Debian Med Project
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Summary
Imaging
Pakiety Debian Med do przetwarzania obrazów

Ten metapakiet zainstaluje pakiety Debiana, które mogą być przydatne przy przetwarzaniu obrazów medycznych.

Instaluje kilka pakietów obsługujących DICOM (Digital Imaging and Communications in Medicine), który jest de facto standardem dla zarządzania obrazami medycznymi. Standard ten definiuje struktury danych i usługi, służące do wymiany obrazów medycznych i związanych z nimi informacji. Najnowsza wersja została opublikowana w 2008 roku i składa się z 18 części.

Aby uzyskać więcej informacji, należy odwiedzić stronę NEMA http://medical.nema.org/.

Status oficjalnego standardu DICOM oraz wszystkie uzupełnia i pozycje korygujące przedstawiono na stronie Davida Clunie: http://www.dclunie.com/dicom-status/status.html, gdzie można znaleźć bezpośrednie łącza do najnowszego wydania ftp://medical.nema.org/medical/dicom/2008/.

Description

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

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

Links to other tasks

Debian Med Imaging packages

Official Debian packages with high relevance

Aeskulap
Przeglądarka obrazów medycznych i sieciowy klient DICOM
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Aeskulap pozwala na przeglądanie specjalistycznych obrazów przechowywanych w formacie DICOM. Dodatkowo jest w stanie kwerendować i odbierać obrazy DICOM z węzłów archiwów (tzw. PACS) przez sieć. Aeskulap, jako program otwartoźródłowy, celuje w zastąpieniu komercyjnych przeglądarek DICOM.

Screenshots of package aeskulap
Amide
Oprogramowanie do obrazowania medycznego
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AMIDE: analizator zobrazowanych danych medycznych (ang. Amide's a Medical Imaging Data Examiner). AMIDE jest narzędziem do przeglądania i analizowania zestawów danych obrazów medycznych. Do jego możliwości można zaliczyć: jednoczesne przetwarzanie złożonych zbiorów danych importowanych z różnych formatów plików, łączenie obrazów, przedstawianie określonych analiz i rysunków w postaci trójwymiarowej, renderowanie objętości i wyrównywanie obrazów ciał stałych.

Amide importuje większość klinicznych plików DICOM (z wykorzystaniem biblioteki DCMTK).

Please cite: Andreas Markus Loening and Sanjiv Sam Gambhir: AMIDE: A Free Software Tool for Multimodality Medical Image Analysis. (PubMed) Molecular Imaging 2(3):131-7 (2003)
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1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17673/simage/large-7640f62c8ac17498b7e825bdc3e3be71.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17677/simage/large-8f7aaa9529343865541ebc968e464c74.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17678/simage/large-deeb0fc832965282d8e7bd9a43b6065e.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/16980/simage/large-bad825aa1bf433c09104699fb7be429c.png
0.9.1-2https://screenshots.debian.net/shrine/screenshot/356/simage/large-a3b9d7e99aafc8e159ad1288d6031445.png
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1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17675/simage/large-d5d4f705acb3ff24758ea101b026c05b.png
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Ants
advanced normalization tools for brain and image analysis
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Advanced Normalization Tools (ANTS) is an ITK-based suite of normalization, segmentation and template-building tools for quantitative morphometric analysis. Many of the ANTS registration tools are diffeomorphic, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD).

This package provides environment-modules configuration. Use 'module load ants' to make all cmdline tools available in your shell.

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

Please cite: Martin Uecker, Sebastian Rosenzweig, H. Christian M. Holme, Moritz Blumenthal, Zhengguo Tan, Xiaoqing Wang, Jonathan I. Tamir and Michael Lustig: BART Toolbox for Computational Magnetic Resonance Imaging.
Bart-view
viewer for multi-dimensional complex-valued data
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The Berkeley Advanced Reconstruction Toolbox (BART) is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging.

This package provides an image viewer as an optional component of the BART framework. The viewer is designed for multi-dimensional complex-valued data.

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

  • save2gdf: converter between different file formats, including but not limited to SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF, BDF, CWFB.
  • biosig2gdf: converts biosig data files into GDF, to simplify parsing and loading by scripting languages (e.g. loadgdf.{py,r})
  • rec2bin, bin2rec, heka2itx, save2aecg, save2scp: several converter tools based on save2gdf
  • biosig_fhir: packs biosignal data into HL7/FHIR binary template file.
  • physicalunits: converter for encoding and decoding of physical units according to ISO 11073-10101
Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
Camitk-imp
workbench application for the CamiTK library
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CamiTK helps researchers and clinicians to easily and rapidly collaborate in order to prototype CAMI applications, that feature medical images, surgical navigation and biomechanical simulations.

camitk-imp is the CamiTK workbench application where you can test all available extensions for prototyping. It provides an easy and interactive access to all available data and algorithm parameters, including the one you build yourself using the CamiTK SDK.

For example, camitk-imp can visualize medical images from a lot of different (standard) formats, offers image processing and segmentation algorithms to reconstruct a mesh geometry and run a biomechanical simulation.

Please cite: Céline Fouard, Aurélien Deram, Yannick Keraval and Emmanuel Promayon: CamiTK: a Modular Framework Integrating Visualization, Image Processing and Biomechanical Modeling. :323-354 (2012)
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Caret
Zestaw narzędzi do edycji i komputerowych rekonstrukcji anatomicznych
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Program umożliwia tworzenie, przeglądanie i zarządzanie rekonstrukcjami powierzchni kory mózgowej i móżdżkowej, przeglądanie objętości oraz wyświetlanie danych eksperymentalnych dotyczących powierzchni i objętości. Oprócz głównej aplikacji z graficznym interfejsem, pakiet caret oferuje również wszechstronne narzędzie wiersza poleceń caret_command, które daje dostęp do znacznej części funkcji obsługiwanych przez Caret.

