsinkelse, der kan konfigureres, vil ImageVis3D successivt gengive finere niveauer af detaljer, indtil data er synlige på deres standardopløsning.

Udvikling af ImageVis3D er sponsoreret af NIH/NCRR Center for Integrative Biomedical Computing (CIBC) og DOE Visualization And Analytics Center for Enabling Technologies (VACET).

Invesalius
3D-medicinsk billedkontruktionsprogram
Versions of package invesalius
ReleaseVersionArchitectures
jessie3.0~b5-4all
buster3.1.99992-3all
bullseye3.1.99994-1all
sid3.1.99994-1all
stretch3.0.1-1all
Popcon: 12 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

InVesalius opretter 3D-medicinsk billedkontruktion baseret på en sekvens af 2D DICOM-filer hentet fra CT- eller MRI-udstyr. InVesalius er oversat til en række sprog (i øjeblikket tilgængelig på engelsk, portugisisk, fransk, spansk, tyrkisk, italiensk, tjekkisk, japansk, catalansk, koreansk, rumænsk og tysk) og tilbyder flere værktøjer:

  • DICOM-understøttelse inklusive: (a) ACR-NEMA version 1 og 2; (b) DICOM version 3.0 (inklusive diverse kodninger af JPEG - med og uden kvalitetstab, RLE)
  • Funktioner til billedmanipulation (zoom, panorer, rotation, lysstyrke /kontrast etc.).
  • Segmentering baseret på 2D-dias
  • Forhåndsdefinerede tærskelintervaller jævnfør væv under undersøgelse
  • Segmentering baseret på watershed
  • Regionsvoksende segmentering
  • Editionværktøjer (svarer til Paint Brush) baseret på 2D-dias
  • Semiautomatisk segmentering baseret på Watershed
  • 3D-overfladeoprettelse
  • 3D-overfladeforbindelsesværktøjer
  • 3D-overfladeeksport (inklusive: binær STL, OBJ, VRML, Inventor)
  • Enhedsoptegningsprojektion i høj kvalitet
  • Forhåndsdefinitioner for enhedsoptegning
  • Enhedsoptegning af crop-niveau
  • Billedeksport (inklusive: BMP, TIFF, JPG, PostScript, POV-Ray)
  • Minimum, Maksimum eller gennemsnitlig intensitetprojektion, maksimum intensitetforskelsakkumulering og konturbaserede visualiseringer
Screenshots of package invesalius
Ismrmrd-tools
Kommandolinjeværktøjer for ISMRMRD
Versions of package ismrmrd-tools
ReleaseVersionArchitectures
bullseye1.4.2.1-6amd64,arm64,armel,i386,mips64el,mipsel,ppc64el,s390x
sid1.4.2.1-6amd64,arm64,armel,i386,mips64el,mipsel,ppc64el,s390x
buster1.4.0-1amd64,arm64,armel,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch1.3.3-1amd64,arm64,armel,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 7 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

ISMRMRD-formatet kombinerer en blanding af fleksible datastrukturer (XML-teksthoveder) og faste strukturer (svarende til C-structs) til at repræsentere MRI-data.

Derudover specificerer ISMRMRD-formatet også et billedteksthoved for lagring af nykonstruerede billeder og det medfølgende C++-bibliotek, der tilbyder en passende måde at skrive sådanne billeder til HDF5-filer sammen med generiske arrayer for lagring mindre veldefinerede datastrukturer, f.eks. coil-sensitivitetskort eller andre kalibreringsdata.

Denne pakke indeholder værktøjerne for kommandolinjen.

Itksnap
semiautomatisk segmentering af strukturer i 3D-billeder
Versions of package itksnap
ReleaseVersionArchitectures
wheezy2.2.0-1.1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
buster3.6.0-3amd64,i386
jessie2.2.0-1.1amd64,armel,armhf,i386
squeeze2.0.0+cvs20100615-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
sid3.6.0-5amd64,i386
bullseye3.6.0-5amd64,i386
stretch3.4.0-2amd64,i386
Debtags of package itksnap:
fieldmedicine:imaging
roleprogram
Popcon: 19 users (5 upd.)*
Versions and Archs
License: DFSG free
Git

SNAP tilbyder semiautomatisk segmentering af strukturer i medicinske billeder (f.eks. magnetisk ressonansbilleder af hjernen) med brug af aktiv konturmetoder, samt som manuel skitsetegning og billednavigering. Funktioner værd at nævne er:

  • Lænket markør for let 3D-navigering
  • Manuel segmentering i tre ortogonale planer på en gang
  • Understøttelse af mange forskellige 3D-billedformater, inklusiv NIfTI
  • Understøttelse af sammenfaldende, lænket visning og segmentering af flere billeder
  • Begrænset understøttelse af farvebilleder (f.eks. diffusion tensor-kort)
  • 3D-skæringsværktøj for hurtig efterbehandling af segmenteringsresultater
Please cite: Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee and Guido Gerig: User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability. Neuroimage 31:1116-1128 (2006)
Screenshots of package itksnap
King
Interaktivt system for tredimensionel vektorgrafik
Versions of package king
ReleaseVersionArchitectures
sid2.23.161103+dfsg1-4all
bullseye2.23.161103+dfsg1-4all
stretch2.23.161103+dfsg1-1all
jessie2.21.120420+dfsg-1all
buster2.23.161103+dfsg1-3all
wheezy2.21.120420-2all
Popcon: 4 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

KiNG (Kinemage, Next Generation) er et interaktivt system for tredimensionel vektorgrafik. Den understøtter et sæt af grafikprimitiver, som gør det egnet til mange typer af grafer, plot og andre illustrationer; selvom dets første brug var at vise makromolekylære strukturer for biofysisk forskning. KiNG bygger på Mage, JavaMage og »kinemage«-konceptet (kinetisk billede) for at levere et Javaprogram med alle funktioner og en brugervenlig grænseflade samt integrerede redigeringsfunktioner. KiNG-jarfilen kan bruges i en netside som et Javapanelprogram eller Javaobjekt til at fremme nem adgang til kinemages eller koordinere filer fra en internetbrowser.

Libgdcm-tools
Grassroots DICOM-værktøjer og redskaber
Versions of package libgdcm-tools
ReleaseVersionArchitectures
jessie2.4.4-3+deb8u1amd64,armel,armhf,i386
wheezy2.2.0-14.1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze2.0.16-2amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
bullseye3.0.8-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid3.0.8-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.8.8-9amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch2.6.6-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package libgdcm-tools:
fieldmedicine:imaging
interfacecommandline
roleprogram
scopeutility
useconverting
works-withimage, image:raster
Popcon: 17 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

Grassroots DICOM er et C++-bibliotek for DICOm-medicinske filer. Den omsluttes automatisk om python/C#/Java (med swig). Den understøtter RAW,JPEG (med og uden kvalitetstab),J2K,JPEG-LS, RLE og deflated.

Installer denne pakke for programmerne gdcmconv, gdcmdiff, gdcmdump, gdcmpap3, gdcmgendir, gdcmimg, gdcminfo, gdcmpdf, gdcmraw, gdcmscanner, gdcmscu, gdcmtar, gdcmxml.

Please cite: David Rodríguez González, Trevor Carpenter, Jano I. van Hemert and Joanna Wardlaw: An open source toolkit for medical imaging de-identification. (PubMed,eprint) European Radiology 20(8):1896-1904 (2010)
Lipsia
analysis suite for MRI and fMRI data
Versions of package lipsia
ReleaseVersionArchitectures
squeeze1.6.0-4amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

Leipzig Image Processing and Statistical Inference Algorithms (LIPSIA)

This is a software package for the data processing and evaluation of functional magnetic resonance images. The analysis of fMRI data comprises various aspects including filtering, spatial transformation, statistical evaluation as well as segmentation and visualization. All these aspects are covered by LIPSIA. For the statistical evaluation, a number of well established and peer-reviewed algorithms were implemented in LIPSIA that allow an efficient and user-friendly processing of fMRI data sets. As the amount of data that must be handled is enormous, an important aspect in the development of LIPSIA was the efficiency of the software implementation.

LIPSIA operates exclusively on data in the VISTA data format. However, the package contains converters for medical image data in iBruker, ANALYZE and NIfTI format -- converting VISTA images into NIfTI files is also supported.

Please cite: Gabriele Lohmann, Karsten Müller, Volker Bosch, Heiko Mentzel, Sven Hessler, Lin Chen, S. Zysset and D. Yves von Cramon: Lipsia—a new software system for the evaluation of functional magnetic resonance images of the human brain. Computerized Medical Imaging and Graphics 25:449-457 (2001)
Remark of Debian Med team: lipsia was removed from Debian (see #674295)

The bug log (http://bugs.debian.org/674295) explains the reasons for the removal and the conditions when a new version might be back

Medcon
Medicinsk billedkonverteringsværktøj (DICOM, ECAT, ...)
Versions of package medcon
ReleaseVersionArchitectures
wheezy0.10.7-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
sid0.16.3+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster0.16.1+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie0.13.0-2amd64,armel,armhf,i386
squeeze0.10.5-2.1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
bullseye0.16.3+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch0.14.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
upstream0.21.0
Debtags of package medcon:
fieldbiology
interfacecommandline
roleprogram
uitoolkitgtk
useconverting
works-withimage, image:raster
x11application
Popcon: 24 users (17 upd.)*
Newer upstream!
License: DFSG free
Git

Dette projekt står for Medical Image Conversion, dvs. et medicinsk billedkonverteringsværktøj. Programmet er udgivet under (L)GPL. Den fulde C-kildekode fra biblioteket følger med. Det er et fleksibelt kommandolinjeredskab med en pæn grafisk grænseflade, som anvender GTK+- værktøjssættet. Formater som aktuelt understøttes er: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 og PNG.

Programmet giver også mulighed for at læse ej understøttede filer uden komprimering, at udskrive billedpunktsværdier eller at udtrække/ændre rækkefølge på specificerede billeder. Det er muligt at hente de rå binære/ascii-billedarray'er eller at skrive PNG for skrivebordsprogrammer.

Dette er kommandolinjeværktøjet for jobbehandling.

Mia-tools
Kommandolinjeværktøjer for billedbehandling i gråtone
Versions of package mia-tools
ReleaseVersionArchitectures
bullseye2.4.7-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie2.2.2-1amd64,i386
stretch2.4.3-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.4.6-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid2.4.7-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
experimental2.4.7-8~exp1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 10 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

Kommandolinjeværktøjer til at køre almene billedbehandlingsopgaver på 2D- og 3D-gråtonebilleder, og grundlæggende operationer på triangulære mesher. Understøttede billedbehandlingsalgoritmer er billedfiltrering, kombinering, billedregistrering, bevægelseskompensation for billedserier og estimering af forskellig statistik over billeder. Denne pakke indeholder også nipype-grænsefladerne for disse kommandolinjeværktøjer.

The package is enhanced by the following packages: mia-tools-doc
Please cite: Gert Wollny, Jean-Jaques Hublin, Maria-J Ledesma-Carbayo, Matthew M. Skinner, Peter Kellman and Thomas Hierl: MIA - A Free and Open Source Software for Gray Scale Medical Image Analysis. (eprint) Source Code for Biology and Medicine 8:20 (2013)
Mia-viewit
Fremviserprogram for 3D-datasæt oprettet af MIA
Versions of package mia-viewit
ReleaseVersionArchitectures
bullseye1.0.5-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.0.5-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie1.0.1-1amd64,i386
stretch1.0.4-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.0.5-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package mia-viewit:
uitoolkitgtk
Popcon: 7 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

MIA-fremviserprogram for visualiseringen af 3D-datasæt. Grænsefladerne og understøttede datatyper fokuserer på resultaterne, som kan indhentes ved at køre programmer fra pakken mia-tools.

Screenshots of package mia-viewit
Mialmpick
Værktøjer for landmærkevalg i 3D-datasæt
Versions of package mialmpick
ReleaseVersionArchitectures
jessie0.2.10-2amd64,armel,armhf,i386
stretch0.2.13-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid0.2.15-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye0.2.15-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster0.2.14-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package mialmpick:
uitoolkitgtk
Popcon: 5 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

Dette værktøj tilbyder en simpel 3D-optegner, som kan visualisere overflader direkte fra 3D-volumeer og kan bruges til at angive 3D-landemærker. Det er bedst egnet for CT-datasæt.

