Debian Med Project
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Summary
Imaging
paquets Debian Med de traitement et visualisation d'images

Ce métapaquet installera les paquets Debian qui peuvent être utiles dans le cadre du traitement et de la visualisation d'images médicales.

D’une part, il installe plusieurs paquets prenant en charge divers formats de fichier d’image, comme DICOM (« Digital Imaging and Communications in Medecine ») qui est le standard de facto pour la gestion d'images médicales, ou NIFTI. D’autre part, il fournit divers paquets logiciels pouvant être utilisés pour la visualisation et le traitement d’images, soit à partir d’une interface graphique, de la ligne de commande ou implantées dans un flux de travail.

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
Afficheur d'images médicales et client réseau DICOM
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Aeskulap est capable de charger une série d'images spéciales stockéees au format DICOM pour les réviser. De plus, il est capable de questionner et d'extraire des images DICOM à partir de noeuds d'archive (appelés PACS) à travers le réseau. Le but d'Aeskulap est de devenir un remplaçant open source aux visualiseurs DICOM commerciaux disponibles.

Screenshots of package aeskulap
Amide
programme pour l'imagerie médicale
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AMIDE (« AMIDE's a Medical Image Data Examiner ») est un outil pour la visualisation et l'analyse de jeux de données d'imagerie médicale. On peut noter parmi ses fonctionnalités la prise en charge simultanée de données importées de fichiers aux formats divers, la fusion d'images, la définition de régions d'intérêt tridimensionnelles, le rendu des volumes et l'alignement de structures solides.

Amide importe la plupart des fichiers cliniques DICOM (grâce à la bibliothèque DCMTK).

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)
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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
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Ants
outils de normalisation élaborés pour l'analyse d'images du cerveau
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ANTS (« Advanced Normalization Tools ») est un ensemble d'outils basé sur ITK pour la normalisation, segmentation et construction de modèles pour l'analyse morphométrique quantitative. De nombreux outils d'acquisition d'ANTS sont difféomorphiques, mais les transformations de forme (élastique et BSpline) sont disponibles. Les composants uniques d'ANTS incluent : métriques de similarité multivariées, repères cartographiques, capacité à utiliser des images étiquetées pour assister la cartographie et une implémentation optimale en temps, espace et ressources, des difféomorphismes. La stratégie de normalisation symétrique (SyN) fait partie des outils ANTS en tant que transformation de forme libre directement manipulée (DMFFD).

Ce paquet fournit une configuration de modules d'environnement. Lancer « module load ants » rend tous les outils en ligne de commande accessibles dans l'interpréteur de commande.

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Bart
outils pour l'imagerie par résonance magnétique computationnelle
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BART (« Berkeley Advanced Reconstruction Toolbox ») est un environnement libre de reconstruction d'images pour l'imagerie par résonance magnétique computationnelle. Il consiste en une bibliothèque de programmation et un boîte à outils de programmes en ligne de commande. La bibliothèque fournit des opération courantes sur les tableaux multidimensionnels, les transformations de Fournier et par ondelettes, ainsi que des implémentations génériques d'algorithmes d'optimisation itérative. Les outils en ligne de commande fournissent un accès direct aux opérations de base sur les tableaux multidimensionnels et des implémentations efficaces de plusieurs algorithmes de calibration et de reconstruction pour l'imagerie parallèle et l'acquisition comprimée.

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
visualisateur de données multidimensionnelles et de valeur complexe
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BART (« Berkeley Advanced Reconstruction Toolbox ») est un environnement libre de reconstruction d'images pour l’informatique de l'imagerie par résonance magnétique (IRM).

Ce paquet fournit un visualisateur d’images en tant que composant optionnel de l’environnement BART. Il est conçu pour les données multidimensionnelles et de valeur complexe.

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

  • save2gdf: converter between different file formats, including but not limited to SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF, BDF, CWFB.
  • biosig2gdf: converts biosig data files into GDF, to simplify parsing and loading by scripting languages (e.g. loadgdf.{py,r})
  • rec2bin, bin2rec, heka2itx, save2aecg, save2scp: several converter tools based on save2gdf
  • biosig_fhir: packs biosignal data into HL7/FHIR binary template file.
  • physicalunits: converter for encoding and decoding of physical units according to 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
banc de test pour la bibliothèque CamiTK
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CamiTK aide les chercheurs et les cliniciens à collaborer facilement et rapidement afin de prototyper des applications CAMI incluant des images médicales, une navigation chirurgicale et des simulations biomécaniques.

Camitk-imp est le banc de test de CamiTK dans laquelle toutes les extensions disponibles peuvent être testées pour faire du prototypage. Elle fournit un accès simple et interactif à toutes les données disponibles et aux paramètres des algorithmes, y compris ceux créés par les développeurs avec le SDK de CamiTK.

Par exemple, camitk-imp peut visualiser les images médicales depuis beaucoup de formats standard, propose des algorithmes de traitement et de segmentation d'images pour reconstruire un maillage et lancer une simulation biomécanique.

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)
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Caret
outil d'edition et de reconstruction anatomique assistées par ordinateur
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Ce logiciel permet de créer, de visualiser et de manipuler des modélisations surfaciques en 3D du cerveau et du cortex, de visualiser les volumes et d'afficher les données expérimentales des surfaces et des volumes. Alors que Caret est avant tout conçu pour être une interface graphique, il est également un outil utilisable en console avec ses commandes au format 'caret_command' , ce qui rend directement accessibles de nombreuses fonctionnalités du programme.

Caret peut télécharger et utiliser les atlas stéréotaxiques (humain, singe, souris et rat) depuis une base de données libre.

Certaines fonctionnalités de Caret ne sont opérationnelles que si des données complémentaires, fournies dans le paquet caret-data, sont installées. Cela inclut :

  • construction de surface à partir des volumes via les atlas PALS ;
  • morphing à résolutions multiples ;
  • projection de « foyers » via les atlas PALS ;
  • base de données de surfaces de base ;
  • aplatissement de surface.

