Debian Med Project
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Summary
Imaging development
paquets Debian Med de traitement et visualisation d'images —⋅développement

Ce métapaquet installera les paquets Debian qui peuvent être utiles pour développer des applications pour le traitement et la visualisation d'images médicales.

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 development packages

Official Debian packages with high relevance

Cimg-dev
bibliothèque puissante de calcul d'images
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La bibliothèque CImg est une boîte à outils C++ fournissant de simples classes et fonctions permettant de charger, enregistrer, traiter et afficher des images dans votre propre code C++. Il vient sous la forme d'un seul fichier en-tête CImg.h devant être inclus dans votre programme source. Il contient de puissants algorithmes de traitement d'images pour charger/enregistrer/redimensionner/pivoter, filtrer, dessiner des objets (texte, lignes, faces, ellipses, ...), etc.

Les images sont instanciées par une classe capable de représenter des images en 4 dimensions (de signaux scalaires à une dimension aux volumes 3D de pixels représentés par un vecteur), avec des modèles de type de pixel. Il dépend d'un nombre minimal de bibliothèques : vous pouvez le compiler avec une bibliothèque C standard. Pas besoin de bibliothèque exotique ou de dépendance complexe.

The package is enhanced by the following packages: cimg-doc cimg-examples
Ctn-dev
Fichiers de développement pour CTN, une implémentation de DICOM
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DICOM est un standard pour le stockage, l'annotation et l'utilisation en réseau d'images dans le monde de l'imagerie médicale.

Ce paquet inclut les fichiers d'en-têtes et les bibliothèques statiques utilisées pour créer des programmes qui utilisent la bibliothèque 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)
Gmic
Manipulation générique d’image « Magic for Image Computing » de GREYC
Maintainer: Bernd Zeimetz
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G'MIC est cadre d’application ouvert et plein de fonctionnalités pour le traitement d’image, fournissant différentes interfaces utilisateur pour convertir, manipuler, filtrer ou visualiser une collection d’images, depuis des signaux scalaires 1d jusqu’à des séquences 3d+t d’images volumétriques multispectrales.

Ce paquet fournit les binaires du gmic autonome.

Screenshots of package gmic
Libbart-dev
fichiers de développement pour BART
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BART (« Berkeley Advanced Reconstruction Toolbox ») est un environnement libre de reconstruction d'images pour l'imagerie par résonance magnétique computationnelle.

Ce paquet fournit les en-têtes et les bibliothèques statiques.

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.
Libbiosig-dev
bibliothèque d'entrées sorties de données biomédicales –⋅fichiers de développement
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BioSig est une bibliothèque pour accéder à des fichiers dans plusieurs formats de données biomédicales (incluant EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro et TMS32). La liste complète des formats de fichiers pris en charge est disponible à l'adresse http://pub.ist.ac.at/~schloegl/biosig/TESTED.

Ce paquet fournit les en-têtes de développement et une bibliothèque statique.

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)
Libcamitk-dev
boîte à outils d'intervention médicale assistée par ordinateur – fichiers de développement
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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.

Ce paquet fournit les fichiers de développement nécessaires pour construire les applications CamiTK. Ce paquet fournit également l'assistant CamiTK pour créer de nouvelles extensions.

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)
Libcifti-dev
development files for CiftiLib
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CIFTI (Connectivity Informatics Technology Initiative) standardizes the file formats for storage of connectivity data. These formats are developed by the Human Connectome Project and other interested parties.

CiftiLib is a C++ library for CIFTI-1 and CIFTI-2 file I/O, supporting both on-disk and in-memory access. It also provides facilities for reading and writing generic NIfTI-1 and NIfTI-2 files.

This package provides the development files.

Libedf-dev
European Data Format library - devel
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EDFlib is a programming library for C/C++ to read/write EDF+/BDF+ files. (It also reads old-type EDF/BDF files.) EDF means European Data Format. BDF is the 24-bits version of EDF.

Headers and shared libraries for edflib.

Libgdcm2-dev
bibliothèques de développement et fichiers d'en-tête pour Grassroots DICOM
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Grassroots DiCoM est une bibliothèque C++ pour les fichiers médicaux DICOM. Elle est automatiquement adaptée pour python/C#/Java (en utilisant swig). Elle gère les fichiers RAW, JPEG (avec et sans pertes), J2K, JPEG-LS, RLE et deflate.