Please cite: Gert Wollny, Fritjhof Kruggel, Thomas Hierl and Jörg Hendricks: Assessment, validation, and visualisation of bony changes in crano-facial surgery (eprint) :459-464 (2004)
Minc-tools
Medicinsk billedformatværktøjer for MNI
Versions of package minc-tools
ReleaseVersionArchitectures
bullseye2.3.00+dfsg-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.3.00+dfsg-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze2.0.18+cvs20100518-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
stretch2.3.00+dfsg-1.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie2.2.00-6amd64,armel,armhf,i386
wheezy2.1.10-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
sid2.3.00+dfsg-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package minc-tools:
fieldmedicine, medicine:imaging
interfacecommandline
roleprogram
scopeutility
useanalysing, converting
works-withimage, image:raster
Popcon: 14 users (5 upd.)*
Versions and Archs
License: DFSG free
Git

Denne pakke indeholder værktøjer til at manipulere MINC-filer.

Minc-filformatet er et stærkt fleksibelt medicinsk billedfilformat bygget oven på det NetCDF-generaliserede dataformat. Formatet er simpelt, selvbeskrivende, kan udvides, flytbart og n-dimensionelt med programmeringsgrænseflader for dataadgang på lavt niveau og manipulering af diskenhed (volume) på højt niveau. Oven på bibliotekerne er en programpakke af generiske manipulationsværktøjer for billedfiler. Formatet, biblioteket og værktøjer er designet for brug i forskningsmiljøer for medicinsk billedfremstilling: De er simple og funktionsrige og gør intet for at vise en pæn brugerflade for brugerne.

Mriconvert
Redskab til konvertering af medicinske billedfiler
Versions of package mriconvert
ReleaseVersionArchitectures
stretch2.1.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid2.1.0-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
wheezy2.0.235-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
buster2.1.0-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2.1.0-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie2.0.7-2amd64,armel,armhf,i386
Debtags of package mriconvert:
fieldmedicine:imaging
roleprogram
uitoolkitwxwidgets
Popcon: 14 users (53 upd.)*
Versions and Archs
License: DFSG free
Git

MRIConvert er et redskab til konvertering af medicinske billedfiler, der konverterer DICOM-filer til volumen-formaterne NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager og MetaImage volume.

Screenshots of package mriconvert
Mricron
Magnetisk resonansbilledkonvertering, visning og analyse
Versions of package mricron
ReleaseVersionArchitectures
buster0.20140804.1~dfsg.1-3amd64,arm64,armel,armhf,i386
stretch0.20140804.1~dfsg.1-2amd64,arm64,armel,armhf,i386
sid1.0.20190902+dfsg-2amd64,arm64,armel,armhf,i386,ppc64el
bullseye1.0.20190902+dfsg-2amd64,arm64,armel,armhf,i386,ppc64el
wheezy0.20120505.1~dfsg.1-1amd64,armel,armhf,i386,powerpc,sparc
jessie0.20140804.1~dfsg.1-1amd64,armel,armhf,i386
Debtags of package mricron:
uitoolkitgtk
Popcon: 61 users (24 upd.)*
Versions and Archs
License: DFSG free
Git

Dette er et visualiserings- og analyseværktøj baseret på en grafisk brugerflade for (funktionelle) magnetiske resonansbilleder. MRIcon kan bruges til at oprette 2D- eller 3D-optegninger af statistiske overlagskort på billeder med hjerneanatomi. Derudover tegner det anatomiske regioner-af-interesse (ROI), eller læsionskortlægning, samt grundlæggende analyse af funktionelle tidsserier (f.eks. oprettelse af plot af peristimulus signal-change).

Udover »mricorn« tilbyder denne pakke også »dcm2nii«, der understøtter konvertering af DICOM- og PAR/REC-billeder til NIfTI-formatet og »npm« for ikkeparametrisk dataanalyse.

Please cite: Chris Rorden, Hans-Otto Karnath and Leonardo Bonilha: Improving lesion-symptom mapping. (PubMed) Journal of Cognitive Neuroscience 19(7):1081-1088 (2007)
Mrtrix3
Diffusion-vægtet MRI-hvidt stof traktografi
Versions of package mrtrix3
ReleaseVersionArchitectures
sid3.0~rc3+git135-g2b8e7d0c2-5amd64,arm64
bullseye3.0~rc3+git135-g2b8e7d0c2-5amd64,arm64
buster3.0~rc3+git135-g2b8e7d0c2-3amd64,arm64,i386
Popcon: 9 users (5 upd.)*
Versions and Archs
License: DFSG free
Git

Værktøjssæt til at udføre diffusion-vægtet MRI-hvidt stof traktografi i hjernen ved tilstedeværelse af krydsende fibre, via Constrained Spherical Deconvolution og en probabilistisk streamlines-algoritme. Magnetiske resonansbilleder i DICOM-, ANALYZE- eller ikke komprimeret NIfTI-format er understøttet.

Please cite: Donald Tournier, Robert Smith amd David Raffelt, Rami Tabbara, Thijs Dhollander, Maximilian Pietsch, Daan Christiaens, Ben Jeurissene, Chun-Hung Yeh and Alan Connelly: MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage 202:116137 (2019)
Registry entries: Bio.tools 
Nifti-bin
Værktøjer leveret med NIfTI-biblioteket
Versions of package nifti-bin
ReleaseVersionArchitectures
bullseye3.0.1-8amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch2.0.0-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid3.0.1-8amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie2.0.0-2amd64,armel,armhf,i386
squeeze2.0.0-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy2.0.0-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
buster2.0.0-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package nifti-bin:
fieldmedicine, medicine:imaging
interfacecommandline
roleprogram, shared-lib
scopeutility
usechecking, converting
Popcon: 10 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

Niftilib er et sæt af i/o-biblioteker for læsning og skrivning af filer i NIfTI-1-dataformatet. NIfTI-l er et binært filformat for lagring af medicinske billeddata, f.eks. magnetisk resonansbillede (MRI) og funktionel MRI (fMRI) hjernebilleder.

Denne pakke tilbyder værktøjerne som leveres med biblioteket (nifti_tool, nifti_stats og nifti1_test).

Nifti2dicom
Konverter 3D-medicinbilleder til DICOM 2D-serien
Versions of package nifti2dicom
ReleaseVersionArchitectures
stretch0.4.11-1amd64,i386
bullseye0.4.11-3amd64,i386
buster0.4.11-1amd64,i386
sid0.4.11-3amd64,i386
jessie0.4.9-1amd64,armel,armhf,i386
Popcon: 9 users (5 upd.)*
Versions and Archs
License: DFSG free
Git

Nifti2Dicom er et konverteringsværktøj, som konverterer 3D NIfTI-filer (og andre formater understøttet af ITK, inklusive Analyze, MetaImage Nrrd og VTK) til DICOM. Til forskel fra andre konverteringsværktøjer så kan det importere en DICOM- fil, som bruges til at importere patienten og studere DICOM-mærker, og giver dig mulighed for at redigere accessionsnummeret og andre DICOM-mærker, for at oprette en gyldig DICOM, som kan importeres i en PACS.

Denne pakke indeholder værktøjerne for kommandolinjen.

Odil
C++11-bibliotek for DICOM-standarden - program
Versions of package odil
ReleaseVersionArchitectures
bullseye0.12.1-1all
buster0.10.0-3all
sid0.12.1-1all
stretch0.7.3-1all
Popcon: 8 users (5 upd.)*
Versions and Archs
License: DFSG free
Git

Odil udnytter C++-konstruktioner til at tilbyde en brugervenlig API for forskellige dele af DICOM-standarden. Inkluderet i Odil er undtagelsesbaseret fejlhåndtering, generisk adgang til datasætelementer, JSON- og XML-repræsentation af datasæt og generisk implementering af beskeder, klienter og servere for forskellige DICOM-protokoller.

Denne pakke indeholder programmet for kommandolinjen.

Odin
Udvikl, simuler og kør magnetiske resonanssekvenser
Versions of package odin
ReleaseVersionArchitectures
sid2.0.4-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie1.8.8-1amd64,armel,armhf,i386
buster2.0.3-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze1.8.1-3amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
bullseye2.0.4-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
wheezy1.8.5-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Popcon: 15 users (18 upd.)*
Versions and Archs
License: DFSG free
Git

ODIN er en ramme for magnetisk resonansbilledoprettelse (MRI). Den dækker hele værktøjskæden for MRI, fra dataindhentelse på lavt niveau til billedrekonstruktion. Specielt forsøger programmet at lave hurtige prototyper for MRI-sekvenser. Sekvenserne kan programmeres via en højniveau, objektorienteret, C++-programmeringsgrænseflade. Den tilbyder avancerede sekvensanalyseværktøjer, såsom interaktiv plotning af k-space baner, en brugerflade for en hurtig compile-link-test cyklus og en funktionsrig MRI-simulator, som understøtter forskellige virtuelle prøver. For hurtig og fleksibel billedrekonstruktion indeholder ODIN en flertrådet databehandlingsramme, der kan tilpasses.

Screenshots of package odin
Openmeeg-tools
openmeeg library -- command line tools
Versions of package openmeeg-tools
ReleaseVersionArchitectures
wheezy2.0.0.dfsg-5amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mipsel,powerpc,s390,s390x,sparc
squeeze2.0.0.dfsg-2amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Debtags of package openmeeg-tools:
roleprogram
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

OpenMEEG consists of state-of-the art solvers for forward problems in the field of MEG and EEG. Solvers are based on the symmetric Boundary Element method [Kybic et al, 2005], providing excellent accuracy, particularly for superficial cortical sources. OpenMEEG can compute four types of lead fields (EEG, MEG, Internal Potential and Electrical Impedence Tomography).

This package provides command line interface to openmeeg functionality.

Please cite: Alexandre Gramfort, Théodore Papadopoulo, Emmanuel Olivi and Maureen Clerc: OpenMEEG: opensource software for quasistatic bioelectromagnetics. (PubMed,eprint) BioMedical Engineering OnLine 9:45 (2010)
Openslide-tools
Manipulerings- og konverteringsværktøjer for OpenSlide
Versions of package openslide-tools
ReleaseVersionArchitectures
sid3.4.1+dfsg-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.4.1+dfsg-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster3.4.1+dfsg-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch3.4.1+dfsg-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie3.4.0-1amd64,armel,armhf,i386
wheezy3.2.6-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package openslide-tools:
roleprogram
scopeutility
Popcon: 41 users (22 upd.)*
Versions and Archs
License: DFSG free
Git

OpenSlide er et C-bibliotek, som tilbyder en simpel grænseflade til at læse whole-slide-billeder også kendt som virtuelle dias.

Whole-slide-billeder, også kendt som virtuelle dias, er store, højopløste billeder brugt i digital patologi. Læsning af disse billeder med normale billedværktøjer eller biblioteker er en udfordring, da disse værktøjer typisk er designet for billeder som komfortabelt kan udpakkes i RAM eller en swap-fil. Whole-slide-billeder overgår normalt RAM-størrelsen og fylder ofte en masse gigabyte, når de er udpakket. Derudover er whole-slide typisk i flere opløsninger, og kun en lille mængde af billeddata er krævet ved en bestemt opløsning.

Dette bibliotek understøtter i øjeblikket:

  • Aperio (.svs, .tif)
  • Hamamatsu (.vms, .vmu, .ndpi)
  • Leica (.scn)
  • MIRAX (.mrxs)
  • Sakura (.svslide)
  • Trestle (.tif)
  • Generic tiled TIFF (.tif)

Denne pakke indeholder kommandolinjeværktøjer for filmanipulering.

Registry entries: OMICtools 
Orthanc
Simpel RESTful DICOM-server for medicinske billeder
Versions of package orthanc
ReleaseVersionArchitectures
buster1.5.6+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch1.2.0+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.9.1+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie0.8.4+dfsg-1amd64,armel,armhf,i386
bullseye1.9.1+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 97 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

Orthanc forsøger at tilbyde en simpel, men funktionsrig DICOM-server for medicinske billeder. Orthanc kan omdanne enhver computer, der afvikler Windows eller Linux til et Vendor Neutral Archive (med andre ord et mini-PACS-system). Dets arkitektur er simpel, så ingen kompleks databaseadministration er krævet eller installation af tredjepartsafhængigheder.

Det som gør Orthanc unik er det faktum, at det tilbyder en RESTful-API. Takket være denne vigtige funktioner er det muligt at afvikle Orthanc fra ethvert computersprog. DICOM-mærkerne for lagrede medicinske billeder kan hentes i JSON-filformatet. Derudover kan PNG-billeder oprettes løbende fra DICOM-instanser af Orthanc.

Orthanc lader sine brugere fokusere på indholdet af DICOM-filerne og skjuler kompleksiteten for DICOM-formatet og for DICOM-protokollen.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Screenshots of package orthanc
Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)
Versions of package orthanc-wsi
ReleaseVersionArchitectures
sid1.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster0.6-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 49 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

Orthanc-WSI brings support of whole-slide imaging for digital pathology into Orthanc, the lightweight, RESTful Vendor Neutral Archive for medical imaging.

