Debian Science Project
Summary
Cognitive neuroscience
Debian Science - pakker for kognitiv neurovidenskab

Denne metapakke installerer Debianpakker, som kan være nyttige for videnskabsfolk, der udfører kognitiv neurovidenskabelig forskning. Dette omhandler den fulde forskningsproces fra udførelse af psykofysiske eksperimenter, over dataindhentelse og analyse, til visualisering og opsætning af videnskabelige resultater.

Udvalget af pakker er målrettet anvendelsen af analyseteknikker. Metodeudviklere henvises til metapakkerne science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging og med-imaging-dev for en række yderligere programmer, som kan være nyttige i konteksten kognitiv neurovidenskab.

Description

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

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

Links to other tasks

Debian Science Cognitive neuroscience packages

Official Debian packages with high relevance

Amide
Program til medicinsk billedbehandling
Versions of package amide
ReleaseVersionArchitectures
squeeze0.9.2-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
bullseye1.0.5-12amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.0.5-12amd64,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
jessie1.0.5-2amd64,armel,armhf,i386
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
Debtags of package amide:
fieldmedicine, medicine:imaging
roleprogram
Popcon: 32 users (15 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)
Caret
Værktøjssæt til computerbaseret anatomisk rekonstruktion og redigering
Versions of package caret
ReleaseVersionArchitectures
jessie5.6.4~dfsg.1-3amd64,armel,armhf,i386
squeeze5.6.1.3~dfsg.1-4amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy5.6.4~dfsg.1-3amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package caret:
roleprogram
uitoolkitqt
Popcon: 1 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)
Dicom3tools
DICOM-medicinske billedfiler - manipulerings- og konverteringsværktøjer
Versions of package dicom3tools
ReleaseVersionArchitectures
sid1.00~20190724083540-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
squeeze1.0~20100510-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy1.0~20120505-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie1.00~20140902075059-1amd64,armel,armhf,i386
stretch1.00~20170109062447-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
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
Debtags of package dicom3tools:
fieldmedicine, medicine:imaging
roleprogram
useconverting
works-withimage
Popcon: 23 users (6 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
buster2.33.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2.33.1-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2.33.1-1amd64,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
Debtags of package dicomnifti:
interfacecommandline
roleprogram
scopeutility
useconverting
Popcon: 16 users (9 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.

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: 13 users (0 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)
Itksnap
semiautomatisk segmentering af strukturer i 3D-billeder
Versions of package itksnap
ReleaseVersionArchitectures
sid3.6.0-5amd64,i386
bullseye3.6.0-5amd64,i386
buster3.6.0-3amd64,i386
stretch3.4.0-2amd64,i386
wheezy2.2.0-1.1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze2.0.0+cvs20100615-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
jessie2.2.0-1.1amd64,armel,armhf,i386
Debtags of package itksnap:
fieldmedicine:imaging
roleprogram
Popcon: 19 users (6 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
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)
Medcon
Medicinsk billedkonverteringsværktøj (DICOM, ECAT, ...)
Versions of package medcon
ReleaseVersionArchitectures
jessie0.13.0-2amd64,armel,armhf,i386
squeeze0.10.5-2.1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy0.10.7-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
stretch0.14.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.16.1+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.16.1+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.16.1+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream0.16.2
Debtags of package medcon:
fieldbiology
interfacecommandline
roleprogram
uitoolkitgtk
useconverting
works-withimage, image:raster
x11application
Popcon: 27 users (10 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.

