Debian Med Project
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Summary
Imaging development
Debian Med-billedbehandlings- og visualiseringspakker - pakkeudvikling

Denne metapakke vil installere Debianpakker, som kan være nyttige for udvikling af programmer til medicinsk billedbehandling og visualisering.

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
Funktionsrigt billedbehandlingsbibliotek
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CImg biblioteket er en C++-værktøjskasse, som tilbyder simple klasser og funktioner til at indlæse, gemme, behandle og fremvise billeder i din egen C++-kode. Det består blot af en enkelt teksthovedfil CImg.h, som skal inkluderes i dit kildeprogram. Det indeholder nyttige billedbehandlingsalgoritmer til at indlæse/gemme, skalere/rotere, filtrere, objekttegne (tekst, linjer, ansigter, ellipser ...) osv.

Billeder instantieres gennem en klasse som er i stand til at repræsentere billeder i op til 4 dimensioners bredde (fra 1-D skalar-signaler til 3-D volumener af billedpunkter med vektorværdier), med skabelontyper for billedpunkter. Det forudsætter et minimalt antal af biblioteker: Du kan kompilere det kun med standardbiblioteker for C. Intet behov for eksotiske biblioteker og komplekse afhængigheder.

The package is enhanced by the following packages: cimg-doc cimg-examples
Ctn-dev
Udviklerfiler til Central Test Node, en DICOM implementering
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DICOM er en standard for billede-opbevaring, beskrivelse, og netværksstyring. Det er meget udbredt til medicinsk billedhåndtering.

Denne pakke inkluderer header-filerne og de statiske biblioteker brugt til oprettelse af programmer som gør brug af CTN-biblioteket.

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
GREYC's Magic for Image Computing
Maintainer: Bernd Zeimetz
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G'MIC er en åben ramme med alle funktioner for billedbehandling, der tilbydere flere forskellige brugergrænseflader til at konvertere, manipulere, filtrere og visualisere generiske billeddatasæt, fra 1D scalarsignaler til 3d+t-sekvenser for flerspektrale volumetriske billeder.

Denne pakke indeholder den uafhængige gmic-binære fil.

Screenshots of package gmic
Libbart-dev
Udviklingsfiler for BART
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Berkeley Advanced Reconstruction Toolbox (BART) er en fri ramme til billedrekonstruktion for Computational Magnetic Resonance Imaging.

Denne pakke tilbyder teksthoveder og statiske biblioteker.

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
I/O-bibliotek for biomedicinske data - udviklingsfiler
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BioSig er et bibliotek for adgang til filer i flere forskellige biomedicinske dataformater (inklusive EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro, TMS32). Den fulde liste over understøttede filformater er tilgængelig på http://pub.ist.ac.at/~schloegl/biosig/TESTED .

Denne pakke tilbyder hovedfiler og det statiske bibliotek.

Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
Libcamitk-dev
Computer Assisted Medical Intervention Tool Kit - udvikling
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Hjælper forskere og klinikassistenter med nemt og hurtigt at samarbejde i prototypefremstillingen af CAMI-programmer, som har medicinske billeder, kirurgisk navigation og biomekaniske simuleringer.

Denne pakke indeholder udviklingsfiler krævet til at bygge CamiTK-programmer. Denne pakke tilbyder også CamiTK-guideprogrammet til at oprette nye udvidelser.

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-bibliotek - udvikling
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EDFlib er et programmeringsbibliotek for C/C++ til at læse/skrive EDF+/BDF+-filer. (Læser også ældre EDF/BDF-filer). EDF betyder European Data Format (europæisk dataformat). BDF er 24-bit versionen af EDF.

Teksthoveder og delte biblioteker for edflib.

Libgdcm2-dev
Grassroots DICOM-udviklingsbiblioteker og teksthoveder
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Grassroots DICOM er et C++-bibliotek for DICOm-medicinske filer. Den omsluttes automatisk om python/C#/Java (med swig). Den understøtter RAW,JPEG (med og uden kvalitetstab),J2K,JPEG-LS, RLE og deflated.

Teksthoveder og statiske biblioteker for libgdcm. Disse er ikke krævet for at bruge GDCM, men er krævede for at bygge udvidelsesmoduler eller programmer som lænker mod 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-bibliotek for GDF'en - udviklingsbiblioteket
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GDF (General Dataformat for Biosignals) er lavet for at tilbyde et generisk lager for biosignaler, såsom EEG, ECG, MEG etc.

Denne pakke tilbyder teksthovedfilerne.