Ce paquet contient les bibliothèques statiques et les fichiers d'en-tête pour libgdcm. Ils ne sont pas nécessaires pour utiliser GDCM, mais sont indispensable pour lier des programmes ou greffons à libgdcm.

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)
Libgdf-dev
IO library for the GDF -- development library
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GDF (General Dataformat for Biosignals) is intended to provide a generic storage for biosignals, such as EEG, ECG, MEG etc.

This package provides the header files.

Please cite: Alois Schlögl: GDF – A general dataformat for BIOSIGNALS. The Computing Research Repository abs/cs/0608052 (2006)
Libgiftiio-dev
IO library for the GIFTI cortical surface data format - headers
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GIFTI is an XML-based file format for cortical surface data. This reference IO implementation is developed by the Neuroimaging Informatics Technology Initiative (NIfTI).

This package provides the header files and static library.

Registry entries: SciCrunch 
Libinsighttoolkit5-dev
boîte à outils de traitement d'image pour le recalage et la segmentation - développement
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ITK est une boîte à outils libre pour le recalage et la segmentation. La segmentation consiste à identifier et classer des données trouvées dans un échantillon numérisé d'une représentation. Typiquement, la représentation échantillonnée est une image acquise par une instrumentation médicale telle que les imageurs de tomodensitométrie ou IRM. Le recalage consiste à aligner ou développer des correspondances entre les données. Dans un environnement médical par exemple, une image de tomodensitométrie peut être alignée avec une image IRM afin de combiner les informations contenues dans les deux.

Ce paquet contient les fichiers nécessaires pour bâtir vos propres applications ITK.

Libismrmrd-dev
development files 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 development files.

Libmaxflow-dev
Development files for the maxflow-mincut algorithm
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This library implements an efficient minimum cut/maximum flow algorithms on graphs that can be used for exact or approximate energy minimization in low-level vision. The algorithm provides a high performance that makes near real-time performance possible. This package provides the development files for the library.

Please cite: Yuri Boykov and Vladimir Kolmogorov: An Experimental Comparison of Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision. (eprint) IEEE Transactions on Pattern Analysis and Machine Intelligence 6(9):1124 - 1137 (2004)
Libmdc2-dev
Medical Image (DICOM, ECAT, ...) conversion tool (development)
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This project stands for Medical Image Conversion. Released under the (L)GPL, it comes with the full C-source code of the library, a flexible command line utility and a neat graphical front-end using the GTK+ toolkit. The currently supported formats are: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 and PNG.

Static library, include files and documentation for developers.

Libmia-2.4-dev
library for 2D and 3D gray scale image processing, development files
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libmia comprises a set of libraries and plug-ins for general purpose 2D and 3D gray scale image processing and basic handling of triangular meshes. The libraries provide a basic infrastructure and generic algorithms, that can be specialized by specifying the appropriate plug-ins. This package provides the development files for the library.

The package is enhanced by the following packages: libmia-2.4-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)
Libmialm-dev
Development files for the MIA landmark library
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This library implements handling for landmarks and 3D view positioning for optimal landmark visibility, and in-and output of these landmarks. This library is part of the MIA tool chain for medical image analysis. This package contains the development files - headers, shared libraries, and pkg-config files.

Please cite: Gert Wollny, Fritjhoff Kruggel, Thomas Hierl and Jörg Hendricks: Assessment, validation, and visualisation of bony changes in crano-facial surgery. (eprint) (2004)
Libmiaviewit-dev
development files for the 3D visualization library
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The MIA addon library for simple 3D visualizations provides an interface for the visualization of 3D data generated by using mia-tools These are the development files.

Libminc-dev
environnement de développement pour le format d'images médicales MNI
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Ce paquet fournit la bibliothèque et les en-têtes pour libminc2 et libminc_io.

Le format Minc est un format très souple pour les images médicales. La version 1 de Minc se base sur le format générique NetCDF. La version 2 se base sur le format HDF. Cette bibliothèque gère les deux formats. Dans chaque cas, le format est simple, auto-descriptif, extensible, portable et multidimensionnel, avec des interfaces de programmation pour l'accès bas niveau aux données et la manipulation haut niveau de volumes. Les bibliothèques sont utilisées par une gamme d'outils génériques de manipulation d'images. Le format, les bibliothèques et les outils sont conçus pour être utilisés dans un environnement de recherche sur les images médicales : elles sont simples et puissantes et n'ont pas pour objectif de fournir une interface élégante aux utilisateurs.