Caret potrafi pobierać i wykorzystywać stereotaktyczne atlasy (ludzi, małp, myszy i szczurów) z otwartej bazy danych dostępnej w Internecie.

Niektóre funkcje związane z Caret dostępne są po zainstalowaniu dodatkowych plików danych, zawartych w pakiecie caret-data. Do funkcji tych należą:

  • odwzorowywanie objętości na płaską powierzchnię za pośrednictwem atlasu PALS,
  • przekształcanie (morfing) w wielu rozdzielczościach,
  • odwzorowywanie ognisk patologicznych za pośrednictwem atlasu PALS,
  • rejestrowanie w oparciu o powierzchnię,
  • spłaszczanie powierzchni.

Aktualnie pakiet caret-data znajduje się wyłącznie w repozytorium NeuroDebian. Dodatkowe informacje dostępne są na stronie: http://neuro.debian.net.

Please cite: David C. Van Essen, Heather A. Drury, James Dickson, John Harwell, Donna Hanlon and Charles H. Anderson: An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex. (PubMed,eprint) Journal of American Medical Informatics Association 8(5):443-459 (2001)
Conquest-common
ConQuest DICOM Server - common files
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A full featured DICOM server that has been developed based on and heavily extending the public domain UCDMC DICOM code. Some possible applications of the ConQuest DICOM software are:

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

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

Ctn
Central Test Node - oprogramowanie wykorzystujące standard DICOM do obrazowania medycznego
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DICOM jest standardem przechowywania obrazów, nanoszenia uwag oraz ich wymiany w sieci. Jest szeroko stosowany w obrazowaniu medycznym. Oprogramowanie Central Test Node (CTN) zapewnia implementację tego standardu.

Pakiet zawiera program w postaci binarnej oraz wstępną konfigurację do programu CTN.

Please cite: S.M. Moore, S.A. Hoffman and D.E. Beecher: DICOM Shareware: A Public Implementation of the DICOM Standard 2165:772–781 (1994)
Ctsim
Symulator tomografii komputerowej
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CTSim dostarcza interaktywny symulator tomografii komputerowej. Tomografia komputerowa jest techniką przybliżonego opisu wnętrza obiektu na podstawie pomiaru promieniowania rentgenowskiego wchłoniętego przez ten obiekt.

CTSim posiada graficzny interfejs użytkownika oraz możliwość zarządzania z wiersza poleceń. CTSim udostępnia bardzo dobry system szkoleniowy, służący do przeglądania danych uzyskanych w trakcie symulacji oraz rekonstrukcji obiektu.

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Dcm2niix
next generation DICOM to NIfTI converter
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dcm2niix is the successor of dcm2nii, a popular tool for converting images from the complicated formats used by scanner manufacturers (DICOM, PAR/REC) to the simpler NIfTI format used by many scientific tools. It works for all modalities (CT, MRI, PET, SPECT) and sequence types.

Dcmtk
OFFIS DICOM toolkit, narzędzia wiersza poleceń
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DCMTK zawiera zbiór bibliotek i aplikacji do rozpatrywania, tworzenia i konwertowania plików obrazów DICOM, obsługiwania mediów w trybie offline, wysyłania i odbierania obrazów za pośrednictwem połączenia sieciowego, jak również przykładowe serwery do przechowywania obrazów i listy zadań.

Pakiet zawiera aplikacje użytkowe DCMTK.

Uwaga: Niniejsza wersja została skompilowana z obsługą libssl.

Dicom3tools
Narzędzia do zarządzania i konwersji plików obrazów medycznych DICOM
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Pakiet zawiera narzędzia wiersza poleceń do tworzenia, modyfikowania, przesyłania i sprawdzania poprawności plików z atrybutami DICOM. Obsługuje przekształcanie niektórych własnościowych formatów obrazów medycznych do DICOM. Umożliwia współpracę ze starszym formatem danych ACR/NEMA i niektórymi własnościowymi wersjami tego formatu, takimi jak SPI.

Dicomnifti
Konwertowanie plików DICOM na format NIfTI
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Program dinifti przetwarza obrazy MRI przechowywane w formacie DICOM na format NIfTI. Format NIfTI uważany jest za nowy standard formatu obrazu do obrazowania medycznego i może być używany np. z FSL, AFNI, SPM, Carey lub Freesurfer.

Dinifti konwertuje pojedyncze pliki, ale także obsługuje w pełni zautomatyzowane konwersje wsadowe kompletnych katalogów DICOM. Ponadto, konwertowane pliki NIfTI mogą być odpowiednio nazywane, dzięki informacjom * obrazach z plików DICOM.

Dicomscope
OFFIS DICOM Viewer
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DICOMscope is a free DICOM viewer which can display uncompressed, monochrome DICOM images from all modalities and which supports monitor calibration according to DICOM part 14 as well as presentation states.

DICOMscope offers a print client (DICOM Basic Grayscale Print Management) which also implements the optional Presentation LUT SOP Class.

The development of this prototype was commissioned by the "Committee for the Advancement of DICOM" and demonstrated at the European Congress of Radiology ECR 1999. An enhanced version was developed for the "DICOM Display Consistency Demonstration" at RSNA InfoRAD 1999.

The current release has been demonstrated at ECR 2001 and contains numerous extensions, including a print server, support for encrypted DICOM communication, digital signatures and structured reporting.

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Fslview
Przeglądarka dla danych (f)MRI i DTI
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Ten pakiet oferuje przeglądarkę dla trzy- i czterowymiarowych danych MRI, jak również obrazów DTI. FSLView jest w stanie wyświetlić pliki ANALYZE i NIFTI. Przeglądarka obsługuje wielorakie tryby wyświetlania 2d (ortogonalnie, przeźrocza albo w jednej płaszczyźnie), jak również renderowanie objętościowe 3d. Dodatkowo FSLView może wizualizować serie czasowe i nakładać metryczne i stereotaktycznie dane atlasowe.

FSLView jest częścią FSL.