Actuellement, le paquet caret-data n'est accessible que depuis les dépôts NeuroDebian. Pour de plus amples informations, merci de consulter le site : http://neuro.debian.net

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 - common files
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A full featured DICOM server that has been developed based on and heavily extending the public domain UCDMC DICOM code. Some possible applications of the ConQuest DICOM software are:

  • DICOM training and testing
  • Demonstration and research image archives
  • Image format conversion from a scanner with DICOM network access
  • DICOM image viewing and slide making
  • DICOM image selection, (limited) editing, and splitting and merging of series
  • Advanced scriptable image modification, filtering, forwarding and conversion
  • DICOM caching and archive merging

This package contains common files. You'll need a package providing conquest-dicom-server (e.g. conquest-mysql, conquest-postgres, conquest-sqlite or conquest-dbase).

Ctn
Nœud de Test Central, une implémentation de DICOM pour l'imagerie médicale
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Le logiciel « Central Test Node » (CTN, Nœud de Test Central) est une implémentation de DICOM qui a été conçue pour être utilisée aux rencontres annuelles de la RSNA (Société Radiologique d'Amérique du Nord), dans le but de permettre les démonstrations collaboratives faites par les vendeurs de systèmes d'imagerie médicale. Le but était de fournir une implémentation centralisée qui facilitait la participation des vendeurs, basée sur le standard DICOM.

Ce paquet fournit les programmes et les fichiers de configuration pour 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
Simulateur de tomographie calculée
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CTSim fournit un simulateur interactif de tomographie. La tomographie calculée est la technique permettant d'estimer l'intérieur d'un objet en mesurant l'absorption des rayons X à travers cet objet.

CTSim inclut des outils en ligne de commande et une interface graphique. Il possède des modes éducatifs permettant de voir une simulation de la collecte des données ainsi que de la reconstruction.

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Dcm2niix
convertisseur de dernière génération DICOM vers NIfTI
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Dcm2niix est le successeur de dcm2nii, un outil populaire pour convertir des images des formats compliqués utilisés par les fabricants de numériseur à balayage (DICOM, PAR/REC) au format NIfTI plus simple utilisé par beaucoup d’outils scientifiques. Il fonctionne pour toutes les modalités (CT, MRI, PET, SPECT) et tous les types de séquence.

Dcmtk
utilitaires en ligne de commande de la boîte à outils OFFIS DICOM
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DCMTK contient une collection de bibliothèques et d'applications pour examiner, construire et convertir des images DICOM, gérer les média hors ligne, envoyer et recevoir des images à travers le réseau ainsi que stocker les images et gérer des listes de travaux.

Ce paquet contient les utilitaires DCMTK.

Note : cette version a été compilée avec la prise en charge de libssl.

Dicom3tools
outils de conversion et de manipulation de fichiers d'imagerie médicale DICOM
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Utilitaires en ligne de commande pour créer, modifier, vidanger et valider des fichiers d'attributs DICOM. Il gère la conversion de certains formats d'imagerie médicale propriétaires en DICOM. Il gère l'ancien format de données ACR/NEMA et certaines de ses versions propriétaires telle que SPI.

Dicomnifti
Convertit les fichiers DICOM au format NIfTI
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Le programme dinifti convertit des images d'IRM du format DICOM au format NIfTI. Les fichiers au format NIfTI peuvent être lus par les programmes FSL, AFNI et SPM, Caret ou Freesurfer.

Dinifti convertit les fichiers un par un, ou à la chaîne au sein d'un répertoire, et peut donner des noms cohérents aux fichiers NIfTI en utilisant les informations présentes dans les fichiers DICOM.

Dicomscope
visualisateur DICOM d’OFFIS
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DICOMscope est un visualisateur libre DICOM pouvant afficher des images DICOM non compressées et monochromes pour toutes les modalités, et prenant en charge la calibration du moniteur selon la quatorzième section de DICOM ainsi que les caractéristiques de présentation.

DICOMscope fournit un client d’impression (DICOM Basic Grayscale Print Management) qui met en œuvre la classe facultative de présentation SOP LUT.

Le développement du prototype a été commandé par le « Committee for the Advancement of DICOM » et montré au congrès européen de radiologie (ECR) de 1999. Une version améliorée a été développée pour le « DICOM Display Consistency Demonstration » lors de l’InfoRAD de la RSNA de 1999.

La publication actuelle a été montrée lors de l’ECR de 2001 et contient de nombreuses extensions, comprenant un serveur d’impression, la prise en charge de communications DICOM chiffrées, les signatures numériques et des rapports structurés.

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Fslview
Visualiseur de données (f)MRI et DTI
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Ce paquet fournit un visualiseur pour données 3d et 4d au format MRI ainsi que pour des images DTI. FSLView est capable d'afficher des fichiers ANALYZE et NIFTI. Le visualiseur supporte plusieurs modes pour voir en 2d (orthogonal, lightbox ou simple slices) mais également pour du rendu d'objet 3d. De plus, FSLView est capable de visualiser des séries de temps et de recouvrer des données d'atlas métrique et stéréotaxique.

FSLView fait partie de 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)
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Gdf-tools
bibliothèque d’E/S pour les signaux biomédicaux – assistants
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GDF (General Dataformat for Biosignals – format général de données pour les signaux biomédicaux) vise à fournir un stockage générique pour les signaux biomédicaux, tels EEG, ECG, MEG, etc.

Ce paquet fournit l’outil livré avec la bibliothèque (gdf_merger).