Libnifti2-dev
IO libraries for the NIfTI-1 data format (development)
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Niftilib is a set of i/o libraries for reading and writing files in the NIfTI-1 data format. NIfTI-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images.

This package provides the header files and static libraries of libnifti2.

Libodil-dev
C++11 library for the DICOM standard (development files)
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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 development files.

Libopencv-dev
fichiers de développement pour opencv
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Il s'agit d'un métapaquet qui fournit le paquet de développement nécessaire au développement d'OpenCV (Open Computer Vision).

La bibliothèque Open Computer Vision est un ensemble d'algorithmes et de codes d'exemple pour divers problèmes de vision par ordinateur. La bibliothèque est compatible avec IPL (Image Processing Library d'Intel) et, s'il est disponible, IPP d'Intel (Integrated Performance Primitives) pour de meilleures performances.

OpenCV fournit des types de données et des opérateurs portables de bas niveau et un ensemble de fonctionnalités de haut niveau pour l'acquisition vidéo, le traitement et l'analyse d'image, l'analyse structurale, l'analyse du mouvement et le suivi d'objet, la reconnaissance d’objet, la calibration de caméra et la reconstruction⋅3D.

Please cite: Gary Bradski and Adrian Kaehler: Learning OpenCV: Computer Vision with the OpenCV Library (2008)
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Libopenigtlink-dev
Open IGT Link is a simple network protocol - development
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Open IGT Link is a simple network protocol intended for trackers, robots and other devices to send data to the main application. Some devices might also accept commands.

For example applications may include:

  • Stereotactic surgical guidance using optical position sensor and medical image visualization software.
  • Intraoperative image guidance using real-time MRI and medical image visualization software
  • Robot-assisted intervention using robotic device and surgical planning software

This package contains the development files needed to build your own IGT applications.

Libopenslide-dev
fichiers de développement pour la bibliothèque 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 fichiers de développement nécessaires à la construction d'application avec OpenSlide.

Libpapyrus3-dev
DICOM compatible file format library
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PAPYRUS 3.0 file format based on the new DICOM 3.0 Standard addresses the open interchange of medical images in files or on removable storage media. This specific implementation of the DICOM standard is intended as a generic solution for interchange of multi-modality medical images on removable media. It can also be used for convenient exchange of image data between different computer systems through industry standard file transfer mechanisms. Finally it can also be used for storage and archival of medical image data in a DICOM compatible format.

This package contains the libraries needed to run PAPYRUS 3.0 applications.

Please cite: O. Ratib, H. Hoehn, C. Girard and C. Parisot: PAPYRUS 3.0: DICOM-compatible file format. (PubMed,eprint) Medical Informatics 19(2):171-178 (1994)
Libsight-dev
Sight header files
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The Surgical Image Guidance and Healthcare Toolkit aims to ease the creation of applications based on medical imaging. It includes various features such as 2D and 3D digital image processing, visualization, augmented reality and medical interaction simulation. It runs on many different environments (Windows, Linux, macOS), is written in C++, and features rapid interface design using XML files.

Sight was formerly known as FW4SPL. It was renamed in 2018, firstly to make its purpose clearer, and secondly as part of a major change in design and in the governance of the development team.

This package contains the development files.

Libsimpleitk1-dev
development files for SimpleITK
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SimpleITK is an image analysis toolkit with a large number of components supporting general filtering operations, image segmentation and registration. It is built on top of the Insight Segmentation and Registration Toolkit ITK with the intent of providing a simplified interface to ITK. SimpleITK itself is written in C++ but is available for a large number of programming languages.

This package provides the development files.

Libteem-dev
Tools to process and visualize scientific data and images - development
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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 provides the Teem header files required to compile C++ programs that use Teem to do 3D visualisation.

Libvigraimpex-dev
development files for the C++ computer vision library
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Vision with Generic Algorithms (VIGRA) is a computer vision library that puts its main emphasis on flexible algorithms, because algorithms represent the principle know-how of this field. The library was consequently built using generic programming as introduced by Stepanov and Musser and exemplified in the C++ Standard Template Library. By writing a few adapters (image iterators and accessors) you can use VIGRA's algorithms on top of your data structures, within your environment.

This package contains the header and development files needed to build programs and packages using VIGRA.

Libvistaio-dev
Development files for the libvistaio library
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Vistaio is a library that handles loading and storing of data in a cross-platform manner. Its virtue is that the otherwise binary files provide an ascii header that makes it easy to get information about the contens of a file. It supports a variety of data types like images, vector fields and graphs. This is the development package containing the header files, and pkg-config script, and man pages.