Minc-tools
Medicinsk billedformatværktøjer for MNI
Versions of package minc-tools
ReleaseVersionArchitectures
bullseye2.3.00+dfsg-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
squeeze2.0.18+cvs20100518-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy2.1.10-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie2.2.00-6amd64,armel,armhf,i386
stretch2.3.00+dfsg-1.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.3.00+dfsg-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid2.3.00+dfsg-3amd64,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: 9 users (17 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
bullseye2.1.0-4amd64,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
sid2.1.0-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.1.0-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch2.1.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie2.0.7-2amd64,armel,armhf,i386
Debtags of package mriconvert:
fieldmedicine:imaging
roleprogram
uitoolkitwxwidgets
Popcon: 15 users (11 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
bullseye0.20140804.1~dfsg.1-3amd64,arm64,armel,armhf,i386
buster0.20140804.1~dfsg.1-3amd64,arm64,armel,armhf,i386
stretch0.20140804.1~dfsg.1-2amd64,arm64,armel,armhf,i386
wheezy0.20120505.1~dfsg.1-1amd64,armel,armhf,i386,powerpc,sparc
sid0.20140804.1~dfsg.1-3amd64,arm64,armel,armhf,i386
jessie0.20140804.1~dfsg.1-1amd64,armel,armhf,i386
Debtags of package mricron:
uitoolkitgtk
Popcon: 42 users (47 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, Leonardo Bonilha: Improving lesion-symptom mapping. (2007)
Other screenshots of package mricron
VersionURL
0.20140804.1~dfsg.1-2+b1https://screenshots.debian.net/screenshots/000/016/011/large.png
0.20140804.1~dfsg.1-2+b1https://screenshots.debian.net/screenshots/000/016/012/large.png
Screenshots of package mricron
Nifti-bin
Værktøjer leveret med NIfTI-biblioteket
Versions of package nifti-bin
ReleaseVersionArchitectures
wheezy2.0.0-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
stretch2.0.0-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.0.0-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2.0.0-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2.0.0-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
squeeze2.0.0-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
jessie2.0.0-2amd64,armel,armhf,i386
Debtags of package nifti-bin:
fieldmedicine, medicine:imaging
interfacecommandline
roleprogram, shared-lib
scopeutility
usechecking, converting
Popcon: 16 users (10 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
sid0.4.11-1.1amd64,i386
bullseye0.4.11-1.1amd64,i386
buster0.4.11-1amd64,i386
stretch0.4.11-1amd64,i386
jessie0.4.9-1amd64,armel,armhf,i386
Popcon: 5 users (12 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.

Openmeeg-tools
openmeeg library -- command line tools
Versions of package openmeeg-tools
ReleaseVersionArchitectures
squeeze2.0.0.dfsg-2amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy2.0.0.dfsg-5amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mipsel,powerpc,s390,s390x,sparc
Debtags of package openmeeg-tools:
roleprogram
Popcon: 3 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)
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.

Praat
program for taleanalyse og -syntese
Versions of package praat
ReleaseVersionArchitectures
sid6.1.09-1amd64,arm64,i386,ppc64el,s390x
squeeze5.1.42-1amd64,armel,i386,ia64,mips,mipsel,powerpc,s390,sparc
wheezy5.3.16-1amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc
jessie5.4.0-1amd64,armel,armhf,i386
stretch6.0.23-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster6.0.48-1amd64,arm64,i386,mips64el,ppc64el,s390x
bullseye6.1.08-1amd64,arm64,i386,mips64el,ppc64el,s390x
sid6.1.08-1mips64el
Debtags of package praat:
fieldlinguistics
interfacex11
roleprogram
scopeapplication
uitoolkitmotif
works-withaudio
x11application
Popcon: 30 users (18 upd.)*
Versions and Archs
License: DFSG free
Git

Ifølge programmets forfattere så udfører praat »fonetik via computeren«. Via sin grafiske grænseflade, flere funktioner for taleanalyse er tilgængelige: spektogrammer, cochleogrammer, og tonehøjde og formant- udtræk. Artikulær syntese samt syntese fra tonehøjde, formant og intensitet er også tilgængelig. Andre egenskaber indgår segmentering, brug af etiketter med brug af det fonetiske alfabet, samt beregning af statistikker. Praat er konfigurerbar og udvidelig gennem dets eget skriptsprog og har bestemmelser for kommunikation med andre programmer.

Please cite: Paul Boersma: Praat, a system for doing phonetics by computer. Glot International 5(9/10):341-345 (2001)
Screenshots of package praat
Psignifit
Tilpasser og tester hypoteser om psykometriske funktioner
Versions of package psignifit
ReleaseVersionArchitectures
jessie2.5.6-3amd64,armel,armhf,i386
stretch2.5.6-3.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.5.6-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2.5.6-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2.5.6-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
squeeze2.5.6-3amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy2.5.6-3amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package psignifit:
fieldstatistics
interfacecommandline
roleprogram
Popcon: 11 users (12 upd.)*
Versions and Archs
License: DFSG free
Git

Psignifit tillader tilpasning af psykometriske funktioner til datasæt, mens der bevares fuld kontrol over et stort antal parametre. Data kan enten læses fra tekstfiler eller videresendes via en datakanal.