Please cite: Alois Schlögl: GDF – A general dataformat for BIOSIGNALS. The Computing Research Repository abs/cs/0608052 (2006)
Ginkgocadx
logiciel d’imagerie médicale et visualisateur DICOM complet
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Ginkgo CADx fournit une solution de visualisation DICOM avec des capacités performantes et la prise en charge d’extensions :

 – interface simple et personnalisable à l’aide de profils ;
 – visualisation pleine de fonctionnalités d’image DICOM ;
 – ensemble d’outils complet (mesure, marquage, texte…) ;
 – prise en charge de plusieurs secteurs médicaux (neurologie, radiologie,
   dermatologie, ophtalmologie, échographie, endoscopie…) ;
 – prise en charge de la normalisation DICOM à partir de JPEG, PNG, GIF
   et TIFF ;
 – prise en charge entière de l’intégration du matériel (EMH) : flux
   produits conformes aux normes HL7 et IHE ;
 – station de travail PACS (système d'archivage et de transmission
   d'images), (C-FIND, C-MOVE, C-STORE…) ;
 – extensibilité à l’aide d’ajouts personnalisables :
   – composition mosaïquée d’image rétinienne,
   – diagnostic automatique à partir d’analyse rétinienne,
   – diagnostic automatique du psoriasis.
Gwyddion
outil d'analyse et de visualisation de données SPM (« Scanning Probe Microscopy »)
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Gwyddion est un programme modulaire pour la visualisation et l’analyse des données de microscopie à sonde locale (SPM – Scanning Probe Microscopy). Il est principalement conçu pour l’analyse des données du champ de hauteur obtenues par des techniques telles que (entre autres) :

 – le microscope à force atomique (AFM – Atomic Force Microscopy) ;
 – le microscope à force magnétique (MFM – Magnetic Force Microscopy) ;
 – le microscope à effet tunnel (STM – Scanning Tunneling Microscopy) ;
 – le microscope optique en champ proche (SNOM ou NSOM – Near-field
   Scanning Optical Microscopy).
Il peut aussi être utilisé pour n’importe quelle analyse de champ de

hauteur et d’image.

Ce paquet fournit l'application principale et ses modules. Il contient également un générateur d'aperçu pour GNOME (et Xfce) permettant de créer des aperçus pour tous les types de fichier pris en charge par 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)
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Imagej
programme de traitement d’image ciblant les images de microscopie
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Ce programme peut afficher, éditer, analyser, traiter, enregistrer et imprimer des images 8, 16 et 32 bits. Il peut lire de nombreux formats d'image, dont TIFF, GIF, JPEG, BMP, DICOM, FITS et RAW. Il prend en charge les « stacks », une série d'images partageant une même fenêtre.

ImageJ peut calculer des statistiques de zones et pixels à partir de sélections de l'utilisateur. Il peut mesurer les distances et les angles. Il peut créer des histogrammes de densité et des affichages de profils linéaires. Il prend en charge les fonctions standard de traitement d'images telles que la manipulation du contraste, l'accentuation, l'adoucissement, la détection d'arêtes et le filtrage médian.

La calibration spatiale est disponible pour fournir des mesures de dimensions réelles dans des unités comme le millimètre. La calibration de la densité ou des niveaux de gris est également disponible.

ImageJ est développé par Wayne Rasband (wayne@codon.nih.gov) dans la Research Services Branch du National Institute of Mental Health à 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)
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Imagevis3d
application de bureau pour le rendu volumique direct de grands volumes de données
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ImageVis3D est une application de rendu volumique direct conçue particulièrement pour le rendu de grands volumes de données. Cela est réalisé en divisant l’ensemble de données selon plusieurs niveaux de détail, avec chaque niveau décomposé en plusieurs briques (primitive de rendu atomique). L’interaction se produit au niveau de détail le plus grossier, qui peut être rendu instantanément sur la plupart des systèmes modernes. Après un délai personnalisable, ImageVis3D affichera successivement des niveaux de détail plus fin, jusqu’à ce que toutes les données soient visibles dans leur résolution d’origine.

Le développement d’ImageVis3D est parrainé par « NIH/NCRR Center for Integrative Biomedical Computing (CIBC) » et « DOE Visualization And Analytics Center for Enabling Technologies (VACET) ».

Invesalius
logiciel de reconstruction d’images médicales en 3D
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InVesalius génère des reconstructions d’images médicales en 3D en se basant sur une série de fichiers DICOM de 2D obtenus avec des équipements de tomodensitométrie ou d’imagerie par résonance magnétique. InVesalius est internationalisé (actuellement disponible en anglais, portugais, français, espagnol, turc, italien, tchèque, japonais, catalan, coréen, roumain et allemand) et fournit plusieurs outils :

 — prise en charge de DICOM dont : (a) ACR-NEMA version 1 et 2 ;
  (b) DICOM version 3.0 (dont divers encodages de JPEG — sans perte et
   avec pertes —, RLE) ;
 — fonctions de manipulation d’image (zoom, panoramique, rotation, lumière
   et contraste, etc.) ;
 — segmentation basée sur des tranches en 2D ;
 — intervalles de seuil prédéfinis selon le tissu en vue ;
 — segmentation par ligne de partage des eaux ;
 — segmentation par région croissante ;
 — outils d’édition (similaires à Paint Brush) basés sur des tranches 2D ;
 — segmentation semi-automatique basée sur lignes de partage des eaux ;
 — création de surface en 3D ;
 — outils de connexité de surface 3D ;
 — exportation de surface 3D (dont : STL binaire, OBJ, VRML, Inventor) ;
 — projection de rendu de volume de haute qualité ;
 — préréglages prédéfinis de rendu de volume ;
 — plan de coupe de rendu de volume ;
 — exportation d’image (dont : BMP, TIFF, JPG, PostScript, POV-Ray) ;
 — visualisations basées sur la projection par intensité minimale,
   maximale ou moyenne, accumulation et contour de différences maximales
   d’intensité.
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Ismrmrd-tools
command-line tools for ISMRMRD
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The ISMRMRD format combines a mix of flexible data structures (XML header) and fixed structures (equivalent to C-structs) to represent MRI data.

In addition, the ISMRMRD format also specifies an image header for storing reconstructed images and the accompanying C++ library provides a convenient way of writing such images into HDF5 files along with generic arrays for storing less well defined data structures, e.g. coil sensitivity maps or other calibration data.

This package provides the command-line tools.