Libvolpack1-dev
fast volume rendering library (development package)
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VolPack is a software library for fast, high-quality volume rendering with this features:

  • Renders data sampled on a regular, three-dimensional grid.
  • Supports user-specified transfer functions for both opacity and color.
  • Provides a shading model with directional light sources, multiple material types with different reflective properties, depth cueing, and shadows.
  • Produces color (24 bits/pixel) or grayscale (8 bits/pixel) renderings, with or without an alpha channel.
  • Supports arbitrary affine view transformations.
  • Supports a flexible data format that allows an arbitrary C structure to be associated with each voxel.

This is the development package.

Libvtk-dicom-dev
DICOM for VTK - dev
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This package contains a set of classes for managing DICOM files and metadata from within VTK, and some utility programs for interrogating and converting DICOM files.

Development headers

Libvtk9-dev
VTK header files
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The Visualization Toolkit (VTK) is an open-source software system for 3D computer graphics, image processing, and visualization.

This package provides the VTK header files required to compile C++ programs that use VTK to do 3D visualisation.

Please cite: Will Schroeder, Ken Martin and Bill Lorensen: The Visualization Toolkit (4th ed.) (2006)
Libxdf-dev
C++ library for loading XDF files (headers and static lib)
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Libxdf is a cross-platform C++ library for loading multimodal, multi- rate signals stored in XDF files. Libxdf is used in the biosignal viewing application SigViewer. It can also be integrated into other C++ applications.

This package contains the header files and the static library

Octave-bart
liaisons Octave pour BART
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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 les liaisons Octave pour BART.

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.
Octave-dicom
manipulate DICOM files in Octave
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Digital communications in medicine (DICOM) is an information standard, originally created for image transfer, which now deals with a large range of medical data.

This package provides functions to read and (eventually) write DICOM files in Octave, a scientific computation software. The functions in the package are intended to have similar usage as the dicom functions in the Matlab Image Processing Toolbox. In Octave they are separate: most image package users will not use dicom, and its dependency might be considered troublesome.

This Octave add-on package is part of the Octave-Forge project.

Octave-gdf
bibliothèque IO pour GDF – interface pour Octave
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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 les liaisons d’Octave pour libgdf.

Please cite: Alois Schlögl: GDF – A general dataformat for BIOSIGNALS. The Computing Research Repository abs/cs/0608052 (2006)
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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Python3-biosig
liaisons Python⋅3 à la bibliothèque BioSig
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Ce paquet fournit les liaisons Python⋅3 à la bibliothèque BioSig. Son objectif principal est de fournir une interface d'entrées sorties à une grande variété de formats de fichiers biomédicaux, comprenant entre autres SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF et EDF.

Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
Python3-brian
simulator for spiking neural networks
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Brian is a clock-driven simulator for spiking neural networks. It is designed with an emphasis on flexibility and extensibility, for rapid development and refinement of neural models. Neuron models are specified by sets of user-specified differential equations, threshold conditions and reset conditions (given as strings). The focus is primarily on networks of single compartment neuron models (e.g. leaky integrate-and-fire or Hodgkin-Huxley type neurons). Features include:

  • a system for specifying quantities with physical dimensions
  • exact numerical integration for linear differential equations
  • Euler, Runge-Kutta and exponential Euler integration for nonlinear differential equations
  • synaptic connections with delays
  • short-term and long-term plasticity (spike-timing dependent plasticity)
  • a library of standard model components, including integrate-and-fire equations, synapses and ionic currents
  • a toolbox for automatically fitting spiking neuron models to electrophysiological recordings
Please cite: D.F. Goodman and R. Brette: Brian: A Simulator for Spiking Neural Networks in Python. (PubMed,eprint) Frontiers in Neuroinformatics 2(5) (2008)
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-gdcm
Grassroots DICOM Python bindings
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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.

Python bindings to the GDCM DICOM library.

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)
Python3-imageio
library for reading and writing image data (Python 3)
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Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats.

This package provides the library for Python 3.

Python3-mia
Python-3 bindings for the MIA image processing library
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MIA comprises a set of tools, libraries, and plug-ins for general purpose 2D and 3D gray scale image processing and basic handling of triangular meshes. The libraries provide a basic infrastructure and generic algorithms, that can be specialized by specifying the appropriate plug-ins. This package provides the Python-3 bindings.