This package contains two command-line tools to convert whole-slide images to and from DICOM. Support for proprietary file formats is available through OpenSlide. The package also contains an Orthanc plugin to display such DICOM images by any standard Web browser. The implementation follows DICOM Supplement 145.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Pixelmed-apps
DICOM-implementering indeholdende billedfremviser og en ECG-fremviser - cli
Versions of package pixelmed-apps
ReleaseVersionArchitectures
bullseye20200416-4all
buster20150917+git20151209.36f3174+dfsg-1all
jessie20140816-1all
stretch20150917-1all
sid20200416-4all
Popcon: 11 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

Dette er et uafhængigt DICOM-værktøjssæt, som implementerer kode til læsning og oprettelse af DICOM-data, DICOM-netværks- og filunderstøttelse, en database for DICOM-objekter, understøttelse for visning af mapper, billeder, rapporter og spektra samt DOCOM- objektvalidering.

Tilbyder kommandolinjeprogrammer til at bruge pixelmed.

Plastimatch
Medicinsk billedrekonstruktion og registrering
Versions of package plastimatch
ReleaseVersionArchitectures
stretch1.6.5+dfsg.1-1amd64,i386
buster1.7.4+dfsg.1-2amd64,i386
bullseye1.9.3+dfsg.1-1amd64,i386
wheezy1.5.11+dfsg0-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie1.5.16+dfsg-2amd64,armel,armhf,i386
sid1.9.3+dfsg.1-1amd64,i386
Debtags of package plastimatch:
fieldmedicine:imaging
roleprogram
Popcon: 8 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

Plastimatch er et program for deformationsbilledregistrering, udarbejdet i åben kildekode. Det er designet for højtydende rumfangsregistrering for medicinske billeder, såsom x-røntgen beregnet tomografi (CT), magnetisk resonans billedbehandling (MRI) og positron-emissionstomografi (PET). Inkluderede funktioner:

  • B-spline-metode for deformationsbilledregistrering (GPU- og multikerneaccelereret), inklusive understøttelse for billedmaskering, skelsættende sanktioner, og legalisering
  • Demons method for deformable image registration (GPU-accelereret)
  • Fleratlassegmentering
  • ITK-baserede algoritmer for oversættelse, rigid, affine, flere dæmonmetoder og B-spline-registrering
  • Pipelined, flertrins registreringsrammeværktøj med seamless konvertering mellem de fleste algoritmer og transformeringstyper
  • Landmark-based deformable registrering med brug af thin- plate splines for global registrering
  • Landmark-based deformable registration med brug af radial grundfunktioner for lokale rettelser
  • Bred understøttelse for 3D-billedformater (der bruger ITK), inklusive DICOM, Nifti, NRRD, MetaImage og Analyze
  • Omfattende værktøjskæde for radioterapiforskning, inklusive understøttelse for DICOM- DICOM-RT-, DICOM SRO- og XiO-filformatet, gammaanalyse, kontourmanipulering, kontouroverlapsanalyse og analyse af vektorfelt Plastimatch indeholder også to nyttige redskaber, som ikke er direkte forbundet med billedregistrering:

  • FDK cone-beam CT reconstruction (GPU og accelereret via flere kerner)

  • Digitalt rekonstrueret radiograf-oprettelse (DRR) (GPU- og flerkerneaccelereret)
Screenshots of package plastimatch
Python3-dipy
Python library for the analysis of diffusion MRI datasets
Versions of package python3-dipy
ReleaseVersionArchitectures
bullseye1.3.0-2all
sid1.3.0-2all
Popcon: 5 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

DIPY is a software project for computational neuroanatomy. It focuses on diffusion magnetic resonance imaging (dMRI) analysis and tractography but also contains implementations of other computational imaging methods such as denoising and registration that are applicable to the greater medical imaging and image processing communities. Additionally, DIPY is an international project which brings together scientists across labs and countries to share their state-of-the-art code and expertise in the same codebase, accelerating scientific research in medical imaging.

Here are some of the highlights:

  • Reconstruction algorithms: CSD, DSI, GQI, DTI, DKI, QBI, SHORE and MAPMRI
  • Fiber tracking algorithms: deterministic and probabilistic
  • Native linear and nonlinear registration of images
  • Fast operations on streamlines (selection, resampling, registration)
  • Tractography segmentation and clustering
  • Many image operations, e.g., reslicing or denoising with NLMEANS
  • Estimation of distances/correspondences between streamlines and connectivity matrices
  • Interactive visualization of streamlines in the space of images

This package contains the Python 3 version.

Please cite: Eleftherios Garyfallidis, Matthew Brett, Vassilis Tsiaras, George Vogiatzis and Ian Nimmo-Smith: Identification of corresponding tracks in diffusion MRI tractographies. (eprint) Proc. Intl. Soc. Mag. Reson. Med. 18 (2010)
Python3-nibabel
Python 3-bindinger til diverse neuroimaging-dataformater
Versions of package python3-nibabel
ReleaseVersionArchitectures
buster2.3.2-1all
bullseye3.2.1-2all
stretch2.1.0-1all
sid3.2.1-2all
Popcon: 50 users (12 upd.)*
Versions and Archs
License: DFSG free
Git

NiBabel tilbyder læse- og skriveadgang til nogle almindelige filformater for medicinske og neuromæssige billeder inklusive: ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC samt PAR/REC. De forskellige billedformatklasser giver fuld eller selektiv adgang til hovedinformation (meta) og adgang til billeddata gøres tilgængelig via NumPy-rammer. NiBabel er efterfølgeren til PyNIfTI.

Python3-nipy
Analyse af strukturelle og funktionelle neuroimaging-data
Versions of package python3-nipy
ReleaseVersionArchitectures
sid0.4.3~rc1-1all
Popcon: 2 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

NiPy er en Pythonbaseret ramme til analyse af strukturelle og funktionelle neuroimaging-data. Rammen tilbyder funktionalitet for

  • Generel lineær model (GLM) statistisk analyse
  • Kombineret kurvetidskorrektion og bevægelseskorrektion
  • Generelle rutiner til billedregistrering med fleksible kostfunktioner, optimeringsprogrammer og re-sampling skemaer
  • Billedsegmentering
  • Grundlæggende visualisering af resultater i 2D og 3D
  • Grundlæggende diagnostik af tidsserier
  • Analyse af klynger og aktivitetsmønstre på tværs af emner
  • Reproducerbar analyse for gruppestudier
Please cite: K. Jarrod Millman and Matthew Brett: Analysis of functional magnetic resonance imaging in Python (eprint) Computing in Science & Engineering 9(3):52-55 (2007)
Python3-nipype
Neuroimaging data analysis pipelines in Python3
Versions of package python3-nipype
ReleaseVersionArchitectures
sid1.6.0-2all
bullseye1.6.0-2all
Popcon: 29 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

Nipype interfaces Python to other neuroimaging packages and creates an API for specifying a full analysis pipeline in Python. Currently, it has interfaces for SPM, FSL, AFNI, Freesurfer, but could be extended for other packages (such as lipsia).

Please cite: SS Ghosh, C Burns, D Clark, K Gorgolewski, YO Halchenko, C Madison, R Tungaraza and KJ Millman: Nipype: Opensource platform for unified and replicable interaction with existing neuroimaging tools (eprint) 16th Annual Meeting of the Organization for Human Brain Mapping :106 (2010)
Python3-nitime
timeseries analysis for neuroscience data (nitime)
Versions of package python3-nitime
ReleaseVersionArchitectures
sid0.9-1all
bullseye0.9-1all
Popcon: 1 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

Nitime is a Python module for time-series analysis of data from neuroscience experiments. It contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code.

Python3-pydicom
DICOM-medicinsk fillæsning og -skrivning - Python 3
Versions of package python3-pydicom
ReleaseVersionArchitectures
buster1.2.1-1all
bullseye2.0.0-1all
sid2.0.0-1all
Popcon: 27 users (21 upd.)*
Versions and Archs
License: DFSG free
Git

Pydicom er et rent Pythonmodul til at fortolke DICOM-filer. DICOM er en standard (http://medical.nema.org) til at kommunikere medicinske billeder og relateret information såsom rapporter og radioterapiobjekter.

Pydicom gør det nemt at læse DICOM-filer i naturlige pythoniske strukturer for nem manipulering. Ændrede datasæt kan skrives igen til DICOM-formatfiler.

Denne pakke installerer modulet for Python 3.

Python3-pyxid
interface for Cedrus XID and StimTracker devices
Versions of package python3-pyxid
ReleaseVersionArchitectures
bullseye1.0-4all
sid1.0-4all
Popcon: 1 users (5 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Python3-surfer
visualize Freesurfer's data in Python3
Versions of package python3-surfer
ReleaseVersionArchitectures
sid0.11.0-1all
bullseye0.11.0-1all
Popcon: 0 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

This is a Python3 package for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi’s powerful visualization engine with a high-level interface for working with MRI and MEG data.

PySurfer offers both a command-line interface designed to broadly replicate Freesurfer’s Tksurfer program as well as a Python library for writing scripts to efficiently explore complex datasets.

Qnifti2dicom
Konverter 3D medicinske billeder til DICOM 2D-serier - grafisk brugerflade
Versions of package qnifti2dicom
ReleaseVersionArchitectures
stretch0.4.11-1amd64,i386
jessie0.4.9-1amd64,armel,armhf,i386
sid0.4.11-3amd64,i386
buster0.4.11-1amd64,i386
bullseye0.4.11-3amd64,i386
Popcon: 8 users (4 upd.)*
Versions and Archs
License: DFSG free
Git

Nifti2Dicom er et konverteringsværktøj, som konverterer 3D NIfTI-filer (og andre formater understøttet af ITK, inklusive Analyze, MetaImage Nrrd og VTK) til DICOM. Til forskel fra andre konverteringsværktøjer så kan det importere en DICOM- fil, som bruges til at importere patienten og studere DICOM-mærker, og giver dig mulighed for at redigere accessionsnummeret og andre DICOM-mærker, for at oprette en gyldig DICOM, som kan importeres i en PACS.

Denne pakke indeholder den grafiske brugerflade for Qt5.

Sigviewer
Grafisk brugerflade-fremviser for biosignaler såsom EEG, EMG og ECG
Versions of package sigviewer
ReleaseVersionArchitectures
wheezy0.5.1+svn556-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
bullseye0.6.4-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster0.6.2-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid0.6.4-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie0.5.1+svn556-4amd64,armel,armhf,i386
stretch0.5.1+svn556-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package sigviewer:
interfacex11
roleprogram
uitoolkitqt
useviewing
x11application
Popcon: 9 users (11 upd.)*
Versions and Archs
License: DFSG free
Git

SigViewer er et fremvisnings- og bedømmelsesprogram for biomedicinske signaldata. Det afhænger af biosig4c++-biblioteket, som understøtter et antal dataformater (inklusive EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro, TMS32). Den fuldstændige liste over understøttede filformater er tilgængelig på http://pub.ist.ac.at/~schloegl/biosig/TESTED.

Udover at vise biosignaler undestøtter SigViewer oprettelse af annotationer til at vælge artefakter eller specifikke hændelser.

Screenshots of package sigviewer
Slicer
software package for visualization and image analysis - main application
Versions of package slicer
ReleaseVersionArchitectures
squeeze3.4.0~svn10438-7amd64,i386,ia64,kfreebsd-amd64,kfreebsd-i386,powerpc,s390,sparc
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Svn

Slicer is an application for computer scientists and clinical researchers. The platform provides functionality for segmentation, registration and three-dimensional visualization of multi-modal image data, as well as advanced image analysis algorithms for diffusion tensor imaging, functional magnetic resonance imaging and image-guided therapy. Standard image file formats are supported, and the application integrates interface capabilities to biomedical research software and image informatics frameworks.

3D Slicer main application.

Remark of Debian Med team: slicer was removed from Debian (see #644352)

The bug log (http://bugs.debian.org/644352) explains the reasons for the removal and the conditions when a new version might be back

Sofa-apps
Grafisk brugerflade for SOFA
Versions of package sofa-apps
ReleaseVersionArchitectures
squeeze1.0~beta4-4amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy1.0~beta4-7amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie1.0~beta4-9amd64,armel,armhf,i386
stretch1.0~beta4-11amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.0~beta4-12amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.0~beta4-12amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package sofa-apps:
interfacex11
roleprogram
uitoolkitqt
x11application
Popcon: 5 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

SOFA (»Simulation Open Framework Architecture«) er et open souce- rammeværktøj primært målrettet mod realtidssimulering, med vægt på medicinsk simulering. Det er hovedsagelig rettet mod forskningssamfundet til at hjælpe med at udvikle nye algoritmer, men kan også bruges som et effektivt værktøj for prototyper.