Please cite: S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady and P.M. Matthews: Advances in functional and structural MR image analysis and implementation as FSL. (PubMed) NeuroImage 23:208-219 (2004)
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Gdf-tools
Biblioteka wejścia/wyjścia do GDF - narzędzia pomocnicze
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GDF (General Dataformat for Biosignals - powszechny format danych do biosygnałów) służy do uniwersalnego przechowywania biosygnałów, takich jak EEG, EKG, MEG itd.

Pakiet zawiera narzędzie dostarczane z biblioteką (gdf_merger).

Please cite: Alois Schlögl: GDF – A general dataformat for BIOSIGNALS. The Computing Research Repository abs/cs/0608052 (2006)
Ginkgocadx
Oprogramowanie obrazowania medycznego i kompletna przeglądarka do standardu DICOM
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Ginkgo CADx stanowi kompletne rozwiązanie przeglądarki do standardu DICOM z zaawansowanymi funkcjami i obsługą rozszerzeń.

  • Prosty i konfigurowalny interfejs poprzez profile.
  • W pełni funkcjonalna wizualizacja obrazów DICOM.
  • Kompletny zestaw narzędzi (measure, markers, text, ...).
  • Obsługa wielu modalności (neurologiczne, radiologiczne, dermatologiczne, okulistyczne, USG, endoskopiczne, ...).
  • Obsługa dychotomizacji z JPEG, PNG, GIF i TIFF.
  • Pełna obsługa integracji EMH: standard HL7 i obieg zgodny z IHE.
  • Stacja robocza PACS (C-Find, C-MOVE, C-STORE ...).
  • Rozszerzalny dzięki niestandardowym rozszerzeniom.
  • Kompozycja mozaikowa obrazu siatkówki.
  • Automatyczna analiza diagnostyki siatkówki.
  • Automatyczna diagnostyka łuszczycy.
Gwyddion
Narzędzie do wizualizacji i analizy danych mikroskopii z sondą skanującą (SPM)
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Gwyddion jest modularnym programem do wizualizacji i analizy danych mikroskopii z sondą skanującą (SPM). Przeznaczony jest głównie do analizy danych zawierających wartość pola jako wskaźnik trzeciej współrzędnej położenia - wysokości, otrzymanych przy pomocy następujących technik:

  • Mikroskop Sił Atomowych (AFM),
  • Mikroskop Sił Magnetycznych (MFM),
  • Skaningowy Mikroskop Tunelowy (STM),
  • Mikroskop Optyczny Bliskiego Pola (SNOM lub NSOM) i wiele innych. Może być również użyty do arbitralnej analizy obrazów danych zawierających wartość pola jako wskaźnik trzeciej współrzędnej położenia - wysokości.

Pakiet zawiera główną aplikację i jej moduły. Zawiera również program Thumbnailer do GNOME (i Xfce), który tworzy podgląd wszystkich typów plików obsługiwanych przez program Gwyddion.

Please cite: David Nečas and Petr Klapetek: Gwyddion: an open-source software for SPM data analysis. (eprint) Central European Journal of Physics 10(1):181-188 (2012)
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Imagej
Image processing program with a focus on microscopy images
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It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window.

It can calculate area and pixel value statistics of user-defined selections. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering.

Spatial calibration is available to provide real world dimensional measurements in units such as millimeters. Density or gray scale calibration is also available.

ImageJ is developed by Wayne Rasband (wayne@codon.nih.gov), is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.

Please cite: Caroline A Schneider, Wayne S Rasband and Kevin W Eliceiri: NIH Image to ImageJ: 25 years of image analysis. (PubMed,eprint) Nature methods 9:671-675 (2012)
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Imagevis3d
desktop volume rendering application for large data
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ImageVis3D is a volume rendering application specifically designed to render large data. This is achieved by splitting the dataset into multiple levels of detail (LoD), with each level itself decomposed into multiple bricks (atomic rendering primitive). Interaction occurs at the coarsest LoD, which can be rendered instantaneously on almost all modern systems. After a configurable delay, ImageVis3D will successively render finer levels of detail, until the data are visible at their native resolution.

Development of ImageVis3D is sponsored by the NIH/NCRR Center for Integrative Biomedical Computing (CIBC), and the DOE Visualization And Analytics Center for Enabling Technologies (VACET).

Invesalius
3D medical imaging reconstruction software
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InVesalius generates 3D medical imaging reconstructions based on a sequence of 2D DICOM files acquired with CT or MRI equipments. InVesalius is internationalized (currently available in English, Portuguese, French, Spanish, Turkish, Italian, Czesh, Japanese, Catalan, Korean, Romanian and German) and provides several tools:

  • DICOM support including: (a) ACR-NEMA version 1 and 2; (b) DICOM version 3.0 (including various encodings of JPEG -lossless and lossy-, RLE)
  • Image manipulation features (zoom, pan, rotation, brightness/contrast, etc)
  • Segmentation based on 2D slices
  • Pre-defined threshold ranges according to tissue of interest
  • Segmentation based on watershed
  • Region growing segmentation
  • Edition tools (similar to Paint Brush) based on 2D slices
  • Semi-automatic segmentation based on Watershed
  • 3D surface creation
  • 3D surface connectivity tools
  • 3D surface exportation (including: binary STL, OBJ, VRML, Inventor)
  • High-quality volume rendering projection
  • Pre-defined volume rendering presets
  • Volume rendering crop plane
  • Picture exportation (including: BMP, TIFF, JPG, PostScript, POV-Ray)
  • Minimum, Maximum or Mean Intensity Projection, Maximum Intensity Difference Accumulation and Contour based visualizations
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Ismrmrd-tools
command-line tools for ISMRMRD
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The ISMRMRD format combines a mix of flexible data structures (XML header) and fixed structures (equivalent to C-structs) to represent MRI data.

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

This package provides the command-line tools.