Itksnap
segmentation semi-automatique de structures pour les images en 3D
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SNAP fournit une segmentation semi-automatique de structures pour les images médicales (par exemple, des images de résonance magnétique du cerveau) en utilisant des méthodes de contour actif, ainsi que la délimitation manuelle et la navigation dans les images. Les caractéristiques notables sont :

  – curseur avec liens pour une navigation en 3D fluide ;
  – segmentation manuelle dans les trois plans orthogonaux en même temps ;
  – gestion de beaucoup de formats d’image 3D, y compris NIfTI ;
  – gestion concomitante, visualisations liées et segmentation de plusieurs
    images ;
  – gestion limitée des images en couleur (par exemple, cartes de tenseurs
    de diffusion) ;
  – outils de plan sécant en 3D pour un post-traitement rapide des
    résultats de segmentation.
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)
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King
interactive system for three-dimensional vector graphics
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KiNG (Kinemage, Next Generation) is an interactive system for three-dimensional vector graphics. It supports a set of graphics primitives that make it suitable for many types of graphs, plots, and other illustrations; although its first use was to display macromolecular structures for biophysical research. KiNG builds on Mage, JavaMage, and the "kinemage" (kinetic image) concept to deliver a full-featured Java application with a user-friendly interface and integrated editing features. The KiNG jar file can be used within a web page as a Java applet or Java object to promote easy access to kinemages or coordinate files from a web browser.

Libgdcm-tools
Grassroots DICOM tools and utilities
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Grassroots DiCoM is a C++ library for DICOM medical files. It is automatically wrapped to python/C#/Java (using swig). It supports RAW,JPEG (lossy/lossless),J2K,JPEG-LS, RLE and deflated.

Install this package for the gdcmanon, gdcmconv, gdcmdiff, gdcmdump, gdcmpap3, gdcmgendir, gdcmimg, gdcminfo, gdcmpdf, gdcmraw, gdcmscanner, gdcmscu, gdcmtar, gdcmxml programs.

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
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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)
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Medcon
Outil de conversion d'images médicales (DICOM, ECAT, etc.)
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Ce projet a pour but la conversion d’image médicale (Medical Image Conversion). Publié sous licence (L)GPL, il est livré avec le code source C complet de la bibliothèque, un outil flexible en ligne de commande et une interface graphique soignée utilisant la boîte à outils GTK+. Les formats pris en charge actuellement sont : Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 et PNG.

Le programme permet aussi de lire des fichiers non pris en charge et non compressés, pour afficher les valeurs de pixel ou pour extraire ou réorganiser les images indiquées. Il est possible de récupérer les tableaux d’image binaire ou ASCII RAW ou d’écrire des PNG pour des applications de bureau.

Ceci est l'outil en ligne de commande pour le traitement par lot.

Mia-tools
Command line tools for gray scale image processing
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Command lines tools to run general purpose image processing tasks on 2D and 3D gray scale images, and basic operations on triangular meshes. Supported image processing algorithms are image filtering, combining, image registration, motion compensation for image series, and the estimation of various statistics over images. This package also contains the nipype interfaces for these command line tools.

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
programme de visualisation pour des ensembles de données en 3D créés avec MIA
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Il s’agit du programme de visualisateur de MIA pour l’affichage d’ensembles de données en 3D. Les interfaces et les types de données pris en charge sont axés sur les résultats pouvant être obtenus en exécutant les programmes du paragraphe mia-tools.

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Mialmpick
outils pour le choix de points de repère dans des ensembles de données de volumes en 3D
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Cet outil fournit un moteur simple de rendu pouvant visualiser des surfaces directement à partir de volumes en 3D et pouvant être utilisé pour déterminer des points de repère. Il est le mieux adapté à des ensembles de données de tomodensitométrie (CT).

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
Outils pour le format MNI d'imagerie médicale
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Ce paquet contient des outils permettant de manipuler des fichiers MINC.

Le format de fichiers MINC est un format de fichier très souple basé sur le format généralisé de données NetCDF. Il est simple, auto-décrit, extensible, portable et à N dimensions avec des interfaces de programmation que ce soit pour l'accès aux données de bas niveau ou à des manipulations de haut niveau en masse. Les bibliothèques ont permis l'écriture d'un ensemble d'outils de manipulation de fichiers génériques d'images. Le format, les bibliothèques et les outils sont prévus pour être utilisés dans un environnement de recherche en imagerie médicale : ils sont simples et efficaces sans chercher à fournir une belle interface aux utilisateurs.

Mriconvert
utilitaire de conversion de fichier d’image médicale
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MRIConvert est un utilitaire de conversion de fichier d’image médicale pour des fichiers DICOM vers les formats NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager et MetaImage.

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Mricron
conversion, visualisation et analyse d’images de résonance magnétique
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Il s’agit d’un outil de visualisation et d’analyse basé sur une interface graphique pour les images de résonance magnétique (fonctionnelle). MRIcron peut être utilisé pour créer des rendus en 2D ou 3D des cartes de superposition statistiques d’images d’anatomie de cerveau. De plus, il aide à dessiner des régions anatomiques d’intérêt (ROI), ou des cartes de lésion, ainsi qu’une analyse basique de séries temporelles (par exemple, création de tracés de péristimulus signal-modification).

En plus de « mricron », ce paquet fournit aussi « dcm2nii » qui prend en charge la conversion d’images DICOM et PAR/REC au format NIfTI, et « npm » pour l’analyse de données non paramétriques.

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
tractographie de la substance blanche par IRM pondérée en diffusion
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Ce paquet fournit un ensemble d'outils pour la tractographie de la substance blanche du cerveau, en présence de réseaux de fibres, par IRM pondérée en diffusion du cerveau grâce à des algorithmes de tractographie déterministes ou probabilistes. Les images de résonance magnétique aux formats DICOM, ANALYZE, ou NIfTI non compressé sont prises en charge.

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)
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Nifti-bin
outils livrés avec la bibliothèque NIfTI
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Niftilib est un ensemble de bibliothèques d'entrées-sorties pour lire et écrire des fichiers au format NIfTI-1. NIfTI-1 est un format de fichier binaire pour stocker des images médicales, par exemple des images par résonance magnétique (IRM) et des images de cerveau par résonance magnétique fonctionnelle (IRMf).

Ce paquet fournit les outils livrés avec la bibliothèque (nifti_tool, nifti_stats et nifti1_test).