Denne pakke indeholder hovedprogrammet for SOFA.

Screenshots of package sofa-apps
Teem-apps
Værktøjer til at behandle og visualisere videnskabelige data og billeder - værktøjer for kommandolinjen
Versions of package teem-apps
ReleaseVersionArchitectures
squeeze1.10.0.dfsg1-2amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
sid1.12.0~20160122-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.12.0~20160122-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch1.11.0~svn6057-1.1amd64,armel,armhf,i386,mips,mipsel,s390x
jessie1.11.0~svn5226-1amd64,armel,armhf,i386
wheezy1.11.0~svn5226-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package teem-apps:
interfacecommandline
roleprogram
Popcon: 8 users (8 upd.)*
Versions and Archs
License: DFSG free
Git

Teem er en koordineret gruppe af biblioteker til at repræsentere, behandle og visualisere videnskabelige rasterdata. Teem inkluderer værktøjer for kommandolinjen, som tillader at biblioteksfunktionerne hurtigt kan anvendes på filer og strømme, uden at der skal skrives kode. De mest vigtige og nyttige biblioteker i Teem er:

  • Nrrd (og kommandolinjeværktøjet unu oven på) understøtter en bred vifte af operationer til at transformere N-dimensionelle rasterdata (resample, crop, slice, project, histogram etc.) samt NRRD-filformatet for lagring af tabeller og deres metainformation.
  • Gage: Hurtig convolution-baserede målinger ved arbitrære punktlokationer i diskenhedsdatasæt (skala, vektor, tensor, etc.).
  • Mite: En flertråde ray-casting diskenhedsoptegner med overførselsfunktioner baseret på enhver mængde som Gage kan måle
  • Ten: til at estimere, behandle og visualisere diffusion tensor-felter, inklusive fibertraktografimetoder.

Denne pakke indeholder nogle simple værktøjer for kommandolinjen, som tilbyder hurtig og nem adgang til funktionaliteten i diverse biblioteker.

Tifffile
Læs og skriv billeddata fra og til TIFF-filer
Versions of package tifffile
ReleaseVersionArchitectures
buster20181128-1+deb10u1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy20120421-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
upstream20210408
Popcon: 9 users (2 upd.)*
Newer upstream!
License: DFSG free
Git

Billede og metadata kan læses fra filtyperne TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH, ImageJ, MicroManager, FluoView, SEQ og GEL.

Kun et undersæt af TIFF-specifikationen er understøttet, hovedsagelig uden komprimering og komprimeret med kvalitetstab 2** (0´til 6) bit- heltal, 16-, 32- og 64-bit kommatal, gråskala og RGB(A)-billeder, som ofte bruges i biovidenskabelige billeder. Specifikt er læsning af JPEG/CCITT-komprimerede billeddata eller EXIF/IPTC/GPS/XMP-metadata ikke implementeret. Kun primære informationsposter læses for STK-, FluoView-, MicroManager- og NIH-billedformaterne.

TIFF, Tagged Image File Format, er under kontrol af Adobe Systems. BigTiff tillader filer større end 4 GB. STK, LSM, FluoView, SEQ, GEL og OME-TIFF er tilpassede udvidelser defineret af MetaMorph, Carl Zeiss MicroImaging, Olympus, Media Cybernetics, Melecular Dynamics og Open Microscopy Environment-konsortiet respektivt.

Via-bin
værktøjer for billedanalyser af volumer
Versions of package via-bin
ReleaseVersionArchitectures
wheezy2.0.4-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze1.6.0-3amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Debtags of package via-bin:
roleprogram
useconverting
works-withimage
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

VIA er en programpakke for billedanalyser af volumer for funktionel og strukturel (medicinske) billeder. Programpakken består af forskellige værktøjer fra simpel datahåndtering over fremvisere til komplekse billedtransformationer.

Alle værktøjer opererer på data i VISTA-format. Pakken indeholder flere muligheder for omdannelser f.eks. fra PNG, PGM eller PNM til dette dataformat og tilbage igen.

Voxbo
Behandling, statistisk analyse og billedvisning af hjernedata
Versions of package voxbo
ReleaseVersionArchitectures
stretch1.8.5~svn1246-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie1.8.5~svn1246-1.1amd64,armel,armhf,i386
squeeze1.8.5~svn1172-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy1.8.5~svn1246-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
buster1.8.5~svn1246-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package voxbo:
fieldmedicine:imaging
roleprogram
uitoolkitqt
Popcon: 8 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

Dette er et værktøjssæt til analyse af funktionelle eksperimenter for neurobilledoprettelse (hovedsagelig fMRI) og voxel-baserede læsion-adfærd kortlægning. VoxBo understøtter den modificerede GLM (for autokorrelerede data), samt standard-GLM for ikke automatiske korrelerede data. Værktøjskassen er designet til at være kompatibel med AFNI, FSL, SPM og andre.

Screenshots of package voxbo
Vrrender
DICOM viewer
Versions of package vrrender
ReleaseVersionArchitectures
bullseye20.2.0-2amd64,i386
sid20.2.0-2amd64,i386
Popcon: 2 users (16 upd.)*
Versions and Archs
License: DFSG free
Git

Medical image viewer featuring negatoscope, multi-planar reconstruction, and volume rendering.

Many image formats are handled such as DICOM, mhd, inr.gz, vtk, vti,... Segmentations meshes can also be imported from DICOM and vtk formats, and visualized in mixed rendering with images.

Tools are provided to measure distances of structures in the image and to place landmarks.

Last, VRRender can also connect directly to a PACS, and then request, download or upload DICOM files.

Vtk-dicom-tools
DICOM for VTK - værktøjer
Versions of package vtk-dicom-tools
ReleaseVersionArchitectures
sid0.8.12-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster0.8.9-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch0.7.10-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.8.12-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie0.5.5-2amd64,armel,armhf,i386
Popcon: 9 users (5 upd.)*
Versions and Archs
License: DFSG free
Git

Denne pakke indeholder et sæt af klasser for håndtering af DICOM-filer og metadata inden fra VTK, og nogle redskabsprogrammer til forståelse af og konvertering af DICOM-filer.

Værktøjer for kommandolinjen.

Xmedcon
Medicinsk billedkonverteringsværktøj (DICOM, ECAT, ...) - grafisk brugerflade
Versions of package xmedcon
ReleaseVersionArchitectures
wheezy0.10.7-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
buster0.16.1+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch0.14.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze0.10.5-2.1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
jessie0.13.0-2amd64,armel,armhf,i386
sid0.16.3+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye0.16.3+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream0.21.0
Debtags of package xmedcon:
fieldbiology
interfacecommandline, x11
roleprogram
scopeutility
uitoolkitgtk
useconverting
works-withimage, image:raster
x11application
Popcon: 73 users (13 upd.)*
Newer upstream!
License: DFSG free
Git

Dette projekt står for Medical Image Conversion, dvs. et medicinsk billedkonverteringsværktøj. Programmet er udgivet under (L)GPL. Den fulde C-kildekode fra biblioteket følger med. Det er et fleksibelt kommandolinjeredskab med en pæn grafisk grænseflade, som anvender GTK+- værktøjssættet. Formater som aktuelt understøttes er: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 og PNG.

Programmet giver også mulighed for at læse ej understøttede filer uden komprimering, at udskrive billedpunktsværdier eller at udtrække/ændre rækkefølge på specificerede billeder. Det er muligt at hente de rå binære/ascii-billedarray'er eller at skrive PNG for skrivebordsprogrammer.

Dette er programversionen til X baseret på GTK+. Behandler kun én fil ad gangen.

Screenshots of package xmedcon

Official Debian packages with lower relevance

Cmtk
Beregningsmæssigt værktøjssæt for morfometri
Versions of package cmtk
ReleaseVersionArchitectures
buster3.3.1p1+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid3.3.1p1+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.3.1p1+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie3.2.2-1.3amd64,armel,armhf,i386
stretch3.3.1-1.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy2.2.2-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
upstream3.3.1p2
Popcon: 3 users (0 upd.)*
Newer upstream!
License: DFSG free
Git

Et programværktøjssæt for beregningsmorfometri for biomedicinske billeder, CMTK består af et sæt af kommandolinjeværktøjer og et motorbibliotek til generelle formål for behandling og I/O.

Kommandolinjeværktøjerne tilbyder primært den følgende funktionalitet: registrering (affine og ikke-stive, enkel og flerkanal, parvis og gruppevis), billedkorrektion (MR-biasfeltestimering, interleaved billedartefaktkorrektion), forarbejdning (filtre, kombination af segmenter via afstemninger og STAPLE, formbaseret gennemsnit), statistik (t-test, generel lineær regression).

Please cite: T. Rohlfing: User Guide to The Computational Morphometry Toolkit. (eprint) The Insight Journal (2009)
Registry entries: SciCrunch 
Connectomeviewer
Interaktiv analyse og visualisering for MR Connectomics
Versions of package connectomeviewer
ReleaseVersionArchitectures
wheezy2.1.0-1all
buster2.1.0+dfsg-1all
jessie2.1.0-1all
Popcon: 4 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

Fremviseren, »The Connectome Viewer« er et udvideligt, skriptbart, pythonisk forskningsmiljø for visualisering og (netværks-)analyse i neurobilledbehandling og »connectomics«.

Med brug af formatet »Connectone File Format«, bliver forskellige datatyper såsom netværk, overflader, volume, spor og metadata håndteret og integreret. Fremviseren »The Connectome Viewer« er en del af værktøjssættet »MR Connectome Toolkit«.

Please cite: Gerhard S, Daducci A, Lemkaddem A, Meuli R, Thiran J-P and Hagmann P: The Connectome Viewer Toolkit: An open source framework to manage, analyze, and visualize connectomes. (2011)
Conquest-dbase
ConQuest DICOM-server - DBaseIII-motor
Versions of package conquest-dbase
ReleaseVersionArchitectures
jessie1.4.17d-1amd64,armel,armhf,i386
Popcon: users ( upd.)*
Versions and Archs
License: DFSG free
Git

En DICOM-server, med alle funktioner, som er blevet udviklet baseret på og har udvidet sig med UCDMC DICOM-kode i offentlig ejendom. Nogle mulige programmer for ConQuest DICOM-programmer er:

  • DICOM-træning og test
  • Arkiver for demonstration og videnskabsbilleder
  • Konvertering af billedformat fra en skanner med DICOM-netværksadgang
  • Visning af DICOM-billede og udarbejdelse af dias
  • Valg af DICOM-billede, (begrænset) redigering samt opdeling og sammenføjning af serier
  • Avanceret billedændring, filtrering, videresendelse og konvertering via skripter
  • DICOM-mellemlager og arkivsammenføjning

Denne pakke bruger DBaseIII-filer som databasemotor.

Conquest-mysql
ConQuest DICOM-server - MySQL-motor
Versions of package conquest-mysql
ReleaseVersionArchitectures
jessie1.4.17d-1amd64,armel,armhf,i386
Popcon: users ( upd.)*
Versions and Archs
License: DFSG free
Git

En DICOM-server, med alle funktioner, som er blevet udviklet baseret på og har udvidet sig med UCDMC DICOM-kode i offentlig ejendom. Nogle mulige programmer for ConQuest DICOM-programmer er:

  • DICOM-træning og test
  • Arkiver for demonstration og videnskabsbilleder
  • Konvertering af billedformat fra en skanner med DICOM-netværksadgang
  • Visning af DICOM-billede og udarbejdelse af dias
  • Valg af DICOM-billede, (begrænset) redigering samt opdeling og sammenføjning af serier
  • Avanceret billedændring, filtrering, videresendelse og konvertering via skripter
  • DICOM-mellemlager og arkivsammenføjning

Denne pakke bruger MySQL som databasemotor.

Conquest-postgres
ConQuest DICOM-server - PostgreSQL-motor
Versions of package conquest-postgres
ReleaseVersionArchitectures
jessie1.4.17d-1amd64,armel,armhf,i386
Popcon: users ( upd.)*
Versions and Archs
License: DFSG free
Git

En DICOM-server, med alle funktioner, som er blevet udviklet baseret på og har udvidet sig med UCDMC DICOM-kode i offentlig ejendom. Nogle mulige programmer for ConQuest DICOM-programmer er:

  • DICOM-træning og test
  • Arkiver for demonstration og videnskabsbilleder
  • Konvertering af billedformat fra en skanner med DICOM-netværksadgang
  • Visning af DICOM-billede og udarbejdelse af dias
  • Valg af DICOM-billede, (begrænset) redigering samt opdeling og sammenføjning af serier
  • Avanceret billedændring, filtrering, videresendelse og konvertering via skripter
  • DICOM-mellemlager og arkivsammenføjning

Denne pakke bruger PostgreSQL som databasemotor.