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 500 (2013)
Python3-mne
Python modules for MEG and EEG data analysis
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This package is designed for sensor- and source-space analysis of MEG and EEG data, including frequency-domain and time-frequency analyses and non-parametric statistics.

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-openslide
enveloppe Python 3 de lecture des fichiers d'images « Whole-slide »
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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 le module Python 3 nécessaire à l'exécution d'applications OpenSlide.

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-pyxnat
Interface to access neuroimaging data on XNAT servers
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pyxnat is a simple Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or Python scripts to process the data. It features:

  • resources browsing capabilities
  • read and write access to resources
  • complex searches
  • disk-caching of requested files and resources
Python3-simpleitk
Python bindings for SimpleITK
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SimpleITK is an image analysis toolkit with a large number of components supporting general filtering operations, image segmentation and registration. It is built on top of the Insight Segmentation and Registration Toolkit ITK with the intent of providing a simplified interface to ITK. SimpleITK itself is written in C++ but is available for a large number of programming languages.

This package provides the Python bindings.

Python3-torchvision
Datasets, Transforms and Models specific to Computer Vision
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The torchvision package consists of popular datasets, model architectures, and common image transformations for computer vision.

Python3-vigra
Python3 bindings for the C++ computer vision library
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Vision with Generic Algorithms (VIGRA) is a computer vision library that puts its main emphasis on flexible algorithms, because algorithms represent the principle know-how of this field. The library was consequently built using generic programming as introduced by Stepanov and Musser and exemplified in the C++ Standard Template Library. By writing a few adapters (image iterators and accessors) you can use VIGRA's algorithms on top of your data structures, within your environment.

This package exports the functionality of the VIGRA library to Python3.

R-cran-rniftilib
GNU/R interface to NIFTICLIB
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R interface to nifticlib (nifticlib-2.0.0) (read/write ANALYZE(TM)7.5/NIfTI-1 volume images)

Please cite: Gesa Hartwigsen, Annette Baumgaertner, Cathy J. Price, Maria Koehnke, Stephan Ulmer and Hartwig R. Siebner: Phonological decisions require both the left and right supramarginal gyri. (PubMed,eprint) Proceedings of the National Academy of Sciences of the United States of America 107(38):16494-9 (2010)

Official Debian packages with lower relevance

Libcamp-dev
bibliothèque C++ généraliste de réflexion –⋅fichiers de développement
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CAMP est une bibliothèque C++ généraliste de réflexion développée par Technogerma Systems France (http://www.tegesoft.com). Elle fournit une abstraction pour la plupart des concepts⋅C++ de haut niveau⋅:

 –⋅classes⋅;
 –⋅énumérations⋅;
 –⋅propriétés⋅;
 –⋅fonctions⋅;
 –⋅objets⋅;
 –⋅variables.
En enveloppant tous ces concepts dans des structures abstraites, CAMP

fournit une couche supplémentaire de flexibilité aux programmes et leur permet d'exposer complètement leurs structures de données au moment de l'exécution. De nombreuses applications peuvent tirer avantage de CAMP, afin d'automatiser des tâches qui, autrement, demanderaient beaucoup de travail. Par exemple, CAMP peut être utilisée pour exposer et modifier des attributs d'objet avec une interface utilisateur graphique. Elle peut aussi être utilisée pour créer des liaisons automatiques de classes⋅C++ à des langages de script comme Python ou Lua. La sérialisation d'objets aux formats XML, texte ou binaire pourrait être une autre utilisation. Il est aussi possible de combiner tous ces exemples pour obtenir une interface cohérente et puissante pour la manipulation d'objets en dehors du code⋅C++.

Ce paquet fournit les fichiers nécessaires au développement.

Libeegdev-dev
Biosignal acquisition device library (Development files)
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eegdev is a library that provides a unified interface for accessing various EEG (and other biosignals) acquisition systems. This interface has been designed to be both flexible and efficient. The device specific part is implemented by the means of plugins which makes adding new device backend fairly easy even if the library does not support them yet officially.

The core library not only provides to users a unified and consistent interface to the acquisition device but it also provides many functionalities to the device backends (plugins) ranging from configuration to data casting and scaling making writing new device backend an easy task.

This library is particularly useful to handle the acquisition part of a Brain Computer Interface (BCI) or any realtime multi-electrode acquisition in neurophysiological research.

This package contains the files needed to compile and link programs which use eegdev. It provides also the headers needed to develop new device plugins. The manpages and examples are shipped in this package.