Psignifit udfører beregningen af konfidensintervaller samt goodness-of-fit test.

Dette er udgaven til kommandolinjen.

Screenshots of package psignifit
Python3-nibabel
Python 3-bindinger til diverse neuroimaging-dataformater
Versions of package python3-nibabel
ReleaseVersionArchitectures
bullseye2.5.1-3all
buster2.3.2-1all
stretch2.1.0-1all
sid2.5.1-3all
upstream3.0.1
Popcon: 12 users (38 upd.)*
Newer upstream!
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-pydicom
DICOM-medicinsk fillæsning og -skrivning - Python 3
Versions of package python3-pydicom
ReleaseVersionArchitectures
bullseye1.4.1-1all
buster1.2.1-1all
sid1.4.1-1all
Popcon: 17 users (56 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-statsmodels
Python 3-modul for estimering af statistiske modeller
Versions of package python3-statsmodels
ReleaseVersionArchitectures
buster0.8.0-9all
bullseye0.10.2-2all
experimental0.11.0-1all
sid0.10.2-2all
upstream0.11.0
Popcon: 16 users (77 upd.)*
Newer upstream!
License: DFSG free
Git

Statsmodels Python 3-modul tilbyder klasser og funktioner for estimering af flere kategorier af statistiske modeller. Disse inkluderer i øjeblikket lineære regressionsmodeller, OLS, GLS, WLS og GLS med AR(p)-fejl, generaliserede lineære modeller for flere distributionsfamilier og M-estimatorer for robuste lineære modeller. En omfattende liste over resultatstatistik er tilgængelig for hvert estimeringsproblem.

Please cite: Skipper Seabold and Josef Perktold: Statsmodels: Econometric and statistical modeling with python (eprint) (2010)
Qnifti2dicom
Konverter 3D medicinske billeder til DICOM 2D-serier - grafisk brugerflade
Versions of package qnifti2dicom
ReleaseVersionArchitectures
bullseye0.4.11-1.1amd64,i386
jessie0.4.9-1amd64,armel,armhf,i386
stretch0.4.11-1amd64,i386
buster0.4.11-1amd64,i386
sid0.4.11-1.1amd64,i386
Popcon: 2 users (9 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 Qt4.

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.

Please cite: Steven Pieper, Michael Halle, Ron Kikinis: 3D SLICER. (2004)
Voxbo
Behandling, statistisk analyse og billedvisning af hjernedata
Versions of package voxbo
ReleaseVersionArchitectures
buster1.8.5~svn1246-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch1.8.5~svn1246-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
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
jessie1.8.5~svn1246-1.1amd64,armel,armhf,i386
Debtags of package voxbo:
fieldmedicine:imaging
roleprogram
uitoolkitqt
Popcon: 6 users (3 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
Xmedcon
Medicinsk billedkonverteringsværktøj (DICOM, ECAT, ...) - grafisk brugerflade
Versions of package xmedcon
ReleaseVersionArchitectures
jessie0.13.0-2amd64,armel,armhf,i386
squeeze0.10.5-2.1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
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
bullseye0.16.1+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.16.1+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream0.16.2
Debtags of package xmedcon:
fieldbiology
interfacecommandline, x11
roleprogram
scopeutility
uitoolkitgtk
useconverting
works-withimage, image:raster
x11application
Popcon: 181 users (9 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

Connectomeviewer
Interaktiv analyse og visualisering for MR Connectomics
Versions of package connectomeviewer
ReleaseVersionArchitectures
jessie2.1.0-1all
buster2.1.0+dfsg-1all
wheezy2.1.0-1all
Popcon: 4 users (3 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)
Science-psychophysics
Debian Science - pakker for psykofysik
Versions of package science-psychophysics
ReleaseVersionArchitectures
buster1.10all
wheezy1.0all
stretch1.7all
jessie1.4all
sid1.12all
bullseye1.12all
Debtags of package science-psychophysics:
rolemetapackage
suitedebian
Popcon: 2 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

Denne metapakke vil installere Debianpakker, som kan være nyttige for udførsel af eksperimenter relateret til fysisk stimuli og deres fysiologiske effekter.

Udvalget af pakker er målrettet programmer for stimuli. For yderligere programmer relateret til analyse af de indhentede data se science-neuroscience-cognitive, med-imaging afhængig af domænanvendelsen. Kig derudover i science-bci da disse pakker ofte tilbyder en fuldstændig ramme inklusiv stimulilevering.