Conquest-sqlite
ConQuest DICOM-server - SQLite-motor
Versions of package conquest-sqlite
ReleaseVersionArchitectures
jessie1.4.17d-1amd64,armel,armhf,i386
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

En DICOM-server, med alle funktioner, som er blevet udviklet baseret på og har udvidet sig med UCDMC DICOM-kode i offentlig ejendom. Nogle mulige programmer for ConQuest DICOM-programmer er:

  • DICOM-træning og test
  • Arkiver for demonstration og videnskabsbilleder
  • Konvertering af billedformat fra en skanner med DICOM-netværksadgang
  • Visning af DICOM-billede og udarbejdelse af dias
  • Valg af DICOM-billede, (begrænset) redigering samt opdeling og sammenføjning af serier
  • Avanceret billedændring, filtrering, videresendelse og konvertering via skripter
  • DICOM-mellemlager og arkivsammenføjning

Denne pakke bruger SQLite som databasemotor.

Elastix
Værktøjskasse for rigid og ikkerigid registrering af billeder
Versions of package elastix
ReleaseVersionArchitectures
bullseye4.9.0-2amd64,i386
wheezy4.5-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
stretch4.8-10amd64,i386
jessie4.7-2amd64,i386
sid4.9.0-2amd64,i386
buster4.9.0-1amd64,i386
Debtags of package elastix:
roleprogram
Popcon: 3 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

Billedregistrering baseret på den velkendte Insight Segmentation and Registration Toolkit (ITK). Programmet består af en samling af algoritmer, som ofte bruges til at løse (medicinske) billedregistreringsproblemer. Det modulære design i elastix lader brugeren hurtigt konfigurere, teste og sammenligne forskellige registreringsmetoder for et specifik program. En kommandolinjegrænseflade aktiverer automatiseret behandling af et stort antal datasæt, ved hjælp af skripter.

Please cite: Denis P. Shamonin, Esther E. Bron, Boudewijn P. F. Lelieveldt, Marion Smits, Stefan Klein and Marius Staring: Fast parallel image registration on CPU and GPU for diagnostic classification of Alzheimer's disease. (PubMed,eprint) frontiers in Neuroinformatics 7(50):1-15 (2014)
Imagemagick
Programmer til billedmanipulering - binære filer
Versions of package imagemagick
ReleaseVersionArchitectures
stretch6.9.7.4+dfsg-11+deb9u8amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie-security6.8.9.9-5+deb8u19amd64,armel,armhf,i386
jessie6.8.9.9-5+deb8u12amd64,armel,armhf,i386
wheezy6.7.7.10-5+deb7u4amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x
wheezy-security6.7.7.10-5+deb7u22amd64,armel,armhf,i386
buster6.9.10.23+dfsg-2.1+deb10u1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch-security6.9.7.4+dfsg-11+deb9u12amd64,arm64,armel,armhf,i386
sid6.9.11.60+dfsg-1.2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye6.9.11.60+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster-security6.9.10.23+dfsg-2.1+deb10u1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze6.6.0.4-3+squeeze4amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
squeeze-security6.6.0.4-3+squeeze4amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy6.7.7.10-5+deb7u3sparc
upstream6.9.12.8
Debtags of package imagemagick:
interfacecommandline, x11
roleprogram
scopeutility
uitoolkitxlib
useconverting, editing, viewing
works-withimage, image:raster
works-with-formatgif, jpg, pdf, png, postscript, svg, tiff
x11application
Popcon: 4619 users (1150 upd.)*
Newer upstream!
License: DFSG free
Git

ImageMagick er en programpakke til at oprette, redigere og komponere bitmap-billeder. Det kan læse, konvertere og skrive billeder i en række formater (over 100), inklusive DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG og TIFF. Brug ImageMagick til at oversætte, vende, spejle, rotere, skalere, trapezere og transformere billeder, justere billeder, farver, anvende forskellige specialeffekter eller tegne tekst, linjer, polygoner, ellipser og Bézier-kurver.

Denne pakke inkluderer henvisninger til kanaldybdens specifikke binære filer og manualsider.

Dette er en tom pakke. Du kan fjerne den igen.

Other screenshots of package imagemagick
VersionURL
8:6.9.10.23+dfsg-2.1https://screenshots.debian.net/shrine/screenshot/17101/simage/large-c1677229fbbd02feddc63c6c5909c91d.png
8:6.9.10.23+dfsg-2.1https://screenshots.debian.net/shrine/screenshot/17102/simage/large-7accb1f69a04ce81ca66eea624943e3c.png
8:6.9.10.23+dfsg-2.1https://screenshots.debian.net/shrine/screenshot/17103/simage/large-ad1b7939603ccb9d836b2a1bf21d1398.png
8:6.9.10.23+dfsg-2.1https://screenshots.debian.net/shrine/screenshot/17099/simage/large-3f9df5a59c2fc47a548b97a2c24399d1.png
8:6.9.10.23+dfsg-2.1https://screenshots.debian.net/shrine/screenshot/17104/simage/large-53d9e8e5acedc676d80b94c8c731f6e3.png
8:6.9.10.23+dfsg-2.1https://screenshots.debian.net/shrine/screenshot/17105/simage/large-fde1fc133f12e8c800696d548eef90a2.png
8:6.9.10.23+dfsg-2.1https://screenshots.debian.net/shrine/screenshot/17100/simage/large-846e8bf4b6f2e4e621d00a033b73a874.png
Screenshots of package imagemagick
Imview
Program for billedfremvisning og analyse
Versions of package imview
ReleaseVersionArchitectures
sid1.1.9h-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
squeeze1.1.9c-7amd64,armel,i386,ia64,mips,mipsel,powerpc,s390,sparc
jessie1.1.9c-12amd64,armel,armhf,i386
stretch1.1.9c-17amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.1.9h-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye1.1.9h-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package imview:
roleprogram
works-withimage, image:raster
Popcon: 50 users (26 upd.)*
Versions and Archs
License: DFSG free
Git

Imview er et program som

  • Viser et stort antal billedformater
  • Viser 2D- eller 3D-billeder (som dias) med en udbygget zoom- og panoreringsfunktion.
  • Virker med flerspektral, tidsserier eller flersidedokumenter (f.eks.: satellitbilleder, TIFF-stakke, animerede GIF'er og heterogene flerkomponentfiler).
  • Viser alle billedpunktstyper (1-bit til 64-bit data, heltal eller kommatal.
  • Arbitrær 1-D-profil af 2-D-billeder (eller af 2-D-dias af 3-D-billeder) kan vises.
  • Har understøttelse for arbitrære farvekort for alle billedpunktstyper (dvs.: falsk farvevisning).
  • Har standardfaciliteter for billedmanipulering (lysstyrke/kontrast, gamma, zoon, beskær, rotation etc.).
  • Kan kontrolleres eksternt via sokler og tekstkommandoer (for nem integrering i forskellige analysesystemer for billeder).
  • Billeder kan overføres til Imvies via sokler eller delt hukommelse.
  • Og meget mere!
Please cite: Hugues Talbot: ImView: a portable image display application (eprint)
Openwalnut-qt4
Multi-modal medical and brain data visualization tool.
Versions of package openwalnut-qt4
ReleaseVersionArchitectures
wheezy1.2.5-1.1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package openwalnut-qt4:
interfacex11
roleprogram
uitoolkitqt
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free

OpenWalnut is a tool for multi-modal medical and brain data visualization. Its universality allows it to be easily extended and used in a large variety of application cases. It is both, a tool for the scientific user and a powerful framework for the visualization researcher. Besides others, it is able to load NIfTI data, VTK line data and RIFF-format CNT/AVR-files. OpenWalnut provides many standard visualization tools like line integral convolution (LIC), isosurface-extraction, glyph-rendering or interactive fiber-data exploration. The powerful framework of OpenWalnut allows researchers and power-users to easily extend the functionality to their specific needs.

This package contains the QT4 GUI for OpenWalnut.

Please cite: Sebastian Eichelbaum, Mario Hlawitschka, Alexander Wiebel, Gerik Scheuermann: OpenWalnut - An Open-Source Visualization System (2010)
Orthanc-dicomweb
Udvidelsesmodul til at udvide Orthanc med understøttelse for WADO og DICOMweb
Versions of package orthanc-dicomweb
ReleaseVersionArchitectures
bullseye1.5+dfsg-2amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.5+dfsg-2amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch0.3+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.6+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 4 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

Orthanc DICOMweb er et udvidelsesmodul til Orthanc, det simple RESTful Vendor Neutral Archive for medicinske billeder. Det udvider Orthanc-kernen med understøttelse for WADO- (nu kendt som WADO-URI) og DICOMweb-standarderne (QIDO-RS, STOW-RS, WADO-RS).

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Orthanc-gdcm
DICOM transcoder/decoder for Orthanc using GDCM (notably for JPEG2k)
Versions of package orthanc-gdcm
ReleaseVersionArchitectures
sid1.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

This package installs a plugin for Orthanc, the lightweight, RESTful Vendor Neutral Archive for medical imaging. The plugin extends Orthanc with a transcoder/decoder of DICOM images that is built on the GDCM library, whereas the built-in transcoder/decoder of Orthanc uses DCMTK.

This plugin is notably necessary for Orthanc to be able to transcode and decode JPEG2k transfer syntaxes.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Orthanc-imagej
ImageJ-udvidelsesmodul til at importere billeder fra Orthanc
Versions of package orthanc-imagej
ReleaseVersionArchitectures
stretch1.1+dfsg-1all
buster1.2+dfsg-1all
sid1.2+dfsg-3all
bullseye1.2+dfsg-3all
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

Dette ImageJ-udvidelsesmodul gør det muligt for ImageJ at gennemse indholdet af en Orthanc-server og importere 2D/3D DICOM-billeder fra Orthanc til ImageJ. Orthanc er en simpel RESTful DICOM-server for sundhedspleje og medicinsk forskning.

Dette udvidelsesmodul forenkler indekseringen af DICOM-billeder, når ImageJ bruges (f.eks. for kvalitetskontrol af DICOM-modaliteter, eller til pædagogisk brug). Der er heller ikke noget behov for at udføre en kompleks netværkskonfiguration, da udvidelsesmodulet direkte bruger REST API'en for Orthanc. Dette gør dens installation og dens brug ret ligefrem.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Orthanc-mysql
Udvidelsesmoduler til at bruge MySQL eller MariaDB som en databasemotor for Orthanc
Versions of package orthanc-mysql
ReleaseVersionArchitectures
buster2.0-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid3.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 4 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

Orthanc MySQL er et sæt med to udvidelsesmoduler til Orthanc, et simpelt, RESTful Vendor Neutral Archive til medicinske billeder. Disse udvidelsesmoduler overskriver SQLite-motoren til Orthanc med en MySQL- eller MariaDB-motor. De bringer skalerbarhed til Orthanc, hvilket gør programmet klar til virksomheder.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Orthanc-postgresql
Udvidelsesmoduler til at bruge PostgreSQL som en databasemotor til Orthanc
Versions of package orthanc-postgresql
ReleaseVersionArchitectures
sid3.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster3.2-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch2.0-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 3 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

Orthanc PostgreSQL er et sæt af to udvidelsesmoduler til Orthanc, et simpelt RESTful Vendor Neutral Archive for medicinske billeder. Disse udvidelsesmoduler overskriver SQLite-standardmotoren for Orthanc med en PostgreSQL-motor. De bringer skalering til Orthanc, hvilket gør den klar for virksomhedsbrug.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Orthanc-webviewer
Netfremviser af medicinske billeder for Orthanc
Versions of package orthanc-webviewer
ReleaseVersionArchitectures
bullseye2.7-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch2.2-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.5-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid2.7-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 12 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

Orthanc-netfremviser er et udvidelsesmodul til Orthanc, et simpelt, RESTful Vendor Neutral Archive for medicinske billeder. Modulet udvider Orthanc med en integreret internetfremviser for DICOM-billeder.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Paraview
Parallel visualiseringsprogram
Versions of package paraview
ReleaseVersionArchitectures
squeeze3.8.0-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
sid5.9.0-2amd64,arm64,i386,mips64el,ppc64el,s390x
bullseye5.9.0-2amd64,arm64,i386,mips64el,ppc64el,s390x
buster5.4.1+dfsg4-3.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch5.1.2+dfsg1-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie4.1.0+dfsg+1-1amd64,armel,armhf,i386
wheezy3.14.1-6amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package paraview:
roleprogram
uitoolkitqt
useviewing
Popcon: 164 users (110 upd.)*
Versions and Archs
License: DFSG free
Git

ParaView er et program til flere platforme, udviklet i åben kildekode og designet til at visualisere datasæt med en størrelse der varierer fra lille til meget stor.