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
Værktøjssæt til billedbehandling for registrering og segmentering - udvikling
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ITK er et programværktøjssæt, i åben kildekode, for udførelse af registrering og segmentering. Segmentering er processen med at identificere og klassificere data fundet i en digitalt samlet repræsentation. Typisk er den samlede repræsentation et billede indhentet fra medicinske instrumenter såsom CT- eller MRI-skannere. Registrering er opgaven med at justere eller finde ligheder mellem dataene. For eksempel, i det medicinske miljø, kan en CT-skan justeres med en MRI-skan for at kombinere informationen indeholdt i begge.

Denne pakke indeholder udviklingsfilerne krævet for at bygge dine egne ITK- programmer.

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

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

Denne pakke tilbyder udviklingsfilerne.

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
Udviklingsfiler for 3D-visualiseringsbiblioteket
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MIA addon-biblioteket for simple 3D-visualiseringer tilbyder en grænseflade for visualisering af 3D-data oprettet ved at bruge mia-tools. Dette er udviklingsfilerne.

Libminc-dev
MNI medical image format development environment
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This package contains the library and headers for libminc2 and libminc_io.

The Minc file format is a highly flexible medical image file format. Minc version 1 is built on top of the NetCDF generalized data format. Minc version 2 is built on top of the HDF data format. This library handles both formats. In each case the format is simple, self-describing, extensible, portable and N-dimensional, with programming interfaces for both low-level data access and high-level volume manipulation. On top of the libraries is a suite of generic image-file manipulation tools. The format, libraries and tools are designed for use in a medical-imaging research environment : they are simple and powerful and make no attempt to provide a pretty interface to users.

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
Udviklingsfiler for opencv
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Dette er en metapakke, der tilbyder udviklingspakken nødvendig for udvikling af OpenCV (Open Computer Vision).

Open Computer Vision Library er en samling af algoritmer og eksempelkode for diverse computer vision-problemer. Biblioteket er kompatibelt med IPL (Intels Image Processing Library) og, hvis tilgængeligt, kan det bruger IPP (Intels Integrated Performance Primitives) for bedre ydelse.

OpenCV tilbyder datatyper og operatorer på lavt niveau, der kan flyttes samt et sæt af funktioner på højt niveau for videooptagelse, billedbehandling og analyse, strukturel analyse, bevægelsesanalyse og objektsporing, objektgenkendelse, kamerakalibrering og 3D-rekonstruktion.

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 er en simpel netværksprotokol - udvikling
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Open IGT Link er en simpel netværksprotokol lavet for trackere, robotter og andre enheder til at sende data til hovedprogrammet. Nogle enheder kan måske også acceptere kommandoer.

For eksempel kan programmer inkluderer:

  • Stereotaktisk kirurgisk vejledning ved hjælp af optisk positionssensor og programmer for medicinsk billedvisualisering.
  • Intraoperativ billedvejledning ved hjælp af realtids MRI og programmer for medicinsk billedvisualisering.
  • Robotassisteret indgriben ved hjælp af robotenhed og kirurgiske planlægningsprogrammer.

Denne pakke indeholder udviklingsfilerne krævet for at bygge dine egne IGT-programmer.

Libopenslide-dev
Development files for the OpenSlide library
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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:

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

This package contains development files needed to build OpenSlide applications.

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
Udviklingsfiler for C++-computervisionsbiblioteket
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Vision med generiske algoritmer (VIGRA) er et computervisionbibliotek, som placerer sit hovedfokus på fleksible algoritmer, da algoritmerne repræsenterer den grundlægende viden indenfor dette felt. Biblioteket blev som konsekvent bygget med brug af generisk programmering som introduceret af Stepanov og Musser og eksemplicificeret i C++ Standard Template Library. Ved at skrive nogle få adaptere (billediteratorer og accessorer) kan du bruge VIGRA's algoritmer oven på dine datastrukturer, inden i dit miljø.

Denne pakke indeholder teksthovederne og udviklingsfilerne krævet for at bygge programmer og pakker med brug af 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
Optegningsbibliotek for hurtig diskenhed - udviklingspakke
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VolPack er et softwarebibliotek til hurtigt, højkvalitets diskenhedsoptegning med disse funktioner:

  • Optegner data indsamlet på et regulært, tredimensionelt gitter.
  • Understøtter brugerangivne overførelsesfunktioner for både gennemsigtighed og farve.
  • Tilbyder en skyggemodel med retningsbestemte lyskilder, flere materialetyper med forskellige reflektive egenskaber, dybdeforslag og skygger.
  • Udarbejder farve- (24 bit/billedpunkt) eller gråskalaoptegninger (8 bit/billedpunkt), med eller uden en alfakanal.
  • Understøtter arbitrær affin visningstransformation.
  • Understøtter et fleksibelt dataformat som tillader at en arbitrær C-struktur kan forbindes med hver voxel.