Science-typesetting
Debian Science - opsætningspakker
Versions of package science-typesetting
ReleaseVersionArchitectures
squeeze0.12all
stretch1.7all
jessie1.4all
wheezy1.0all
sid1.12all
bullseye1.12all
buster1.10all
Debtags of package science-typesetting:
rolemetapackage
suitedebian
Popcon: 6 users (15 upd.)*
Versions and Archs
License: DFSG free
Git

Denne metapakke vil installere Debian Science-pakker relateret til opsætning. Du er måske også interesseret i deb-mærket use::typesetting.

Debian packages in contrib or non-free

Fsl
transitional dummy package
Versions of package fsl
ReleaseVersionArchitectures
jessie5.0.7-4 (non-free)all
squeeze4.1.6-4 (non-free)all
sid5.0.8-6 (non-free)all
buster5.0.8-6 (non-free)all
wheezy4.1.9-7 (non-free)all
bullseye5.0.8-6 (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)

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 Science team: How to work together with 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

Debruijn
De Bruijn cycle generator
Versions of package debruijn
ReleaseVersionArchitectures
VCS1.6-2all
Versions and Archs
License: BSD-4-clause
Git
Version: 1.6-2

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

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
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 Science team: The 'tktools' (tkmedit, tksurfer and tkregister2) under the
 CorTechs license are not readily redistributable thus excluded.
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

Eeglab
toolbox for processing and visualization of electrophysiological data
Responsible: NeuroDebian Team
License: GPL-2+
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)
Mni-autoreg
MNI average brain (305 MRI) stereotaxic registration model
Responsible: Michael Hanke
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

Remark: Michael Hanke agreed to take over his stuff from mentors http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg and http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg-model to Debian Med svn and start group maintenance.

Mni-n3
MNI Non-parametric Non-uniformity Normalization
Responsible: Michael Hanke
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

Remark: Michael Hanke agreed to take over his stuff from mentors http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-n3 to Debian Med svn and start group maintenance.

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

Fieldtrip - wnpp
toolbox for MEG and EEG analysis
License: GPL-2+
Debian package not available
Language: Matlab/Octave

The software includes algorithms for simple and advanced analysis of MEG and EEG data, such as time-frequency analysis, source reconstruction using dipoles, distributed sources and beamformers and non-parametric statistical testing. It supports the data formats of all major MEG systems (CTF, Neuromag, BTi) and of the most popular EEG systems, and new formats can be added easily. FieldTrip contains high-level functions that you can use to construct your own analysis protocols in Matlab. Furthermore, it easily allows developers to incorporate low-level algorithms for new EEG/MEG analysis methods.

Remark of Debian Science team: The NIMH distributes a "port" of fieldtrip to Octave (at

http://kurage.nimh.nih.gov/meglab/Meg/Software). It needs to be figured out whether this port can be incorporated into the official version, and to what degree it is complete. Packaging fieldtrip is required to complete the packaging of SPM8.

Pysurfer - wnpp
visualize Freesurfer's data in Python
Responsible: NeuroDebian Team
License: BSD-3
Debian package not available
Language: Python

This is a Python 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.

Spm8 - wnpp
analysis of brain imaging data sequences
Responsible: NeuroDebian team
License: GPL-2+
Debian package not available

Statistical Parametric Mapping (SPM) refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM. It is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.

Please register by following this link if you are using spm8.
Please cite: Karl J. Friston, John T. Ashburner, Stephen Kiebel, Thomas E. Nichols and William D. Penny: Statistical Parametric Mapping: The Analysis of Functional Brain Images.. (2007)
Remark of Debian Science team: This software is written for matlab, but initial tests indicate that

some (significant) portion of it might also work with octave. More tests are pending...

No known packages available

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.

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)
Iqr
large-scale multi-level neuronal systems simulator
Responsible: NeuroDebian team
License: GPL-3+
Debian package not available

This graphical environment allows for designing large-scale multi-level neuronal systems that can control real-world devices, such as cameras and mobile robots, in real-time. iqr is an extensible framework with the ability to handle new, user-provided, neuron and synapse types, as well as custom interfaces to other hardware systems. iqr employes an XML-based format for system descriptions.

Please cite: Ulysses Bernardet, Paul F.M.J. Verschure: iqr: A tool for the construction of multi-level simulations of brain and behaviour.. (2010)
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 203233