Nifti2dicom
convert 3D medical images to DICOM 2D series
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Nifti2Dicom is a conversion tool that converts 3D NIfTI files (and other formats supported by ITK, including Analyze, MetaImage Nrrd and VTK) to DICOM. Unlike other conversion tools, it can import a DICOM file that is used to import the patient and study DICOM tags, and allows you to edit the accession number and other DICOM tags, in order to create a valid DICOM that can be imported in a PACS.

This package includes the command line tools.

Odil
C++11 library for the DICOM standard (application)
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Odil leverages C++ constructs to provide a user-friendly API of the different parts of the DICOM standard. Included in Odil are exception-based error handling, generic access to datasets elements, standard JSON and XML representation of datasets, and generic implementation of messages, clients and servers for the various DICOM protocols.

This package contains the command-line application.

Odin
développement, simulation et exécution de séquences de résonance magnétique
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ODIN est un cadriciel pour l’imagerie par résonance magnétique (IRM). Il couvre toute la chaîne d’outils pour l’IRM, du plus bas niveau d’acquisition des données jusqu’à la reconstruction de l’image. En particulier, il vise à réaliser un prototypage rapide de séquences IRM. Les séquences peuvent être programmées en utilisant une interface de programmation en C++, orientée objet et de haut niveau. Il fournit des outils de pointe pour l’analyse de séquences tels que le tracé interactif de trajectoires d’espace des phases, une interface utilisateur pour un cycle rapide compilation-lien-test et un simulateur d’IRM puissant prenant en charge différents échantillons virtuels. Pour une reconstruction rapide et modulable, ODIN fournit un cadriciel grandement personnalisable et de traitement de données multiprocessus.

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Openmeeg-tools
openmeeg library -- command line tools
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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
outils de manipulation et conversion pour OpenSlide
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OpenSlide est une bibliothèque C fournissant une interface simple pour lire des images de lame de microscope, aussi appelées lames virtuelles.

Les images « Whole-slide », aussi appelées lames virtuelles (virtual slides), sont des images de grande taille et haute résolution utilisées en pathologie numérique. La lecture de ces images en utilisant les outils ou bibliothèques standard est un défi parce que ces outils sont classiquement utilisés pour des images pouvant être compressées ou décompressées confortablement en mémoire vive ou dans un fichier d’échange (swap). Les images de lames virtuelles dépassent couramment la taille de la RAM, occupant, non compressées, souvent des dizaines de gigaoctets. De plus, ces images ont plusieurs résolutions, et seulement une petite partie des données peuvent être nécessaires et cela dans une résolution particulière.

Cette bibliothèque actuellement prend en charge : – Aperio (.svs, .tif) ; – Hamamatsu (.vms, .vmu, .ndpi) ; – Leica (.scn) ; – MIRAX (.mrxs) ; – Sakura (.svslide) ; – Trestle (.tif) ; – Generic tiled TIFF (.tif).

Ce paquet fournit les outils en ligne de commande pour la manipulation de fichier.

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Orthanc
Lightweight, RESTful DICOM server for medical imaging
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Orthanc aims at providing a simple, yet powerful DICOM server for medical imaging. Orthanc can turn any computer running Windows or Linux into a Vendor Neutral Archive (in other words, a mini-PACS system). Its architecture is lightweight, meaning that no complex database administration is required, nor the installation of third-party dependencies.

What makes Orthanc unique is the fact that it provides a RESTful API. Thanks to this major feature, it is possible to drive Orthanc from any computer language. The DICOM tags of the stored medical images can be downloaded in the JSON file format. Furthermore, standard PNG images can be generated on-the-fly from the DICOM instances by Orthanc.

Orthanc lets its users focus on the content of the DICOM files, hiding the complexity of the DICOM format and of the DICOM protocol.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
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Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)
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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 implementation containing Image Viewer and a ECG Viewer - cli
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This is a stand-alone DICOM toolkit that implements code for reading and creating DICOM data, DICOM network and file support, a database of DICOM objects, support for display of directories, images, reports and spectra, and DICOM object validation.

Provide command line applications for using pixelmed

Plastimatch
reconstruction d’images médicales et recalage
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Plastimatch est un logiciel au code source ouvert pour le recalage d’images fluctuantes (« deformable »). Il est conçu pour un enregistrement volumétrique de haute performance d’images médicales, telles que scanographie, imagerie par résonance magnétique (IRM) ou tomoscintigraphie par émission de positons (TEP). Les propriétés du logiciel sont :

 — méthode « B-spline » pour le recalage d’images fluctuantes (accélérations
     graphique GPU et multi-cœur), y compris le masquage d’image, « landmark
     penalties » et régularisation ;
 — méthode « Demons » pour l’enregistrement d’images fluctuantes (accélération
     graphique GPU) ;
 — segmentation multi-atlas ;
 — algorithmes basés sur ITK pour les multiples méthodes de translation,
     rigides, affines, démons multiples, et enregistrement « B-spline z ;
 — cadriciel d’enregistrement multi-étape parallélisé avec une conversion
     homogène entre la plupart des algorithmes et les types de transformation ;
 — enregistrement d’images fluctuantes en fonction de repères en utilisant
     des splines de fines tranches pour un enregistrement global ;
 — enregistrement d’images fluctuantes en fonction de repères en utilisant
     des fonctions basiques en utilisant des fonctions basiques radiales ;
 — vaste prise en charge des formats de fichier d’image 3D (avec ITK),
     intégrant DICOM, Nifti, NRRD, MetaImage et Analyze ;
 — chaîne d’outils extensibles pour la recherche en radiothérapie, comprenant
     la prise en charge des formats de fichier DICOM, DICOM-RT, DICOM SRO et
     XiO, l’analyse gamma, les manipulations de contour, l’analyse des
     recoupements et l’analyse des champs de vecteurs ;
Plastimatch prend aussi en charge deux utilitaires pratiques qui ne concernent

pas directement le recalage d’image :

 — reconstruction FDK cone-beam CT (accélérations graphique GPU et
     multi-cœur) ;
 — génération de radiographies reconstruites de manière numérique
     (accélérations graphique GPU et multi-cœur).
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Python3-dipy
Python library for the analysis of diffusion MRI datasets
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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
Python3 bindings to various neuroimaging data formats
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NiBabel provides read and write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC, as well as PAR/REC. The various image format classes give full or selective access to header (meta) information and access to the image data is made available via NumPy arrays. NiBabel is the successor of PyNIfTI.