Dette er udviklingspakken.

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

Udviklingsteksthoveder.

Libvtk9-dev
VTK-teksthovedfiler
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Visualization Toolkit (VTK) er et programsystem for 3D-computergrafik, billedbehandling og visualisering.

Denne pakke tilbyder VTK-teksthovedfiler krævet for at kompilere C++-programmer, som bruger VTK til at udføre 3D-visualisering.

Please cite: Will Schroeder, Ken Martin and Bill Lorensen: The Visualization Toolkit (4th ed.) (2006)
Libxdf-dev
C++-bibliotek til at indlæse XDF-filer - teksthoveder og statisk bibliotek
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Libxdf er et C++-bibliotek for flere platforme til at indlæse multimodal, multi-rate signaler lagret i XDF-filer. LIbxdf bruges i biosignal-visningsprogrammet SigViewer. Det kan også integreres i andre C++-programmer.

Denne pakke indeholder teksthovedfilerne og det statiske bibliotek.

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

Denne pakke tilbyder Octavebindingerne for 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
Manipuler DICOM-filer i Octave
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Digital communications in medicine (DICOM) er en informationsstandard, oprindelige oprettet for billedoverførsel, der nu håndterer et stort antal medicinske data.

Denne pakke tilbyder funktioner til at læse og (eventuelt) skrive DICOM-filer i Octave, et videnskabeligt beregningsprogram. Funktionerne i pakken er lavet til lignende brug som dicom-funktionerne i Matlab Image Processing Toolbox. I Octave er de adskilt: de fleste billedpakkebrugere vil ikke bruge dicom og dets afhængighed kan anses for at være problematisk.

Denne Octave-udvidelsespakke er en del af projektet Octave-Forge.

Octave-gdf
IO-bibliotek for GDF'en - Octavegrænseflade
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GDF (General Dataformat for Biosignals) er lavet for at tilbyde et generisk lager for biosignaler, såsom EEG, ECG, MEG etc.

Denne pakke tilbyder Octavebindinger for libgdf.

Please cite: Alois Schlögl: GDF – A general dataformat for BIOSIGNALS. The Computing Research Repository abs/cs/0608052 (2006)
Odin
Udvikl, simuler og kør magnetiske resonanssekvenser
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ODIN er en ramme for magnetisk resonansbilledoprettelse (MRI). Den dækker hele værktøjskæden for MRI, fra dataindhentelse på lavt niveau til billedrekonstruktion. Specielt forsøger programmet at lave hurtige prototyper for MRI-sekvenser. Sekvenserne kan programmeres via en højniveau, objektorienteret, C++-programmeringsgrænseflade. Den tilbyder avancerede sekvensanalyseværktøjer, såsom interaktiv plotning af k-space baner, en brugerflade for en hurtig compile-link-test cyklus og en funktionsrig MRI-simulator, som understøtter forskellige virtuelle prøver. For hurtig og fleksibel billedrekonstruktion indeholder ODIN en flertrådet databehandlingsramme, der kan tilpasses.

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Python3-biosig
Python 3-bindinger for BioSig-biblioteket
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Denne pakke tilbyder Python 3-bindinger for BioSig-biblioteket. Primære formål - I/O-grænseflade til en række biomedicinske filformater, inklusive men ikke begrænset til SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF.

Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
Python3-brian
Simulator for spikingneurale netværk
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Brian er en ur-drevet simulator for spikingneurale netværk. Det er designet med vægt på fleksibilitet og udvidelse, for hurtig udvikling og raffinement af neurale modeller. Neuronmodeller er specificeret af sæt af brugerangivne differentialligninger, tærskelbetingelser og nulstillingsbetingelser (givet som strenge). Fokus er primært på netværk med »single compartment neuron«-modeller (f.eks. leaky integrate-and-fire- eller Hodgkin-Huxley-neuroner). Inkluderede funktioner:

  • et system for angivelse af kvantiteter med fysiske dimensioner
  • præcis numerisk integration for lineære differentialligninger
  • Euler, Runge-Kutta og eksponentiel Eulerintegration for ikkelineære differentialligninger
  • synaptiske forbindelser med forsinkelser
  • korttids og langtids plasticitet (spike-timing-afhængig plasticitet)
  • et bibliotek med modelkomponenter, inklusive integrate-and-fire ligninger, synapser og ionic-strømme
  • en værktøjskasse for automatisk tilpasning af spiking neuron-modeller til elektrofysiologiske optagelser
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
Pythonbibliotek til analyse af diffusion MRI-datasæt
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DIPY er et program til beregningsneuroanatomi. Det fokuserer på diffusionsmagnetisk resonansbilleddannelsesanalyse (dMRI) og traktografi, men indeholder også implementeringer af andre beregningsmæssige billedbehandlingsmetoder, som f.eks. fjernelse af støj og registrering, der er anvendelige til større medicinsk billeddannelse og billedbehandlingsfællesskaber. Derudover er DIPY et internationalt projekt, som samler forskere på tværs af laboratorier og lande for at dele deres moderne kode og ekspertise i den samme kodebase, hvilket fremskynder videnskabelig forskning inden for medicinsk billeddannelse.

Her er nogle af højdepunkterne:

  • Genopbygningsalgoritmer: CSD, DSI, GQI, DTI, DKI, QBI, SHORE og MAPMRI
  • Fibersporingsalgoritmer: deterministisk og sandsynlig
  • Medfølgende lineær og ikke-lineær registrering af billeder
  • Hurtige operationer ved strømlinjeformning (udvælgelse, resampling, registrering)
  • Traktografisegmentering og gruppering
  • Mange billedoperationer, f.eks. ændr af størrelse eller fjernelse af støj NLMEANS
  • Estimering af afstande/korrespondance mellem strømlinjer og forbindelsesmatricer
  • Interaktiv visualisering af strømlinjer i billedrummet

Denne pakke indeholder Python 3-versionen.

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

Pythonbindinger for GDCM DICOM-biblioteket.

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-bindinger for MIA-billedbehandlingsbiblioteket
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MIA består af et sæt af værktøjer, biblioteker og udvidelsesmoduler for almen 2D- og 3D-gråskala billedbehandling og grundlæggende håndtering af triangulær mesher. Bibliotekerne tilbyder en grundlæggende infrastruktur og generiske algoritmer, som kan specialiseres ved at angive passende udvidelsesmoduler. Denne pakket tilbyder Python 3-bindingerne.

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
Pythonmoduler for MEG- og EEG-dataanalyse
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Denne pakke er designet for sensor- og kilde-rum analyse af MEG- og EEG-data, inklusive frekvens-domæne og tid-frekvens analyser og ikkeparametrisk statistik.

Python3-nibabel
Python 3-bindinger til diverse neuroimaging-dataformater
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NiBabel tilbyder læse- og skriveadgang til nogle almindelige filformater for medicinske og neuromæssige billeder inklusive: ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC samt PAR/REC. De forskellige billedformatklasser giver fuld eller selektiv adgang til hovedinformation (meta) og adgang til billeddata gøres tilgængelig via NumPy-rammer. NiBabel er efterfølgeren til PyNIfTI.

Python3-nipy
Analyse af strukturelle og funktionelle neuroimaging-data
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NiPy er en Pythonbaseret ramme til analyse af strukturelle og funktionelle neuroimaging-data. Rammen tilbyder funktionalitet for

  • Generel lineær model (GLM) statistisk analyse
  • Kombineret kurvetidskorrektion og bevægelseskorrektion
  • Generelle rutiner til billedregistrering med fleksible kostfunktioner, optimeringsprogrammer og re-sampling skemaer
  • Billedsegmentering
  • Grundlæggende visualisering af resultater i 2D og 3D
  • Grundlæggende diagnostik af tidsserier
  • Analyse af klynger og aktivitetsmønstre på tværs af emner
  • Reproducerbar analyse for gruppestudier
Please cite: K. Jarrod Millman and Matthew Brett: Analysis of functional magnetic resonance imaging in Python (eprint) Computing in Science & Engineering 9(3):52-55 (2007)
Python3-nipype
Neuroimaging data analysis pipelines in Python3
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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
Tidsserieanalyse for neurovidenskabelige data - nitime
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Nitime er et Pythonmodul for analyse af tidsserier for data fra neurovidenskabelige eksperimenter. Det indeholder en kerne af numeriske algoritmer til analyse af tidsseriere både i tids- og spektraldomænet, et sæt af containerobjekter til at repræsentere tidsserier og diverse objekter der vise en grænseflade på højt niveau til det numeriske maskineri og gør gængse analyseopgaver nemt at udtrykke med kompakt og semantisk korrekt kode.