  • Udvikl et visualiseringsprogram i åben kildekode og til flere platforme
  • Understøt distribuerede beregningsmodeller til behandling af store datasæt.
  • Opret en åben, fleksibel og intuitiv brugergrænseflade.
  • Udvikl en arkitektur, der kan udvides, baseret på åbne standarder.

ParaView kører på distribueret og delt hukommelse parallelt samt på systemer kun med en processor. Er blevet testet med succes på Windows, Mac OS X, Linux og diverse Unix-arbejdsstationer, klynger og supercomputere. Under motorhjelmen bruger ParaView visualiseringsværktøjssættet da databehandlings- og optegningsmotoren har en brugergrænseflade skrevet med Qt.

Pngquant
Optimeringsredskab for PNG-billede (Portable Network Graphics)
Versions of package pngquant
ReleaseVersionArchitectures
buster2.12.2-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch2.5.0-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy1.0-4.1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze1.0-4amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
jessie2.3.0-1amd64,armel,armhf,i386
jessie-security2.3.0-1+deb8u1amd64,armel,armhf,i386
sid2.13.1-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
wheezy-security1.0-4.1+deb7u1amd64,armel,armhf,i386
bullseye2.13.1-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package pngquant:
interfacecommandline
roleprogram
scopeutility
usecompressing, converting
works-withimage, image:raster
works-with-formatpng
Popcon: 168 users (68 upd.)*
Versions and Archs
License: DFSG free
Git

pngquant er et kommandolinjekonverteringsredskab til at kvantisere og farvereducere truecolor PNG-billeder, specielt dem med en fuld alfakanal, ned til 8-bit (eller mindre) RGBA-palet PNG'er. Sådanne billeder er normalt to til fire gange mindre end de fulde 32-bit versioner, og delvis gennemsigtighed bevares ret så godt. Dette gør pngquant specielt nyttigt for internetsider og for PlayStation 2-udvikling, hvor et af teksturformaterne er RGBA-palet-baseret (dog ikke PNG-komprimeret). Dette er den samme teknik brugt for mange af billederne på siden for Miscellaneous Transparent PNG'er (http://www.libpng.org/pub/png/pngs- img.html), og der kan ofte ikke ses forskel til den originale fil i truecolor PNG.

Optimeringsprogrammer (såsom pngcrush og optipgn) optimerer komprimeringen, normalt uden kvalitetstab, mens pngquant kvantiserer farver ned til 256 (eller færre) distinkte RGBA-kombinationer, hvilket giver kvalitetstab.

Screenshots of package pngquant
Science-workflow
Håndteringssystem til arbejdsforløb der er nyttig i videnskabelig forskning
Versions of package science-workflow
ReleaseVersionArchitectures
buster1.10all
sid1.14.1all
bullseye1.14.1all
stretch1.7all
Popcon: 5 users (4 upd.)*
Versions and Archs
License: DFSG free
Git

Denne opgave viser nogle pakker, der tilbyder håndteringssystemer for arbejdsforløb, der er nyttige i videnskabelig forskning.

Trimage
Grafisk brugerflade og kommandolinje til at optimere billedfiler
Versions of package trimage
ReleaseVersionArchitectures
wheezy1.0.5-1all
jessie1.0.5-1all
buster1.0.5+git20130126.e47888e-1all
sid1.0.6-1all
bullseye1.0.6-1all
stretch1.0.5-1.1all
Debtags of package trimage:
interfacecommandline, x11
roleprogram
scopeutility
uitoolkitqt
works-withimage
works-with-formatjpg, png
x11application
Popcon: 94 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

Trimage er en grafisk brugerflade og grænseflade for kommandolinjen som optimerer billedfiler via optipng, advpng, pngcrush og jpegoptim, afhængig af filtypen (i øjeblikket er PNG- og JPG-filer understøttet). Alle billedfiler er pakket uden kvalitetstab på det højeste mulige komprimeringsniveau. Trimage tilbyder dig diverse forskellige inddatafunktioner, så de passer til det arbejdsforløb: En normal fildialog, træk og slip og diverse indstillinger for kommandolinjen.

Debian packages in contrib or non-free

Bart-cuda
tools for computational magnetic resonance imaging
Versions of package bart-cuda
ReleaseVersionArchitectures
sid0.6.00-1 (contrib)amd64
bullseye0.6.00-1 (contrib)amd64
upstream0.7.00
Popcon: users ( upd.)*
Newer upstream!
License: DFSG free, but needs non-free components
Git

The Berkeley Advanced Reconstruction Toolbox (BART) is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging. It consists of a programming library and a toolbox of command-line programs. The library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms. The command-line tools provide direct access to basic operations on multi-dimensional arrays as well as efficient implementations of many calibration and reconstruction algorithms for parallel imaging and compressed sensing.

This package provides BART with CUDA support.

Fsl
transitional dummy package
Versions of package fsl
ReleaseVersionArchitectures
squeeze4.1.6-4 (non-free)all
sid5.0.8-6 (non-free)all
buster5.0.8-6 (non-free)all
jessie5.0.7-4 (non-free)all
wheezy4.1.9-7 (non-free)all
Debtags of package fsl:
fieldmedicine:imaging
interfacecommandline, x11
roleprogram
uitoolkittk
useanalysing
x11application
Popcon: 0 users (0 upd.)*
Versions and Archs
License: non-free
Git

The only purpose of this package is to enable upgrades to the new 'fsl-core' package which replaces 'fsl'. This package can safely be removed.

Users aiming to perform a complete FSL installation (including all data components) are advised to install the 'fsl-complete' package from NeuroDebian.

Please cite: Mark Jenkinson, Christian F. Beckmann, Timothy E. J. Behrens, Mark W. Woolrich and Stephen M. Smith: FSL. (PubMed) NeuroImage 62(2):782-790 (2012)
Vmtk
the Vascular Modeling Toolkit
Versions of package vmtk
ReleaseVersionArchitectures
wheezy1.0.1-1 (non-free)all
jessie1.0.1-3 (non-free)all
sid1.3+dfsg-2.3 (non-free)all
buster1.3+dfsg-2.3 (non-free)all
stretch1.3+dfsg-2.1+deb9u1 (non-free)all
Popcon: 0 users (0 upd.)*
Versions and Archs
License: non-free
Git

The Vascular Modeling Toolkit is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

Please cite: < M. Piccinelli, A. Veneziani, D. A. Steinman, A. Remuzzi and L. Antiga: A framework for geometric analysis of vascular structures: application to cerebral aneurysms.. IEEE Trans Med Imaging 28(8):1141-1155 (2009)
Registry entries: SciCrunch  OMICtools 

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

Bioimagesuite
integrated image analysis software suite
Versions of package bioimagesuite
ReleaseVersionArchitectures
VCS2.0-1all
Versions and Archs
License: GPL-2+
Debian package not available
Git
Version: 2.0-1

BioImage Suite has extensive capabilities for both neuro/cardiac and abdominal image analysis and state of the art visualization. Many packages are available that are highly extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. It can be integrated with other biomedical image processing software, such as FSL and SPM. This site provides information, downloads, documentation, and other resources for users of the software.

BioImage Suite was developed at Yale University and has been extensively used at different labs at Yale since 2004.

Please cite: X. Papademetris, M. Jackowski, N. Rajeevan, R. T. Constable and L. Staib: BioImage Suite: An integrated medical image analysis suite. (eprint) Insight Journal (2005)
Remark of Debian Med team: Contact to upstream

There is a forum at BioImage Suite site for discussion of compiling it from source and packaging issues at http://research.yale.edu/bioimagesuite/forum/index.php?board=12.0

Bioimagexd
Analyzing, processing and visualizing of multi dimensional microscopy images
Versions of package bioimagexd
ReleaseVersionArchitectures
VCS1.0-r1799-1all
Versions and Archs
License: GPL-2
Debian package not available
Git
Version: 1.0-r1799-1

BioImageXD is a multi-purpose post-processing tool for bioimaging. The software can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once. Animations of 3D renderings can be created using flying paths or keyframes. BioImageXD has basic image adjustment operations and a collection of noise reduction methods. Processing methods are accompanied with a selection of segmentation methods. Segmentation results can be analysed for tens of parameters or used for motion tracking. Other quantitative analysis methods include for instance voxel and object colocalization methods and internalization analysis. All processing and analysis methods can be build into pipelines and run for hundreds of datasets at once in batch processor.

Cellprofiler
quantitatively measure phenotypes from images automatically
Versions of package cellprofiler
ReleaseVersionArchitectures
VCS3.0.0-1all
Versions and Archs
License: GPL-2
Debian package not available
Git
Version: 3.0.0-1

CellProfiler is cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

Crea
base library of the creaTools medical image processing suite
Versions of package crea
ReleaseVersionArchitectures
VCS0.0.20131107-1all
Versions and Archs
License: CeCILL-B
Debian package not available
Git
Version: 0.0.20131107-1

The CreaTools are a suite of medical image processing and visualization software and development tools. They are developed by CREATIS, a research unit with extensive experience in the medical image processing field.

The CreaTools are a set of tools designed to meet both the needs of the end-users (physicians, students or researchers) and of the developers.

Please cite: J. F. Carrillo, M. Hernández Hoyos, E. E. Dávila Serrano and M. Orkiszw: Recursive tracking of vascular tree axes in 3D medical images. (eprint) Int J Comput Assisted Radiol Surg 1(6):331-339 (2007)
Dicoogle
Java Advanced Imaging API reference implementation
Versions of package dicoogle
ReleaseVersionArchitectures
VCS2.5.0-1all
Versions and Archs
License: free
Debian package not available
Git
Version: 2.5.0-1

This project contains the source code for the core Java Advanced Imaging API reference implementation containing the packages javax.media.jai. and com.sun.media.jai..

Freesurfer
analysis and visualization of functional brain imaging data
Versions of package freesurfer
ReleaseVersionArchitectures
VCS5.1.0+dev+cvs20120104-1all
Versions and Archs
License: FreeSurfer-Software-License-Agreement
Debian package not available
Git
Version: 5.1.0+dev+cvs20120104-1

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. It contains a fully automatic structural stream for processing cross sectional and longitudinal data.

FreeSurfer provides many anatomical analysis tools, including: representation of the cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from the rest of the brain, skull stripping, B1 bias field correction, nonlinear registration of the cortical surface of an individual with an sterotaxic atlas, labeling of regions of the cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures, etc.

This package depends upon the latest version of freesurfer.

Please cite: A. M. Dale, B. Fischl and M. I. Sereno: Cortical surface-based analysis. I. Segmentation and surface reconstruction. (PubMed) Neuroimage 9(2):179-94 (1999)
Remark of Debian Med team: The 'tktools' (tkmedit, tksurfer and tkregister2) under the
 CorTechs license are not readily redistributable thus excluded.
 .
 Here you can see a list where Freesurfer was cited
 http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation
Incf-nidash-oneclick-clients
utility for pushing DICOM data to the INCF datasharing server
Responsible: NeuroDebian Team
License: BSD
Debian package not available
Vcs
Language: Python

A command line utility for anonymizing and sending DICOM data to the XNAT image database at the International Neuroinformatics Coordinating Facility (INCF). This tool is maintained by the INCF NeuroImaging DataSharing (NIDASH) task force.

Insightapplications
InsightToolKit (ITK) based medical imaging applications
Versions of package insightapplications
ReleaseVersionArchitectures
VCS3.20.0-1.1all
Versions and Archs
License: BSD
Debian package not available
Git
Version: 3.20.0-1.1

A variety of applications providing segmentation, registration, and other medical image processing algorithms such as MRI bias field correction.

Jist
Java Image Science Toolkit
Versions of package jist
ReleaseVersionArchitectures
VCS2.0.20100907.dfsg1-1all
Versions and Archs
License: free
Debian package not available
Git
Version: 2.0.20100907.dfsg1-1

Java Image Science Toolkit (JIST) provides a native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces.

Kradview
medical image viewer for DICOM images
Versions of package kradview
ReleaseVersionArchitectures
VCS1.1.0-2all
Versions and Archs
License: GPL-3+
Debian package not available
Git
Version: 1.1.0-2

Kradview is a viewer of images obtained for some different sources: X-ray, NMR and DICOM-compatible imaging devices. Its aim is a easy to use DICOM viewer with instant rendering of images, no matter the size and the zoom of the DICOM image. It covers the "let's see the the X-ray image" need of the medical professional.