Itksnap
Półautomatyczna segmentacja struktury obrazów 3D
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SNAP umożliwia półautomatyczną segmentację struktur w obrazach medycznych (np. obrazach rezonansu magnetycznego mózgu) przy użyciu metod aktywnych konturów, jak również ręcznego wytyczania i nawigacji w ramach obrazu. Godne uwagi cechy to:

  • połączony kursor do łatwej nawigacji 3D;
  • ręczna segmentacja w trzech prostopadłych płaszczyznach jednocześnie;
  • obsługa wielu różnych formatów obrazu 3D, w tym NIfTI;
  • obsługa równoczesnego podglądania i segmentacji wielu obrazów;
  • ograniczona obsługa kolorowych obrazów (np. map tensora dyfuzji);
  • narzędzie przycinania płaszczyzny 3D do przyspieszenia dalszego przetwarzania wyników segmentacji.
Please cite: Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee and Guido Gerig: User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability. Neuroimage 31:1116-1128 (2006)
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King
Interaktywny system do tworzenia trójwymiarowej grafiki wektorowej
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KiNG (Kinemage, Następna Generacja) jest interaktywnym systemem do tworzenia trójwymiarowej grafiki wektorowej. Obsługuje szereg prymitywów graficznych, co czyni go idealnym narzędziem do różnego rodzaju grafów, wykresów i innych ilustracji; mimo, że pierwotnie został zaprojektowany do wyświetlania wielocząsteczkowych struktur dla biofizycznych badań. KiNG opiera się na Mage, JavaMage oraz na koncepcji "kinemage" (kinetyczne obrazy), aby zapewnić w pełni funkcjonalną aplikację Javy z przyjaznym użytkownikowi interfejsem i zintegrowanymi funkcjami edycji. Plik o rozszerzeniu .jar z programem KiNG można użyć wewnątrz strony internetowej jako aplet lub obiekt Javy, w celu umożliwienia łatwego dostępu do obrazów kinemage albo zarządzania plikami za pośrednictwem przeglądarki.

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

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

Please cite: David Rodríguez González, Trevor Carpenter, Jano I. van Hemert and Joanna Wardlaw: An open source toolkit for medical imaging de-identification. (PubMed,eprint) European Radiology 20(8):1896-1904 (2010)
Lipsia
analysis suite for MRI and fMRI data
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Leipzig Image Processing and Statistical Inference Algorithms (LIPSIA)

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

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

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

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

Medcon
Narzędzie do konwersji formatów obrazów medycznych (DICOM, ECAT, ...)
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Program przeznaczony jest do konwertowania formatów obrazów medycznych i rozpowszechniany na podstawie licencji (L)GPL. Pakiet zawiera kompletny kod źródłowy w języku C, elastyczne narzędzie wiersza poleceń oraz przejrzysty interfejs graficzny, stworzony przy użyciu biblioteki GTK+. Aktualnie obsługuje następujące formaty: ACR/NEMA 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 i PNG.

Program umożliwia także odczytywanie nieskompresowanych, oficjalnie nieobsługiwanych plików, wyświetlanie wartości pikseli oraz wyodrębnianie/zmienianie kolejności poszczególnych obrazów. Możliwe jest również uzyskiwanie nieprzetworzonych obrazów w formatach binarnym lub ASCII oraz zapisywanie obrazów w formacie PNG, używanym w aplikacjach pulpitowych.

Jest to narzędzie wiersza poleceń do przetwarzania wsadowego.

Mia-tools
Narzędzia wiersza poleceń do przetwarzania obrazów w skali szarości
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Narzędzia wiersza poleceń do uruchamiania powszechnie stosowanych zadań dotyczących przetwarzania dwu i trójwymiarowych obrazów w skali szarości, oraz podstawowych operacji na trójkątnych oczkach. Obsługiwanymi algorytmami przetwarzania obrazów są: filtrowanie, łączenie, rejestrowanie, kompensowanie ruchu na serii zdjęć, oraz ocena różnych statystyk mających związek z obrazami. Pakiet zawiera również interfejsy nipype do tych narzędzi wiersza poleceń.

The package is enhanced by the following packages: mia-tools-doc
Please cite: Gert Wollny, Jean-Jaques Hublin, Maria-J Ledesma-Carbayo, Matthew M. Skinner, Peter Kellman and Thomas Hierl: MIA - A Free and Open Source Software for Gray Scale Medical Image Analysis. (eprint) Source Code for Biology and Medicine 8:20 (2013)
Mia-viewit
Przeglądarka do zestawów danych 3D utworzonych przy użyciu MIA
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MIA to przeglądarka do wizualizacji zestawów danych 3D. Interfejsy i obsługiwane typy danych skupiają się na wynikach, które można uzyskać, uruchamiając programy z pakietu mia-tools.

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Mialmpick
Narzędzia do wybierania punktów orientacyjnych w zestawach danych wartości 3D
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Narzędzie zapewnia prosty mechanizm renderujący 3D, który może wizualizować powierzchnie bezpośrednio z wielkości 3D i służyć do wyznaczania punktów orientacyjnych 3D. Najlepiej nadaje się do zestawów danych CT.

Please cite: Gert Wollny, Fritjhof Kruggel, Thomas Hierl and Jörg Hendricks: Assessment, validation, and visualisation of bony changes in crano-facial surgery (eprint) :459-464 (2004)
Minc-tools
Narzędzia do formatowania obrazów medycznych MNI
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Pakiet zawiera narzędzia do obsługi plików MINC.

Format pliku Minc to bardzo elastyczny format plików obrazów medycznych, zbudowany na bazie uogólnionego formatu danych NetCDF. Format ten jest prosty, samoopisujący się, rozszerzalny, przenośny i N-wymiarowy, z interfejsami programistycznymi zarówno do niskopoziomowego dostępu do danych, jak i do wysokopoziomowego zarządzania zawartością. Pakiet udostępnia zestaw narzędzi do obsługi plików graficznych, bazujący na bibliotekach. Format, biblioteki i narzędzia przeznaczone są do użytku w środowisku badawczym obrazowania medycznego: są proste i wydajne i nie starają się zapewnić użytkownikom ładnego interfejsu.