Python3-nipy
Analysis of structural and functional neuroimaging data
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NiPy is a Python-based framework for the analysis of structural and functional neuroimaging data. It provides functionality for

  • General linear model (GLM) statistical analysis
  • Combined slice time correction and motion correction
  • General image registration routines with flexible cost functions, optimizers and re-sampling schemes
  • Image segmentation
  • Basic visualization of results in 2D and 3D
  • Basic time series diagnostics
  • Clustering and activation pattern analysis across subjects
  • Reproducibility analysis for group studies
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
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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)
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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 medical file reading and writing (Python 3)
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pydicom is a pure Python module for parsing DICOM files. DICOM is a standard (http://medical.nema.org) for communicating medical images and related information such as reports and radiotherapy objects.

pydicom makes it easy to read DICOM files into natural pythonic structures for easy manipulation. Modified datasets can be written again to DICOM format files.

This package installs the module for Python 3.

Python3-pyxid
interface for Cedrus XID and StimTracker devices
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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
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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
convert 3D medical images to DICOM 2D series (gui)
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Nifti2Dicom is a conversion tool that converts 3D NIfTI files (and other formats supported by ITK, including Analyze, MetaImage Nrrd and VTK) to DICOM. Unlike other conversion tools, it can import a DICOM file that is used to import the patient and study DICOM tags, and allows you to edit the accession number and other DICOM tags, in order to create a valid DICOM that can be imported in a PACS.

This package contains the Qt5 GUI.

Sigviewer
visionneur graphique pour biosignaux tels que EEG, EMG et ECG
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SigViewer est un logiciel pour visualiser et noter des données de signaux biomédicaux. Il repose sur la bibliothèque biosig4c++ gérant un certain nombre de formats de données (dont EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro, TMS32). La liste complète des formats de fichier pris en charge est disponible sur http://pub.ist.ac.at/~schloegl/biosig/TESTED.

En plus d’afficher les biosignaux, SigViewer gère la création d’annotations pour sélectionner des artefacts ou des évènements particuliers.

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Slicer
software package for visualization and image analysis - main application
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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
Interface graphique à SOFA (« Simulation Open Framework Architecture »)
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SOFA est un ensemble libre visant la simulation temps réel, en particulier la simulation médicale. Il est principalement prévu pour aider la communauté de chercheurs à développer de nouveaux algorithmes mais peut aussi être utilisé comme outil de prototypage efficace.

Ce paquet contient l'application principale SOFA.

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Teem-apps
Tools to process and visualize scientific data and images - command line tools
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Teem is a coordinated group of libraries for representing, processing, and visualizing scientific raster data. Teem includes command-line tools that permit the library functions to be quickly applied to files and streams, without having to write any code. The most important and useful libraries in Teem are:

  • Nrrd (and the unu command-line tool on top of it) supports a range of operations for transforming N-dimensional raster data (resample, crop, slice, project, histogram, etc.), as well as the NRRD file format for storing arrays and their meta-information.
  • Gage: fast convolution-based measurements at arbitrary point locations in volume datasets (scalar, vector, tensor, etc.)
  • Mite: a multi-threaded ray-casting volume render with transfer functions based on any quantity Gage can measure
  • Ten: for estimating, processing, and visualizing diffusion tensor fields, including fiber tractography methods.

This package contains some simple command-line tools which provide fast and easy access to the functionality in the various libraries.

Tifffile
Read and write image data from and to TIFF files
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Image and meta-data can be read from TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH, ImageJ, MicroManager, FluoView, SEQ and GEL files.

Only a subset of the TIFF specification is supported, mainly uncompressed and losslessly compressed 2**(0 to 6) bit integer, 16, 32 and 64-bit float, grayscale and RGB(A) images, which are commonly used in bio-scientific imaging. Specifically, reading JPEG/CCITT compressed image data or EXIF/IPTC/GPS/XMP meta-data is not implemented. Only primary info records are read for STK, FluoView, MicroManager, and NIH image formats.

TIFF, the Tagged Image File Format, is under the control of Adobe Systems. BigTIFF allows for files greater than 4 GB. STK, LSM, FluoView, SEQ, GEL, and OME-TIFF, are custom extensions defined by MetaMorph, Carl Zeiss MicroImaging, Olympus, Media Cybernetics, Molecular Dynamics, and the Open Microscopy Environment consortium respectively.

Via-bin
outils d'analyse volumétrique d'images
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VIA est un ensemble de programmes d'analyse volumétrique d'images fonctionnelles et structurales (médicales). L'ensemble comprend divers outils qui vont de la simple gestion de données en passant par des visionneuses, jusqu'à des transformations d'images complexes.

Tous les outils travaillent sur des données au format VISTA. Le paquet contient plusieurs convertisseurs de et vers de nombreux formats d'images tels que PNG, PGM ou PNM.

Voxbo
traitement, analyse statistique et affichage de données d’imagerie cérébrale
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Il s’agit d’une boîte à outils pour l’analyse des expériences d’imagerie par résonance magnétique fonctionnelle (principalement fMRI) et la cartographie basée sur les voxels de comportement de lésion. VoxBo prend en charge le GLM modifié (pour les données autocorrélées), ainsi que le GLM standard pour les données non autocorrélées. La boîte à outils est conçue pour être interopérable avec entre autres, AFNI, FSL et SPM.

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Vrrender
DICOM viewer
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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 pour VTK – outils
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Ce paquet fournit un ensemble de classes pour gérer les fichiers et métadonnées DICOM avec VTK, et quelques utilitaires pour interroger et convertir les fichiers DICOM.

Il s’agit d’outils en ligne de commande.