Libfreeimage-dev
Support library for graphics image formats (development files)
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FreeImage is an Open Source C/C++ library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to use, fast, multithreading safe, and cross-platform (works both with Linux, 32 bit Windows and Mac OS X).

This package contains the headers and static libraries needed to develop programs using FreeImage.

Libics-dev
Image Cytometry Standard file reading and writing (devel)
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This is the reference library for ICS (Image Cytometry Standard), an open standard for writing images of any dimensionality and data type to file, together with associated information regarding the recording equipment or recorded subject.

This package contains the libraries needed to build ICS applications.

Liblimereg-dev
Library for lightweight image registration [development files]
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Liblimereg automatically aligns two images with similar content to each other. Given two 2D images the algorithm returns the rigid transformation parameters detected for the best possible alignment (shift, rotation). There are also functions for a rigid image transformation (shift, rotation) and for creating a difference image out of two images.

This package contains the static library and the header file.

Libnifti-doc
Documentaion pour la bibliothèque API 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 à résonance magnétique (MRI) et des images de cerveau MRI fonctionnelles (fMRI).

Ce paquet fournit la documentation de référence pour la bibliothèque API.

Libxdffileio-dev
Library to read/write EEG data file formats (development files)
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xdffileio is a library that provides a unified interface for writing and reading various biosignal file formats in realtime (i.e. streaming). It has been designed to provide a flexible, consistent and generic interface to all supported file formats while minimizing the overhead the function calls: the heaviest operations (type casting, scaling and formatting) are offloaded into a separated thread. This design makes its particularly suitable to be directly used in a data acquisition loop (like in electrophysiology recording or in Brain-Computer Interfaces (BCI)).

The genericity of the interface makes trivial various operations like transformation of a recorded file or its conversion to another file format. xdffileio currently supports EDF, BDF, GDF1 and GDF2 file formats and more will be added in future.

This package contains the files needed to compile and link programs which use xdffileio.

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.

Debian packages in contrib or non-free

Libvmtk-dev
shared links and header files for vmtk
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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.

This package contains header files and shared library links.

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)
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Python-vmtk
Python interface for vmtk
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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.

This package provides the Python interface for vmtk.

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

Emokit
Emotiv EPOC headset Python interface
License: BSD-3
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Language: Python, C

Emotive is an interface to a budget Emotiv EPOC EEG headset.

Libbio-formats-java
reading and writing proprietary microscopy image data and metadata
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Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats.

Bio-Formats's primary purpose is to convert proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format.

Remark of Debian Med team: This library would enhance the package imagej
Libctk-dev
toolkit for medical imaging application development - devel
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The goals of CTK are as follows:

  • Provide a unified set of basic programming constructs that are useful for medical imaging applications development
  • Facilitate the exchange and combination of code and data
  • Document, integrate, and adapt successful solutions
  • Avoid the duplication of code and data
  • Continuously extend to new tasks within the scope of the toolkit (medical imaging) without burdening existing tasks

This package provides the CTK header files required to compile C++ programs that use CTK.

Libopenmeeg-dev
openmeeg library -- development files
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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 static libraries and header files.

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)
Libopenslide-java
java wrapper for reading whole slide image files
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OpenSlide is a C library that provides a simple interface to read whole-slide images also known as virtual slides.

Whole-slide images, also known as virtual slides, are large, high resolution images used in digital pathology. Reading these images using standard image tools or libraries is a challenge because these tools are typically designed for images that can comfortably be uncompressed into RAM or a swap file. Whole-slide images routinely exceed RAM sizes, often occupying tens of gigabytes when uncompressed. Additionally, whole-slide images are typically multi-resolution, and only a small amount of image data might be needed at a particular resolution.

This library currently supports:

  • Trestle (.tif)
  • Hamamatsu (.vms, .vmu)
  • Aperio (.svs, .tif)
  • MIRAX (.mrxs)
  • Generic tiled TIFF (.tif)

This package contains the java module needed to run OpenSlide applications.

Libvia-dev
library for volumetric image analysis
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VIA is a volumetric image analysis suite. The included libraries provide about 70 image analysis functions.

This package provides the header files and static libraries of vialib, vxlib and viaio.

Unofficial packages built by somebody else

Libmni-perllib-perl
The MNI Perl Library
Responsible: NeuroDebian Team
License: Artistic License

Collection of various Perl module used by other MNI software packages.

Remark of Debian Med team: There was some previous work on this software which is stalled currently

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

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 201414