Mriconvert
Narzędzie do konwersji medycznych plików graficznych
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MRIConvert jest narzędziem do konwersji medycznych plików graficznych, które przetwarza pliki DICOM do następujących formatów: NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager oraz MetaImage.

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Mricron
Konwertowanie, przeglądanie i analizowanie obrazu rezonansu magnetycznego
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Jest to narzędzie z graficznym interfejsem użytkownika, służące do przeglądania i analizowania (funkcjonalnych) obrazów otrzymanych metodą rezonansu magnetycznego. MRIcron może być używany do tworzenia dwu- lub trójwymiarowych wizualizacji map statystycznych, nakładanych na zdjęcia anatomiczne mózgu. Ponadto, pomaga w rysowaniu anatomicznych obszarów zainteresowania (ROI), w odwzorowywaniu zmian oraz w podstawowej analizie funkcjonalnych szeregów czasowych (np. w tworzeniu wykresów przed i po stymulacyjnej zmiany sygnału).

Oprócz samego MRIcron, pakiet dostarcza również narzędzie dcm2nii, obsługujące konwersję obrazów DICOM i PAR/REC do formatu NIfTI oraz npm do nieparametrycznej analizy danych.

Please cite: Chris Rorden, Hans-Otto Karnath and Leonardo Bonilha: Improving lesion-symptom mapping. (PubMed) Journal of Cognitive Neuroscience 19(7):1081-1088 (2007)
Mrtrix3
diffusion-weighted MRI white matter tractography
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Set of tools to perform diffusion-weighted MRI white matter tractography of the brain in the presence of crossing fibres, using Constrained Spherical Deconvolution, and a probabilisitic streamlines algorithm. Magnetic resonance images in DICOM, ANALYZE, or uncompressed NIfTI format are supported.

Please cite: Donald Tournier, Robert Smith amd David Raffelt, Rami Tabbara, Thijs Dhollander, Maximilian Pietsch, Daan Christiaens, Ben Jeurissene, Chun-Hung Yeh and Alan Connelly: MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage 202:116137 (2019)
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Nifti-bin
Narzędzia dostarczane z biblioteką NIfTI
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Niftilib jest zestawem bibliotek wejścia/wyjścia do odczytywania i zapisywania plików w formacie danych NIfTI-1. NIfTI-1 to binarny format pliku do przechowywania danych z obrazów medycznych, np. obrazów mózgu wykonanych metodą obrazowania rezonansu magnetycznego (MRI) oraz wyspecjalizowaną odmianą obrazowania rezonansu magnetycznego (fMRI).

Pakiet zawiera narzędzia, które dostarczane są z biblioteką NIfTI (nifti_tool, nifti_stats i nifti1_test).

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

This package includes the command line tools.

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

This package contains the command-line application.

Odin
develop, simulate and run magnetic resonance sequences
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ODIN is a framework for magnetic resonance imaging (MRI). It covers the whole toolchain of MRI, from low-level data acquisition to image reconstruction. In particular, it aims at rapid prototyping of MRI sequences. The sequences can be programmed using a high-level, object oriented, C++ programming interface. It provides advanced sequence analysis tools, such as interactive plotting of k-space trajectories, a user interface for a fast compile-link-test cycle and a powerful MRI simulator which supports different virtual samples. For fast and flexible image reconstruction, ODIN contains a highly customizable, multi-threaded data-processing framework.

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

This package provides command line interface to openmeeg functionality.

Please cite: Alexandre Gramfort, Théodore Papadopoulo, Emmanuel Olivi and Maureen Clerc: OpenMEEG: opensource software for quasistatic bioelectromagnetics. (PubMed,eprint) BioMedical Engineering OnLine 9:45 (2010)
Openslide-tools
Narzędzia przetwarzania i konwersji plików oparte na OpenSlide
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OpenSlide to biblioteka języka C, dostarczająca interfejs do odczytu obrazów kompletnych slajdów znanych jako wirtualne klisze.

Wirtualne klisze są to duże obrazy o wysokiej rozdzielczości używane w cyfrowej obróbce zdjęć medycznych. Odczyt tych obrazów w standardowych programach jest problematyczny, gdyż narzędzia te pracują z reguły na obrazie dekompresowanym do pamięci operacyjnej lub pliku wymiany. Wirtualne klisze z reguły są większe niż pamięć RAM, po rozpakowaniu zajmując nieraz dziesiątki gigabajtów. Dodatkowo są to obrazy zapisane w wielu rozdzielczościach, i często niezbędna jest jedynie niewielka porcja danych dla wybranej rozdzielczości.

Aktualnie wspierane są następujące formaty:

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

Pakiet zawiera narzędzia do przetwarzania plików, pracujące w wierszu poleceń.

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

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

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

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
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Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)
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Orthanc-WSI brings support of whole-slide imaging for digital pathology into Orthanc, the lightweight, RESTful Vendor Neutral Archive for medical imaging.