Xmedcon
outil de conversion d’image médicale (DICOM, ECAT…) – interface graphique
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Ce projet a pour but la conversion d’image médicale (Medical Image Conversion). Publié sous licence (L)GPL, il est livré avec le code source C complet de la bibliothèque, un outil flexible en ligne de commande et une interface graphique soignée utilisant la boîte à outils GTK+. Les formats pris en charge actuellement sont : Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 et PNG.

Le programme permet aussi de lire des fichiers non pris en charge et non compressés, pour afficher les valeurs de pixel ou pour extraire ou réorganiser les images indiquées. Il est possible de récupérer les tableaux d’image binaire ou ASCII RAW ou d’écrire des PNG pour des applications de bureau.

Il s’agit de la version du programme pour X basée sur GTK+. Le traitement doit être fait fichier par fichier.

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Official Debian packages with lower relevance

Cmtk
boîte à outils de morphométrie computationnelle
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Boîte à outils logicielle pour la morphométrie computationnelle d'images biomédicales, CMTK comprend un ensemble d'outils en ligne de commande et de bibliothèques dorsales généralistes pour le traitement et les E/S.

Les outils en ligne de commande fournissent principalement les fonctionnalités suivantes : enregistrement (affine et non rigide ; simple et multicanal ; par paire et par groupe), collection d'images (estimation du champ de distorsion MR ; correction d'artefacts d'images entrelacées), traitement (filtres ; combinaison de segments avec voting et STAPLE ; moyenne basée sur la forme), statistiques (tests t ; régression linéaire générale).

Please cite: T. Rohlfing: User Guide to The Computational Morphometry Toolkit. (eprint) The Insight Journal (2009)
Registry entries: SciCrunch 
Connectomeviewer
analyse interactive et visualisation pour la connectomique MR
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Connectome Viewer est un environnement extensible, scriptable et en python de visualisation et d'analyse (de réseau) en neuro-imagerie et connectomique.

Grâce au format de fichier Connectome, divers types de données tels que les réseaux, surfaces, volumes, traces et métadonnées sont gérés et intégrés. Connectome Viewer fait partie de la boîte à outils MR Connectome.

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 backend
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A full featured DICOM server that has been developed based on and heavily extending the public domain UCDMC DICOM code. Some possible applications of the ConQuest DICOM software are:

  • DICOM training and testing
  • Demonstration and research image archives
  • Image format conversion from a scanner with DICOM network access
  • DICOM image viewing and slide making
  • DICOM image selection, (limited) editing, and splitting and merging of series
  • Advanced scriptable image modification, filtering, forwarding and conversion
  • DICOM caching and archive merging

This package uses DBaseIII files as database backend.

Conquest-mysql
ConQuest DICOM Server - MySQL backend
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A full featured DICOM server that has been developed based on and heavily extending the public domain UCDMC DICOM code. Some possible applications of the ConQuest DICOM software are:

  • DICOM training and testing
  • Demonstration and research image archives
  • Image format conversion from a scanner with DICOM network access
  • DICOM image viewing and slide making
  • DICOM image selection, (limited) editing, and splitting and merging of series
  • Advanced scriptable image modification, filtering, forwarding and conversion
  • DICOM caching and archive merging

This package uses MySQL as database backend.

Conquest-postgres
ConQuest DICOM Server - PostgreSQL backend
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A full featured DICOM server that has been developed based on and heavily extending the public domain UCDMC DICOM code. Some possible applications of the ConQuest DICOM software are:

  • DICOM training and testing
  • Demonstration and research image archives
  • Image format conversion from a scanner with DICOM network access
  • DICOM image viewing and slide making
  • DICOM image selection, (limited) editing, and splitting and merging of series
  • Advanced scriptable image modification, filtering, forwarding and conversion
  • DICOM caching and archive merging

This package uses PostgreSQL as database backend.

Conquest-sqlite
ConQuest DICOM Server - SQLite backend
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A full featured DICOM server that has been developed based on and heavily extending the public domain UCDMC DICOM code. Some possible applications of the ConQuest DICOM software are:

  • DICOM training and testing
  • Demonstration and research image archives
  • Image format conversion from a scanner with DICOM network access
  • DICOM image viewing and slide making
  • DICOM image selection, (limited) editing, and splitting and merging of series
  • Advanced scriptable image modification, filtering, forwarding and conversion
  • DICOM caching and archive merging

This package uses SQLite as database backend.

Elastix
Boîte à outils pour le recalage rigide et non-rigide d'images
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Recalage d'image basé sur la boîte à outils réputée ITK (Insight Segmentation and Registration Toolkit). Le logiciel consiste en une collection d'algorithmes qui sont habituellement utilisés pour résoudre les problèmes de recalage d'images (médicales). La conception modulaire d'elastix permet à l'utilisateur de rapidement configurer, tester et comparer différentes méthodes de recalage pour un usage particulier. Une interface en ligne de commande autorise le traitement automatique de grandes quantités de jeux de données au moyen de scripts.

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
programmes de manipulation d'image — binaires
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ImageMagick est une suite logicielle pour créer, éditer et composer des images matricielles (« bitmaps »). Il peut lire, convertir et écrire des images dans de nombreux formats (plus de 100), notamment DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG et TIFF. Vous pouvez utiliser ImageMagick pour translater, retourner, refléter, tourner, redimensionner, découper et transformer des images, ajuster les couleurs, appliquer divers effets spéciaux ou encore écrire du texte, des lignes, des polygones, des ellipses et des courbes de Bézier. Toutes les manipulations peuvent être réalisées par des commandes d’interpréteur ou par une interface graphique X11 (display).

Ce paquet contient des liens vers les binaires spécifiques aux diverses tailles de canaux (bits par pixel) et les pages de manuel.

Il s'agit d'un paquet factice. Il peut être purgé ou supprimé en toute sécurité.