Libdcm4che-java
Clinical Image and Object Management
Versions of package libdcm4che-java
ReleaseVersionArchitectures
VCS5.10.6-1all
Versions and Archs
License: Apache-2.0 or LGPL-2
Debian package not available
Git
Version: 5.10.6-1

Dcm4che is a collection of open source applications and utilities for the healthcare enterprise.

At the core of the dcm4che project is a robust implementation of the DICOM standard. The dcm4che DICOM toolkit is used in many production applications across the world.

Remark of Debian Med team: Needs jai_imageio as prerequsite

Building the package using the packaging code in SVN works up to a point were jai_imageio.jar is required. For the status of packaging this prerequisite see the Debian Java mailing list at http://lists.debian.org/debian-java/2011/04/msg00045.html

Mayam
Cross-platform DICOM Viewer
Versions of package mayam
ReleaseVersionArchitectures
VCS0.8-1all
Versions and Archs
License: MPL 1.1/GPL 2.0/LGPL 2.1
Debian package not available
Git
Version: 0.8-1

A Cross-platform DICOM viewer using the dcm4che toolkit.

The current features are:

  • DICOM Listener for Q/R
  • DICOM Send
  • Local DB for storing study information
  • Importing DICOM studies from local disk
  • Parsing DicomDir from local disk or CD
  • Query compressed studies without decompressing them
  • Multiple Studies viewer using Layout,Tab view
  • Export to JPEG (Study, Series, Instance level). Windowing can be applied to a single instance or series of instance while exporting
  • Cine Loop & stack navigation
  • Toggle for Text and Annotation Overlay
  • Windowing Presets Settings (based on modality)
  • Layout Settings (based on modality)
  • AE Management
  • DICOM Tags Viewer
Micromanager
Microscopy Software
Versions of package micromanager
ReleaseVersionArchitectures
VCS1.4.10-1all
Versions and Archs
License: free
Git
Version: 1.4.10-1

µManager is a software package for control of automated microscopes. It lets you execute common microscope image acquisition strategies such as time-lapses, multi-channel imaging, z-stacks, and combinations thereof. μManager works with microscopes from all four major manufacturers (Leica, Nikon, Olympus and Zeiss), most scientific-grade cameras and many peripherals (stages, filter wheels, shutters, etc.) used in microscope imaging (check the list of supported hardware). Since μManager runs as a plugin to ImageJ, image analysis routines are available within the application.

Unencumbered code provides a GUI for microscope image acquisition, a hardware interface layer and hardware interfacing for:

  • ASI stages, filter wheels and shutters
  • Arduino
  • Conix filter changer
  • Velleman K8055 and K8061 digital IO boards
  • Leica DMI microscopes
  • Ludl shutters, stages and filter Wheels
  • Nikon TE2000 microscope
  • Physik Instrumente stages
  • Pecon stage incubators
  • Prior shutters, stages and filter wheels
  • Spectral LMM5 laser controller
  • Sutter shutters, filter wheels and DG4
  • Vincent Uniblitz shutters
  • Yokogawa spinning disk confocal CSU22 and CSUX
  • Zeiss microscopes (two 'generations')
  • iidc1394 compatible cameras (through libdc1394)
Remark of Debian Med team: Partially problematic licenses

Unfortunately there is a pile of dirty licenses involved so I'm not sure this is ready for Debian yet. Some of the code cannot be given out and some drivers require kernel modules to be built. You have to sign NDAs to get access to all the code.

Mipav
quantitative analysis and visualization of medical images
Versions of package mipav
ReleaseVersionArchitectures
VCS5.0.0.20100907-2all
Versions and Archs
License: non-free
Git
Version: 5.0.0.20100907-2

The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders. MIPAV provides an interface for plug-ins and serves as the foundation for other projects (e.g. JIST).

This package provides downloader/installer for non-redistributable closed-source version of MIPAV and a convenience startup wrapper. You will have a choice of reviewing the license and accepting or declining it upon installation.

Mni-colin27-nifti
Talairach stereotaxic space template
Versions of package mni-colin27-nifti
ReleaseVersionArchitectures
VCS1.1-2all
Versions and Archs
License: free
Git
Version: 1.1-2

This template MRI volume was created from 27 T1-weighted MRI scans of a single individual that have been transformed into the Talairach stereotaxic space. The anatomical image is complemented by a brain and a head mask. All images are in 1x1x1 mm resolution.

This package provides the template in NIfTI format.

Openelectrophy
data analysis GUI for intra- and extra-cellular recordings
Versions of package openelectrophy
ReleaseVersionArchitectures
VCS0.0.svn143all
Versions and Archs
License: free
Git
Version: 0.0.svn143

This package provides the startup script for the OpenElectrophy GUI.

Please cite: Samuel Garcia and Nicolas Fourcaud-Trocmé: OpenElectrophy: an electrophysiological data- and analysis-sharing framework. Frontiers in Neuroinformatics 3:14 (2009)
Stabilitycalc
evaluate fMRI scanner stability
Responsible: NeuroDebian Team
License: BSD
Git
Language: Python

Command-line tools to calculate numerous fMRI scanner stability metrics, based on the FBIRN quality assurance test protocal. Any 4D volumetric timeseries image in NIfTI format is support input. Output is a rich HTML report.

Visit - wnpp
interactive parallel visualization and graphical analysis tool
Versions of package visit
ReleaseVersionArchitectures
VCS2.9.1-1all
Versions and Archs
License: free
Debian package not available
Git
Version: 2.9.1-1

VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes.

VisIt was designed to handle very large data set sizes in the terascale range and yet can also handle small data sets in the kilobyte range.

Xnat
platform for data management and productivity tasks in neuroimaging
Versions of package xnat
ReleaseVersionArchitectures
VCS1.7.5.1-1all
Versions and Archs
License: XNAT_SLA
Debian package not available
Git
Version: 1.7.5.1-1

The primary functionality of XNAT is to provide a place to store and control access to neuroimaging data. This includes sophisticated user control, search and retrieval, and archiving capabilities. As open-source software, XNAT also supports a wide variety of research-based processing pipelines, and is able to link up with supercomputer processing power to dramatically shorten image processing time.

Please cite: Daniel S. Marcus, Timothy R. Olsen, Mohana Ramaratnam and Randy L. Buckner: The Extensible Neuroimaging Archive Toolkit (XNAT): An informatics platform for managing, exploring, and sharing neuroimaging data.. (PubMed,eprint) Neuroinformatics 5(1):11-34 (2007)

Unofficial packages built by somebody else

Cdmedicpacs
web interface to PACS to access DICOM study images
License: GPL2

Web based PACS (Picture Archiving and Communication System) to access DICOM studies images, in an easy and quick manner.

  • Easy configuration of PACS nodes (AE,IP,Port) , status, statistics of storage form web interface.
  • Dynamic web page generation from DICOM data +- prospective preparation when system is idle.
  • Automatic video(mp4/gif) generation from Heart MRI at Patient’s heart bit frame rate and XA at 15 fps.
  • Still images in jpeg with Window/Level from DICOM header when present or with Histogram algorithm.
  • Possibility on large Studies of still images to make a single mp4 for Series instead of a bunch of jpeg.
  • Easy web deletion of Series/Studies and auto deletion (Study date/DB insertion) for temporal PACS.
  • Good DICOM interaction with Diagnostic Modalities and commercial DICOM Viewers/Work Stations.
  • Good DICOM interaction with free DICOM Viewers Aeskulap
Fiji
The Fiji image processing suite (based on ImageJ)
Responsible: Mark Longair
License: unknown

Fiji is a project aiming at simplifying:

  • the installation of ImageJ
  • the usage of ImageJ
  • the usage of specific, powerful ImageJ plugins
  • the development of plugins using ImageJ
Remark of Debian Med team: About packaging status the authors said:

See the thread on the Debian Med mailing list at: http://lists.debian.org/debian-med/2009/04/msg00059.html

  • We've been working to get rid of, or replace, any remaining non-DFSG licensed plugins, but there's at least one left. The bug for tracking this is here: http://pacific.mpi-cbg.de/cgi-bin/bugzilla/show_bug.cgi?id=19
  • At the moment Fiji depends on sun-java6 rather than openjdk.
  • The packages are rather large at the moment (about 35MiB). This is mostly due to bundling various components with Fiji that could be satisfied as dependencies in Debian, such as junit, jruby, etc. but I haven't had time to work on separating those out.
  • Fiji uses a modified version of ImageJA (which again is bundled into the fiji package) rather than depending on the imagej Debian package created by people on this list.
  • One of the aims of Fiji was to make Benjamin Schmid's Java3D-based 3D viewer plugin work out-of-the-box, since people often had trouble installing it manually. At the time when I first made these packages there were no java3d packages in Debian, but now that these are in sid we should eventually be able to switch to using those.
Mni-autoreg
MNI average brain (305 MRI) stereotaxic registration model
Responsible: NeuroDebian Team
License: no-free, but GPLed parts

This package provides a version of the MNI Average Brain (an average of 305 T1-weighted MRI scans, linearly transformed to Talairach space) specially adapted for use with the MNI Linear Registration Package.

  • average_305.mnc - a version of the average MRI that covers the whole brain (unlike the original Talairach atlas), sampled with 1mm cubic voxels
  • average_305_mask.mnc - a mask of the brain in average_305.mnc
  • average_305_headmask.mnc - another mask, required for nonlinear mode
Mni-n3
MNI Non-parametric Non-uniformity Normalization
Responsible: NeuroDebian Team
License: BSDish

MNI Non-parametric Non-uniformity Normalization (N3). This package provides the 'nu_correct' tool for unsupervised correction of radio frequency (RF) field inhomogenities in MR volumes. Two packages are provided:

  • mni-n3 - provides 'nu_correct'
  • libebtks-dev - MNI support library with numerical types and algorithms
Opendicom.net
API to DICOM in C# for Mono
Responsible: Albert Gnandt
License: LGPL

The openDICOM.NET project implements a new approach towards DICOM (Digital Imaging and Communications in Medicine) libraries. DICOM is a worldwide standard in Medical IT and is provided by the National Electrical Manufacturers Association (NEMA). This standard specifies the way medical images and meta data like study or patient related data is stored and communicated over different digital medias. Thus, DICOM is a binary protocol and data format.

The openDICOM# Class Library, main part of the openDICOM.NET project, provides an API to DICOM in C# for Mono and the .NET Framework. It is a completely new implementation of DICOM. In contrast to other similar libraries the intention of this implementation is to provide a clean classification with support of unidirectional DICOM data streaming. Another implemented goal is the support of DICOM as XML. This is not standard conform but very use- and powerful within software development, storage and manipulation. Currently, full read support of DICOM output stream and full write support to XML is supposed to be provided. The entire DICOM content can be accessed as sequence or as tree of class instances. Latter is the default representation of DICOM content by the library.

The openDICOM.NET Utils are a collection of console tools for working with the needed data dictionaries in different data formats (binary and textual), query of ACR-NEMA (prior DICOM standard) and DICOM files and transcoding them into image formats like JPEG and XML files. These utils are written in C# for Mono and the .NET Framework and are using the openDICOM# API for processing.

The openDICOM.NET Navigator recapitulates the openDICOM.NET Utils in form of a GTK# GUI. It provides different views with focus on DICOM data sets and visualization. Connectivity to GIMP is also given for single image processing purpose as well as the possibility to run through multi-frame images like a movie.

The openDICOM.NET Beagle Filter Plugin increases the usability of ACR-NEMA and DICOM query within your desktop. It makes DICOM content overall indexable for retrieval. The Beagle search engine relies on Mono/.NET and works in the background of your system, but is able to detect content changes in realtime (depending on your configuration).

All GUI applications focus the popular GNOME desktop, but are 100% platform independent by relying on Mono.

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

Devide - wnpp
Delft Visualization and Image processing Development Environment
Responsible: Mathieu Malaterre
License: BSD
Debian package not available

DeVIDE, or the Delft Visualization and Image processing Development Environment, is a Python-based dataflow application builder that enables the rapid prototyping of medical visualization and image processing applications via visual programming. In other words, by visually connecting functional blocks (think Yahoo pipes), you can create cool visualizations.