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

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

Provide command line applications for using pixelmed

Plastimatch
medical image reconstruction and registration
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Plastimatch is an open source software for deformable image registration. It is designed for high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography(PET). Software features include:

  • B-spline method for deformable image registration (GPU and multicore accelerated), including support for image masking, landmark penalties, and regularization
  • Demons method for deformable image registration (GPU accelerated)
  • Multi-atlas segmentation
  • ITK-based algorithms for translation, rigid, affine, multiple demons methods, and B-spline registration
  • Pipelined, multi-stage registration framework with seamless conversion between most algorithms and transform types
  • Landmark-based deformable registration using thinplate splines for global registration
  • Landmark-based deformable registration using radial basis functions for local corrections
  • Broad support for 3D image file formats (using ITK), including DICOM, Nifti, NRRD, MetaImage, and Analyze
  • Extensive toolchain for radiotherapy research, including support for DICOM, DICOM-RT, DICOM SRO, XiO file format, gamma analysis, contour manipulation, contour overlap analysis, and vector field analysis Plastimatch also features two handy utilities which are not directly related to image registration:

  • FDK cone-beam CT reconstruction (GPU and multicore accelerated)

  • Digitally reconstructed radiograph (DRR) generation (GPU and multicore accelerated)
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Python3-dipy
Python library for the analysis of diffusion MRI datasets
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DIPY is a software project for computational neuroanatomy. It focuses on diffusion magnetic resonance imaging (dMRI) analysis and tractography but also contains implementations of other computational imaging methods such as denoising and registration that are applicable to the greater medical imaging and image processing communities. Additionally, DIPY is an international project which brings together scientists across labs and countries to share their state-of-the-art code and expertise in the same codebase, accelerating scientific research in medical imaging.

Here are some of the highlights:

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

This package contains the Python 3 version.

Please cite: Eleftherios Garyfallidis, Matthew Brett, Vassilis Tsiaras, George Vogiatzis and Ian Nimmo-Smith: Identification of corresponding tracks in diffusion MRI tractographies. (eprint) Proc. Intl. Soc. Mag. Reson. Med. 18 (2010)
Python3-nibabel
Python3 bindings to various neuroimaging data formats
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NiBabel provides read and write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC, as well as PAR/REC. The various image format classes give full or selective access to header (meta) information and access to the image data is made available via NumPy arrays. NiBabel is the successor of PyNIfTI.

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

  • General linear model (GLM) statistical analysis
  • Combined slice time correction and motion correction
  • General image registration routines with flexible cost functions, optimizers and re-sampling schemes
  • Image segmentation
  • Basic visualization of results in 2D and 3D
  • Basic time series diagnostics
  • Clustering and activation pattern analysis across subjects
  • Reproducibility analysis for group studies
Please cite: K. Jarrod Millman and Matthew Brett: Analysis of functional magnetic resonance imaging in Python (eprint) Computing in Science & Engineering 9(3):52-55 (2007)
Python3-nipype
Neuroimaging data analysis pipelines in Python3
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Nipype interfaces Python to other neuroimaging packages and creates an API for specifying a full analysis pipeline in Python. Currently, it has interfaces for SPM, FSL, AFNI, Freesurfer, but could be extended for other packages (such as lipsia).

Please cite: SS Ghosh, C Burns, D Clark, K Gorgolewski, YO Halchenko, C Madison, R Tungaraza and KJ Millman: Nipype: Opensource platform for unified and replicable interaction with existing neuroimaging tools (eprint) 16th Annual Meeting of the Organization for Human Brain Mapping :106 (2010)
Python3-nitime
timeseries analysis for neuroscience data (nitime)
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Nitime is a Python module for time-series analysis of data from neuroscience experiments. It contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code.

Python3-pydicom
DICOM medical file reading and writing (Python 3)
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pydicom is a pure Python module for parsing DICOM files. DICOM is a standard (http://medical.nema.org) for communicating medical images and related information such as reports and radiotherapy objects.

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

This package installs the module for Python 3.

Python3-pyxid
interface for Cedrus XID and StimTracker devices
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pyxid is a Python library for interfacing with Cedrus XID (eXperiment Interface Device) and StimTracker devices. XID devices are used in software such as SuperLab, Presentation, and ePrime for receiving input as part of stimulus/response testing experiments.

pyxid handles all of the low level device handling for XID devices in Python projects.

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

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

Qnifti2dicom
convert 3D medical images to DICOM 2D series (gui)
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Nifti2Dicom is a conversion tool that converts 3D NIfTI files (and other formats supported by ITK, including Analyze, MetaImage Nrrd and VTK) to DICOM. Unlike other conversion tools, it can import a DICOM file that is used to import the patient and study DICOM tags, and allows you to edit the accession number and other DICOM tags, in order to create a valid DICOM that can be imported in a PACS.

This package contains the Qt5 GUI.

Sigviewer
Graficzna przeglądarka biosygnałów takich jak: EEG, EMG i ECG
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SigViewer to oprogramowanie do przeglądania i oceniania biomedycznych danych sygnałowych. Opiera się na bibliotece biosig4c++, która obsługuje pewną liczbę formatów danych (w tym: EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT (Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro i TMS32). Pełna lista obsługiwanych formatów plików dostępna jest pod adresem: http://pub.ist.ac.at/~schloegl/biosig/TESTED.

Oprócz wyświetlania biosygnałów, SigViewer obsługuje tworzenie adnotacji w celu wybierania artefaktów lub określonych zdarzeń.

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

3D Slicer main application.

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

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

Sofa-apps
GUI do Simulation Open Framework Architecture (SOFA)
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SOFA to otwartoźródłowa struktura skoncentrowana przede wszystkim na symulacjach czasu rzeczywistego, z naciskiem na symulacje medyczne. Jest ona przewidziana głównie dla społeczności badawczej, do pomocy w rozwijaniu nowszych algorytmów, ale może być również użyta jako skuteczne narzędzie do prototypów.

Pakiet zawiera główną aplikację SOFA.

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

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

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

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

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

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

Via-bin
tools for volumetric image analysis
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VIA is a volumetric image analysis suite for functional and structural (medical) images. The suite consists of different tools ranging from simple data handling over viewers to complex image transformation.

All tools operate on data in VISTA format. The package contains several converters from e.g. PNG, PGM or PNM to this data format and back.

Voxbo
Przetwarzanie, analiza statystyczna i wyświetlanie danych obrazowych mózgu
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Pakiet zawiera zestaw narzędzi do analiz eksperymentów z zakresu funkcjonalnego obrazowania rezonansu magnetycznego (głównie fMRI) oraz mapowania zmiennych zachowawczych baz vokselowych. VoxBo obsługuje zmodyfikowany GLM (dla danych skorelowanych automatycznie) oraz standardowe GLM dla danych nieskorelowanych automatycznie. Zestaw narzędziowy przeznaczony jest do współdziałania z AFNI, FSL, SPM i innymi.