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Imview
Application de visualisation et d'analyse d'images
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Imview est une application qui :

  • affiche un grand nombre de formats d'images ;
  • affiche des images 2D ou 3D (en tranches) avec une fonctionalité de zoom ;
  • fonctionne pour des documents multi-spectre, animés ou multi-pages (par exemple : images satellites, piles TIFF, GIFs animés et fichiers multi-composants hétérogènes) ;
  • affiche tous les types de pixels (données entières ou en virgule flottante, codées sur 1 à 64 bits) ;
  • permet d'afficher des profils 1D quelconques d'images 2D (ou des tranches 2D d'images 3D) ;
  • supporte des cartes de couleurs quelconques pour tous types de pixels (i.e. : affichage en fausses couleurs) ;
  • fournit les outils classiques de manipulation d'images (luminosité/contraste, correction gamma, zoom, retaillage, rotation, etc.) ;
  • peut être contrôlé à distance à travers des sockets ou des commandes texte (ce qui permet de l'intégrer facilement dans différents systèmes d'analyse d'images) ;
  • peut charger les images depuis une socket ou un espace de mémoire partagée ;
  • et bien plus encore !
Please cite: Hugues Talbot: ImView: a portable image display application (eprint)
Openwalnut-qt4
Multi-modal medical and brain data visualization tool.
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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
Plugin to extend Orthanc with support of WADO and DICOMweb
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Orthanc DICOMweb is a plugin to Orthanc, the lightweight, RESTful Vendor Neutral Archive for medical imaging. It extends the Orthanc core with support of the WADO (now known as WADO-URI) and DICOMweb (QIDO-RS, STOW-RS, WADO-RS) standards.

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)
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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 plugin to import images from Orthanc
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This ImageJ plugin allows ImageJ to browse the content of an Orthanc server, then import 2D/3D DICOM images from Orthanc into ImageJ. Orthanc is a lightweight, RESTful DICOM server for healthcare and medical research.

This plugin simplifies the indexation of DICOM images if using ImageJ (e.g. for quality control of DICOM modalities, or for pedagogical use). There is also no need to carry on any complex network configuration, since the plugin directly uses the REST API of Orthanc. This makes its installation and its use quite straightforward.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Orthanc-mysql
Plugins to use MySQL or MariaDB as a database back-end to Orthanc
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Orthanc MySQL is a set of two plugins to Orthanc, a lightweight, RESTful Vendor Neutral Archive for medical imaging. These plugins override the default SQLite engine of Orthanc with a MySQL or MariaDB back-end. They bring scalability to Orthanc, making it enterprise-ready.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Orthanc-postgresql
Plugins to use PostgreSQL as a database back-end to Orthanc
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Orthanc PostgreSQL is a set of two plugins to Orthanc, a lightweight, RESTful Vendor Neutral Archive for medical imaging. These plugins override the default SQLite engine of Orthanc with a PostgreSQL back-end. They bring scalability to Orthanc, making it enterprise-ready.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Orthanc-webviewer
Web viewer of medical images for Orthanc
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Orthanc Web Viewer is a plugin to Orthanc, a lightweight, RESTful Vendor Neutral Archive for medical imaging. It extends Orthanc with an integrated Web viewer of DICOM images.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Paraview
application parallèle de visualisation
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ParaView est une application multi-plateforme au code source ouvert conçue pour visualiser des ensembles de données allant du plus petit au plus grand. Les buts du projet ParaView incluent les éléments suivants :

 – développer une application de visualisation, multi-plateforme et au code
   source ouvert ;
 – prendre en charge les modèles de calcul distribué pour traiter de grands
   ensembles de données ;
 – créer une interface pour l’utilisateur libre, adaptable et intuitive ;
 – développer une architecture extensible basée sur les normes ouvertes.

ParaView s’exécute aussi bien sur des systèmes distribués avec partage de mémoire que sur des systèmes avec processeur unique, et a été testé avec succès sur Windows, Mac OS X, Linux et sur diverses stations de travail Unix, des grappes et des supercalculateurs. Sous le capot, ParaView utilise la boîte à outils de visualisation « Visualization Toolkit » pour le traitement des données et le moteur de rendu et possède une interface écrite en Qt.

Pngquant
Utilitaire d'optimisation d'images PNG (Portable Network Graphics)
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pngquant est un utilitaire en ligne de commande pour réduire et ajuster des images PNG en couleurs réelles, particulièrement celles avec une couche alpha, vers une palette RGBA 8 bits (ou plus petite). De telles images sont généralement 2 à 4 fois plus légères que les version 32 bits, et la semi-transparence est correctement conservée. Ce paquet est particulièrement utile pour les sites internet et le développement pour la Playstation 2 dont l'un des formats de textures est basé sur des palettes RGBA (PNG non compressé, cependant). C'est la même technique qui est utilisée pour la plupart des images PNG transparentes de cette page http://www.libpng.org/pub/png/pngs-img.html. Les images résultantes sont généralement indiscernables des images d'origine en couleurs réelles.

Des outils comme pngcrush et optipng optimisent la compression, généralement sans perte, tandis que pngquant réduit le nombre de couleurs à 256 (ou moins) combinaisons RGBA, ce qui entraîne une perte de qualité.

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Science-workflow
workflow management systems useful for scientific research
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This task lists some packages providing workflow management systems useful for scientific research.

Trimage
interface graphique et en ligne de commande pour optimiser des fichiers d’image
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Trimage est une interface graphique et en ligne de commande multi-plateforme pour optimiser des fichiers d’image à l’aide de optipng, advpng, pngcrush et jpegoptim, selon le type de fichier (actuellement, les fichiers PNG et JPG sont pris en charge). Tous les fichiers d’image sont compressés sans perte au taux de compression maximal possible. Trimage procure diverses fonctions d’entrée pour adaptation au flux de travail : une boîte simple de dialogue de fichier, le glisser-déposer et des options diverses de ligne de commande.

Debian packages in contrib or non-free

Bart-cuda
tools for computational magnetic resonance imaging
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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
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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
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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
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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
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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
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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
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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
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License: free
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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
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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
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A variety of applications providing segmentation, registration, and other medical image processing algorithms such as MRI bias field correction.

Jist
Java Image Science Toolkit
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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
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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
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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
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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
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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
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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
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License: free
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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
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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
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License: free
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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
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License: XNAT_SLA
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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