See the DeVIDE website at http://visualisation.tudelft.nl/Projects/DeVIDE

Dtitk - wnpp
DTI spatial normalization and atlas construction toolkit
License: GPL-3+
Debian package not available
Language: C++

DTI-TK is a spatial normalization & atlas construction toolkit, designed from ground up to support the manipulation of diffusion-tensor images (DTI) with special cares taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. The key features include:

  • NIfTI support for scalar, vector and DTI volumes
  • tool chains for manipulating DTI volumes: resampling, smoothing, warping, registration & visualization
  • pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies
  • built-in cluster-computing support
  • interoperability with other major DTI tools: AFNI, Camino, DTIStudio & FSL
Please cite: H Zhang, P A Yushkevich, D C Alexander, and J C Gee: Deformable registration of diffusion tensor MR images with explicit orientation optimization. (2006)
Eeglab - wnpp
toolbox for processing and visualization of electrophysiological data
Responsible: NeuroDebian Team
License: GPL-2+
Debian package not available
Language: C, Matlab/Octave

EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data.

Please register by following this link if you are using eeglab.
Please cite: Delorme A and Makeig S: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics (2004)
Isis - wnpp
I/O framework for neuroimaging data
Responsible: NeuroDebian Team
License: GPL-2+
Debian package not available
Language: C++

This framework aids access of and conversion between various established neuro-imaging data formats, like Nifti, Analyze, DICOM and VISTA. ISIS is extensible with plugins to add support for additional data formats.

Jemris - wnpp
high performance computing MRI simulator
Responsible: NeuroDebian Team
License: GPL-2+
Debian package not available

JEMRIS, which stands for "Juelich Extensible MRI Simulator", is a general simulator of MRI (Magnetic Resonance Imaging) data. The general process of simulation consists of preparation by choice or implementation of sequence, sample and coil setup and the invocation of the simulation run itself.

Please cite: Tony Stöcker, Kaveh Vahedipour, Daniel Pflugfelder, N. Jon Shah: High-performance computing MRI simulations. (2010)
Opensourcepacs - wnpp
medical image referral, archiving, routing and viewing system
Responsible: Mathieu Malaterre
License: GPL
Debian package not available

OpenSourcePACS is a free, open source image referral, archiving, routing and viewing system. It adds functionality beyond conventional PACS by integrating wet read functions, implemented through DICOM Presentation State and Structured Reporting standards.

In its first release, OpenSourcePACS delivers a complete wet read system, enabling an imaging clinic or hospital to offer its services over the web to physicians within or outside the institution. In future releases, we hope to incorporate more RIS (dictation, transcription, and reporting) functionality.

OpenSourcePACS is a product of the UCLA Medical Imaging Informatics group (http://www.mii.ucla.edu/).

No known packages available

Blox
medical imaging and visualization program
License: GPL
Debian package not available

The purpose of the project is to develop a quantitative medical imaging and visualization program for use on brain MR, DTI and MRS data. It is a joint project of the Kennedy Krieger Institute and the Johns Hopkins University, Psychiatric Neuroimaging Lab (http://pni.med.jhu.edu/methods/morph.htm).

Brainvisa
image processing factory for MR images
License: Free? (CeCill License)
Debian package not available

BrainVISA is a software, which embodies an image processing factory. A simple control panel allows the user to trigger some sequences of treatments on series of images. These treatments are performed by calls to command lines provided by different laboratories. These command lines, hence, are the building blocks on which are built the assembly lines of the factory. BrainVISA is distributed with a toolbox of building blocks dedicated to the segmentation of T1-weighted MR images. The product of the main assembly line made up from this toolbox is the following: grey/white classification for Voxel Based Morphometry, Meshes of each hemisphere surface for visualization purpose, Spherical meshes of each hemisphere white matter surface, a graph of the cortical folds, a labeling of the cortical folds according to a nomenclature of the main sulci.

Dcm4chee
Clinical Image and Object Management (enterprise)
License: LGPL, MPL, Apache, other (also non-free)
Debian package not available

Contained within the dcm4che project is dcm4chee (the extra 'e' stands for 'enterprise'). dcm4chee is an Image Manager/Image Archive (according to IHE). The application contains the DICOM, HL7 services and interfaces that are required to provide storage, retrieval, and workflow to a healthcare environment. dcm4chee is pre-packaged and deployed within the JBoss application server. By taking advantage of many JBoss features (JMS, EJB, Servlet Engine, etc.), and assuming the role of several IHE actors for the sake of interoperability, the application provides many robust and scalable services.

Dicom4j
Java framework for Dicom
License: GPL
Debian package not available

Java framework for Dicom

Drjekyll
interactive voxel editor for viewing and editing three-dimensional images
License: GPL
Debian package not available

It is specifically aimed at postprocessing of segmented datasets, but offers some functionality for raw data as well. Voxel elements (=voxels) and pixel ("picture element") are viewed as data sets and can be processed by this program as kind of a final polishing process.

Dti-query
dynamic queries of the white matter brain pathways
License: MIT
Debian package not available
Language: C++

This application allows neuroscientists to place and interactively manipulate box-shaped regions (or volumes of interest) to selectively display pathways that pass through specific anatomical areas. A simple and extensible query language allows for arbitrary combinations of these queries using Boolean logic operators. Queries can be further restricted by numerical path properties such as length, mean fractional anisotropy, and mean curvature.

Remark of Debian Med team: Depends on RAPID library that is available under non-commercial

licensing terms.

Ecg2png
convert scanned electrocardiograms into PNG format
License: GPL
Debian package not available

This program is designed to convert scanned 12-lead electrocardiograms into PNG format and a web-friendly image size. It assumes that the electrocardiogram (ECG) is printed with a black line on white paper with a red grid.

The problems this program is designed to solve are (1) an ECG scanned at relatively high resolution (300 to 600 dots per inch) imposes a substantial load on the web browser because it contains about 6 million pixels which may require 18 to 24 MB of RAM to store for display. Also, (2) typical scanners convert a clean paper ECG into a multitude of colors, include green and blue. The resulting file cannot be compressed efficiently because it does not contain as much redundancy, and thus takes more time to transmit over low-speed network connections.

Remark of Debian Med team: Homepage vanished

The homepage of this project that used to be at http://www.cardiothink.com/downloads/ecg2png/ vanished but the source can be downloaded fro instance from http://www.freshports.org/graphics/ecg2png/ .

Gimias
Graphical Interface for Medical Image Analysis and Simulation
License: BSD-like
Debian package not available

GIMIAS is a workflow-oriented environment for solving advanced biomedical image computing and individualized simulation problems, which is extensible through the development of problem-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Physiome community while allowing business-friendly technology transfer and commercial product development.

Hid
database management system for clinical imaging
License: BSD, BIRN
Debian package not available
Language: java

The Human Imaging Database (HID) is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large.

Please register by following this link if you are using hid.
Please cite: Keator, D.B.; Grethe, J.S.; Marcus, D.; Ozyurt, B.; Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.;Notestine, R.; Bockholt, H.J.; Papadopoulos, P.: A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN) (2008)
Maris
package suite for Radiological Workflow
License: GPL
Debian package not available

The MARiS Project goal is to realize a package suite for Radiological Workflow using Open Source tools and technologies in according with IHE guidelines. The architecture of the single packages is based on the concept of IHE actor: this is very useful to develop a system that is an ensemble of single pieces that cooperate together using IHE profiles.

Medisnap
photograph, manage, view, compare, document and archive medical photos
License: GPL-3
Debian package not available

Photograph, manage, view, compare, document and archive medical photos fully integrated into doctor's practice systems. Take a photo and immediately see how the picture gets archived to your current patient automatically.

  • direct support for Olympus E-System cameras
  • network support
  • fully integrated via GDT interface into many medical software systems
  • organise photos by patients effectively
  • define your own localisations
  • compare photos of healing processes at different times
  • work time-optimized and effective, photos automatically get added and archived under the current patient in your system
  • easily print selected photos and archive or give them to your patients
Mesa-test-tools
IHE Test Software for Radiology
License: free
Debian package not available

The MESA software release which is available at http://ihedoc.wustl.edu/mesasoftware/10.15.0/dist/ provides several tools that might cover a wide range of applications for Integrating the Healthcare Enterprise (IHE) testing.

Another important element of the IHE testing process is the set of software tools HIMSS and RSNA have commissioned. Developed by the Electronic Radiology Laboratory at the Mallinckrodt Institute of Radiology, Washington University of St. Louis, the MESA tools are designed for use by participating companies in implementing IHE capabilities in their systems and preparing for the Connectathon. Their purpose is to provide communication partners, test data and test plans to allow organizations to provide a baseline level of testing as they implement the IHE Technical Framework. These tools are made available to participants during the period of an IHE demonstration year and are then released into the public domain at the end of that cycle. The latest version of the MESA Test Tools available in the public domain can be found here.

This kind of software is definitively valuable for information systems vendors and imaging systems vendors.

Because the CTN Debian package is based on an upstream dead project these tools should have a high priority for packaging because the CTN homepage http://erl.wustl.edu/research/dicom/ctn.html says: "The CTN software is also embedded within the MESA tools. The version of CTN software in those tools does not have a separate release number but is more current than version 3.0.6."

Miview
Medical Images viewer and converter
License: GPL-3+
Debian package not available
Language: C++

MIView features - DICOM files browser - volume rendering - reads DICOM v3, NEMA/ACR, Papyrus, Jpeg, GIF, bitmap, TIFF,

  Analyze 7.5, and Nifti1 files
- can convert to raster (jpeg, bitmap, etc) and Analyze/Nifti1
Remark of Debian Med team: At the moment available only for Windows, but author says

there should be no major showstoppers to build it on Linux -- just needs building infrastructure

Mni-icbm152-nlin-2009
MNI stereotaxic space human brain template
Responsible: NeuroDebian Team
License: custom, DFSG-compliant
Debian package not available

This is an unbiased standard magnetic resonance imaging template volume for the normal human population. It has been created by the Montreal Neurological Institute (MNI) using anatomical data from the International Consortium for Brain Mapping (ICBM).

The package provides a 1x1x1 mm and 0.5x0.5x0.5 mm resolution templates (hemissphere-symetric and asymetric non-linearily co-registered versions), some including T1w, T2w, PDw modalities, T2 relaxometry, and tissue probability maps. In addition, it contains a lobe atlas, and masks for brain, eyes and face.

Please cite: V.S. Fonov, A.C. Evans, R.C. McKinstry, C.R. Almli and D.L. Collins: Unbiased nonlinear average age-appropriate brain templates from birth to adulthood. (2009)
Remark of Debian Med team: This package is waiting for the Debian data package archive to become available.
Mrisim
simulator for magnetic resonance imaging data
Responsible: NeuroDebian Team
License: BSD-like
Debian package not available

mrisim is a simple Magnetic Resonance Imaging (MRI) simulation program which produces MINC volumes from a segmented and labelled brain phantom. It allows intrinsic tissue parameters (T1, T2...) and pulse sequence parameters (TR, TE ...) to be specified and then produces simulated images with noise. Currently, no artifacts are implemented.

Omero
coming standard LIMS for microscopy images
License: GPL
Debian package not available

OMERO is client-server software for visualisation, management and analysis of biological microscope images.

Piano
medical image processing library for surgical planning
License: BSD
Debian package not available

Piano is a library containing roughly 75 algorithms and tools for multi-dimensional medical image processing, analysis and visualization. It is used in the field of surgical planning.

Pymeg
suite for analysis of magnetoencephalography (MEG) data
License: GPL-3
Debian package not available
Language: Python
 PyMEG is a project in Python to do various neuroimaging processing
 with magnetoencephalography (MEG) data. The purpose of this project,
 is to create a suite of functions to do MEG analysis in Python.
Remark of Debian Med team: Needs DFSG-ification.
       According to the author is not yet ready for the use by
       mortals -- wasn't released yet.
Stir
Software for Tomographic Image Reconstruction
License: GPL
Debian package not available

STIR is Open Source software for use in tomographic imaging. Its aim is to provide a Multi-Platform Object-Oriented framework for all data manipulations in tomographic imaging. Currently, the emphasis is on (iterative) image reconstruction in PET, but other application areas and imaging modalities can and might be added.

STIR is the successor of the PARAPET software library which was the result of a (European Union funded) collaboration between 6 different partners, the PARAPET project..

Remark of Debian Med team: Even if this is GPLed software the download requires registration.
Tempo
3D visualization of brain electrical activity
License: BSD
Debian package not available
Language: C++, Qt

TEMPO is open source software for 3D visualization of brain electrical activity. TEMPO accepts EEG file in standard EDF format and creates animated sequence of topographic maps. Topographic maps are generated over 3D head model and user is able to navigate around head and examine maps from different viewpoints. Most mapping parameters are adjustable through appropriate graphical user interface controls. Also, individual topographic maps could be saved in PNG format for future examination or publishing.

Remark of Debian Med team: Packaged for OpenSuSE http://en.opensuse.org/TEMPO
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 204157