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

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

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

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

Vtk-dicom-tools
Zarządzanie DICOM z poziomu VTK - narzędzia
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Pakiet zawiera zestaw klas do zarządzania plikami i metadanymi DICOM z poziomu VTK, oraz niektóre narzędzia do odpytywania i konwertowania plików DICOM.

Narzędzia wiersza poleceń.

Xmedcon
Graficzne narzędzie do konwersji obrazów medycznych (DICOM, ECAT, ...)
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Program przeznaczony jest do konwertowania formatów obrazów medycznych i rozpowszechniany na podstawie licencji (L)GPL. Pakiet zawiera kompletny kod źródłowy w języku C, elastyczne narzędzie wiersza poleceń oraz przejrzysty interfejs graficzny, stworzony przy użyciu biblioteki GTK+. Aktualnie obsługuje następujące formaty: ACR/NEMA 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 i PNG.

Program umożliwia także odczytywanie nieskompresowanych, oficjalnie nieobsługiwanych plików, wyświetlanie wartości pikseli oraz wyodrębnianie/zmienianie kolejności poszczególnych obrazów. Możliwe jest również uzyskiwanie nieprzetworzonych obrazów w formatach binarnym lub ASCII oraz zapisywanie obrazów w formacie PNG, używanym w aplikacjach pulpitowych.

Jest to graficzna wersja programu (działająca w środowisku X), z interfejsem opartym na bibliotece GTK+. Program przetwarza tylko jeden plik na raz.

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Cmtk
Computational Morphometry Toolkit
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A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O.

The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear regression).

Please cite: T. Rohlfing: User Guide to The Computational Morphometry Toolkit. (eprint) The Insight Journal (2009)
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Connectomeviewer
Interactive Analysis and Visualization for MR Connectomics
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The Connectome Viewer is a extensible, scriptable, pythonic research environment for visualization and (network) analysis in neuroimaging and connectomics.

Employing the Connectome File Format, diverse data types such as networks, surfaces, volumes, tracks and metadata are handled and integrated. The Connectome Viewer is part of the MR Connectome Toolkit.

Please cite: Gerhard S, Daducci A, Lemkaddem A, Meuli R, Thiran J-P and Hagmann P: The Connectome Viewer Toolkit: An open source framework to manage, analyze, and visualize connectomes. (2011)
Conquest-dbase
ConQuest DICOM Server - DBaseIII backend
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A full featured DICOM server that has been developed based on and heavily extending the public domain UCDMC DICOM code. Some possible applications of the ConQuest DICOM software are:

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

This package uses DBaseIII files as database backend.

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

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

This package uses MySQL as database backend.

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

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

This package uses PostgreSQL as database backend.

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

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

This package uses SQLite as database backend.

Elastix
Zestaw narzędzi do rejestracji obrazów przy użyciu metod rigid i nonrigid
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Rejestracja obrazu oparta na dobrze znanym zestawie narzędziowym ITK (Insight Segmentation and Registration Toolkit). Oprogramowanie składa się z kolekcji algorytmów, które są powszechnie stosowane do rozwiązywania problemów związanych z rejestracją obrazów (medycznych). Modułowa konstrukcja Elastix pozwala użytkownikowi szybko konfigurować, testować i porównywać różne metody rejestracji dla określonej aplikacji. Interfejs wiersza poleceń umożliwia automatyczne przetwarzanie dużych ilości zbiorów danych, z wykorzystaniem skryptów.

Please cite: Denis P. Shamonin, Esther E. Bron, Boudewijn P. F. Lelieveldt, Marion Smits, Stefan Klein and Marius Staring: Fast parallel image registration on CPU and GPU for diagnostic classification of Alzheimer's disease. (PubMed,eprint) frontiers in Neuroinformatics 7(50):1-15 (2014)
Imagemagick
image manipulation programs -- binaries
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ImageMagick is a software suite to create, edit, and compose bitmap images. It can read, convert and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to translate, flip, mirror, rotate, scale, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves. All manipulations can be achieved through shell commands as well as through an X11 graphical interface (display).

This package include links to channel depth specific binaries and manual pages.

This is a dummy package. You can safely purge or remove it.

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Imview
Program do wyświetlania i analizowania obrazów
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Imview to program, który umożliwia:

  • wyświetlanie wielu formatów graficznych;
  • wyświetlanie obrazów 2D lub 3D (jako plastrów) z bardzo dobrymi funkcjami powiększania i panoramowania;
  • współpracę z wielowidmowymi szeregami czasowymi lub wielostronicowymi dokumentami (jak np.: zdjęcia satelitarne, stosy TIFF, animowane GIFy i heterogeniczne pliki wieloskładnikowe);
  • wyświetlanie wszystkich rodzajów pikseli (od 1-bitowych do 64-bitowych danych, całkowitych lub zmiennoprzecinkowych);
  • wyświetlanie arbitralnych profili 1-D z obrazów 2-D (lub plastrów 2-D z obrazów 3-D);
  • obsługiwanie dowolnych map kolorów dla wszystkich rodzajów pikseli (tj. wyświetlanie nierzeczywistych kolorów);
  • obsługiwanie standardowych funkcji do obróbki grafiki (jasność/kontrast, gamma, powiększanie, przycinanie, obracanie itp.);
  • zdalną pracę za pomocą gniazd i poleceń tekstowych (dla łatwej integracji z różnymi systemami analizy obrazu);
  • przesyłanie obrazów do Imview poprzez gniazda lub pamięć współdzieloną;
  • dostęp do wielu innych funkcji.
Please cite: Hugues Talbot: ImView: a portable image display application (eprint)
Openwalnut-qt4
Multi-modal medical and brain data visualization tool.
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OpenWalnut is a tool for multi-modal medical and brain data visualization. Its universality allows it to be easily extended and used in a large variety of application cases. It is both, a tool for the scientific user and a powerful framework for the visualization researcher. Besides others, it is able to load NIfTI data, VTK line data and RIFF-format CNT/AVR-files. OpenWalnut provides many standard visualization tools like line integral convolution (LIC), isosurface-extraction, glyph-rendering or interactive fiber-data exploration. The powerful framework of OpenWalnut allows researchers and power-users to easily extend the functionality to their specific needs.