Python3-openslide
Python 3 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:

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

This package contains the Python 3 module needed to run OpenSlide applications.

Python3-pydicom
DICOM-medicinsk fillæsning og -skrivning - Python 3
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Pydicom er et rent Pythonmodul til at fortolke DICOM-filer. DICOM er en standard (http://medical.nema.org) til at kommunikere medicinske billeder og relateret information såsom rapporter og radioterapiobjekter.

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

Denne pakke installerer modulet for Python 3.

Python3-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
Pythonbindinger for SimpleITK
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SimpleITK er et værktøjssæt for billedanalyse med et stort antal komponenter, der understøtter generelle filtreringsoperationer, billedsegmentering og registrering. Det er bygget oven på Insight Segmentation and Registration Toolkit ITK med det formål at tilbyde en forenklet grænseflade til ITK. SimpleITK er selv skrevet i C++, men er tilgængelig for et stort antal programmeringssprog.

Denne pakke tilbyder Pythonbindingerne.

Python3-torchvision
Datasæts, transformeringer og modeller specifikke for Computer Vision
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Pakken torchvision består af populære datasæt, modelarkitekturer og fælles billedtransformationer 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-grænseflade til NIFTICLIB
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R-grænseflade til nifticlib (nifticlib-2.0.0) (læs/skriv ANALYZE(TM)7.5/NIfTI-1-diskaftryk).

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
C++ multi-purpose reflection library (development files)
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CAMP is a multi-purpose reflection library developed by Technogerma Systems France (http://www.tegesoft.com). It provides an abstraction for most of the high-level concepts of C++

  • Classes
  • Enumerations
  • Properties
  • Functions
  • Objects
  • Variables By wrapping all these concepts into abstract structures, CAMP provides an extra layer of flexibility to programs, and allow them to fully expose their data structures at runtime. Many applications can take advantage of CAMP, in order to automate tasks which would otherwise require a huge amount of work. For example, CAMP can be used to expose and edit objects' attributes into a graphical user interface. It can also be used to do automatic binding of C++ classes to script languages such as Python or Lua. Another possible application would be the serialization of objects to XML, text or binary formats. Or you can even combine all these examples to provide a powerful and consistent interface for manipulating your objects outside C++ code.

This package contains the files needed for development.

Libeegdev-dev
Bibliotek til enheder som registrerer biosignaler - udviklingsfiler
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Eegdev er et bibliotek som tilbyder en samlet grænseflade, der tilgår forskellige EEG-signalsystemer (og andre biosignaler). Denne grænseflade er designet til at være både fleksibel og effektiv. Den enhedsspecifikke del er implementeret gennem udvidelsesmoduler, der gør det rimelig nemt at tilføje nye enhedsmotorer, selv hvis biblioteket endnu ikke understøtter dem officielt.

Kernebiblioteket tilbyder ikke kun brugerne samlede og konsistente grænseflader til registreringsenheden, det tilbyder også mange funktioner til enhedsmotorerne, rækkende fra konfiguration af data-typekonvertering og -skalering, hvilket gør det nemt at skrive nye enhedsmotorer.

Dette bibliotek er særligt nyttigt til håndtering af registreringsdelen for en grænseflade af typen Brain Computer Interface (BCI), eller enhver realtids multi-elektrode-registreringsenhed i neurofysiologisk forskning.

Denne pakke indeholder filerne krævet for at kompilere og lænke programmer, der bruger eegdev. Pakken tilbyder også teksthovederne krævet for at udvikle nye enhedsudvidelsesmoduler. Manualsiderne og eksempler er indeholdt i denne pakke.

Libfreeimage-dev
Støttebibliotek for grafiske billedformater - udviklingsfiler
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FreeImage et et C/C++-biblioteksprojekt for udviklere, der ønsker at støtte populære grafiske billedformater såsom PNG, bMP, JPEG, TIFF og andre som krævet af dagens multimedieprogrammer. FreeImage er nemt at bruge, hurtigt, sikker i brugen af flere tråde og udviklet til flere platforme (fungerer både med Linux, 32-bit Windows og Mac OS X).

Denne pakke indeholder teksthovederne og de statiske biblioteker krævet for at udvikle programmer via 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
NIfTI library API documentation
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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 library API reference documentation.

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

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

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

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