This package contains the QT4 GUI for OpenWalnut.

Please cite: Sebastian Eichelbaum, Mario Hlawitschka, Alexander Wiebel, Gerik Scheuermann: OpenWalnut - An Open-Source Visualization System (2010)
Orthanc-dicomweb
Plugin to extend Orthanc with support of WADO and DICOMweb
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Orthanc DICOMweb is a plugin to Orthanc, the lightweight, RESTful Vendor Neutral Archive for medical imaging. It extends the Orthanc core with support of the WADO (now known as WADO-URI) and DICOMweb (QIDO-RS, STOW-RS, WADO-RS) standards.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Orthanc-gdcm
DICOM transcoder/decoder for Orthanc using GDCM (notably for JPEG2k)
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This package installs a plugin for Orthanc, the lightweight, RESTful Vendor Neutral Archive for medical imaging. The plugin extends Orthanc with a transcoder/decoder of DICOM images that is built on the GDCM library, whereas the built-in transcoder/decoder of Orthanc uses DCMTK.

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

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Orthanc-imagej
ImageJ plugin to import images from Orthanc
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This ImageJ plugin allows ImageJ to browse the content of an Orthanc server, then import 2D/3D DICOM images from Orthanc into ImageJ. Orthanc is a lightweight, RESTful DICOM server for healthcare and medical research.

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

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

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

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

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
Paraview
Program do wizualizacji równoległej
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ParaView to otwartoźródłowa, wieloplatformowa aplikacja zaprojektowana do wizualizacji zestawów danych o rozmiarach począwszy od małych do bardzo dużych. Cele projektu ParaView obejmują:

* Opracowywanie otwartoźródłowych, wieloplatformowych aplikacji do
  wizualizacji.
* Obsługiwanie rozprowadzanych modeli obliczeniowych do przetwarzania
  dużych zbiorów danych.
* Tworzenie otwartego, elastycznego i intuicyjnego interfejsu
  użytkownika.
* Opracowywanie rozszerzalnej architektury w oparciu o otwarte
  standardy.

ParaView działa na rozproszonych i równoległych pamięciach współdzielonych jak również na pojedynczych systemach procesorowych. Został z powodzeniem przetestowany na Windows, Mac OS X, Linux oraz różnych stacjach roboczych Uniksa, klastrach i superkomputerach. Pod maską ParaView używa zestawu narzędzi do wizualizacji jako silnika do renderowania i przetwarzania danych oraz posiada interfejs użytkownika napisany przy użyciu Qt.

Pngquant
Narzędzie do optymalizacji obrazów PNG (Portable Network Graphics)
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Pngquant to narzędzie konwertujące, używane z poziomu wiersza poleceń, które kwantyzuje oraz dodaje dither do obrazów PNG truecolor, aby przekształcić je na pliki z 8-bitową paletą RGBA. Tak przetworzone obrazy są zazwyczaj od dwóch do czterech razy mniejsze niż 32-bitowe oryginały, a ich częściowa przezroczystość zostaje w miarę zgrabnie zachowana. To czyni pngquant szczególnie pożytecznym narzędziem przy tworzeniu stron WWW, a także przy rozwijaniu oprogramowania dla PlayStation 2, którego format tekstur opiera się na palecie RGBA (choć nie są one poddawane kompresji PNG). Jest to ta sama technika, którą zastosowano dla wielu obrazów na stronie Miscellaneous Transparent PNGs (http://www.libpng.org/pub/png/pngs-img.html), a jej rezultaty nierzadko nie dają się odróżnić od oryginalnych plików PNG truecolor.

Optymalizatory (takie, jak pngcrush czy optipng) optymalizują kompresję, zazwyczaj bezstratnie, podczas gdy pngquant kwantyzuje kolory do 256 (lub mniej) różnych kombinacji, co jest procesem stratnym.

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

Trimage
Interfejsy graficzny i wiersza poleceń do optymalizacji plików graficznych
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Trimage to wieloplatformowy graficzny interfejs użytkownika oraz interfejs wiersza poleceń do optymalizacji plików obrazów za pomocą: optipng, advpng, pngcrush i jpegoptim, w zależności od typu pliku (obecnie obsługiwane są pliki PNG i JPG). Wszystkie pliki obrazów kompresowane są bezstratnie na najwyższych dostępnych poziomach kompresji. Trimage oferuje różne funkcje wprowadzania danych, które pasują do osobistego przepływu pracy: Regularne okno dialogowe pliku, przeciąganie i upuszczanie oraz różne opcje wiersza poleceń.

Debian packages in contrib or non-free

Bart-cuda
tools for computational magnetic resonance imaging
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Newer upstream!
License: DFSG free, but needs non-free components
Git

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

This package provides BART with CUDA support.

Fsl
transitional dummy package
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fieldmedicine:imaging
interfacecommandline, x11
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License: non-free
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The only purpose of this package is to enable upgrades to the new 'fsl-core' package which replaces 'fsl'. This package can safely be removed.

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

Please cite: Mark Jenkinson, Christian F. Beckmann, Timothy E. J. Behrens, Mark W. Woolrich and Stephen M. Smith: FSL. (PubMed) NeuroImage 62(2):782-790 (2012)
Vmtk
the Vascular Modeling Toolkit
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The Vascular Modeling Toolkit is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

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

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

Bioimagesuite
integrated image analysis software suite
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License: GPL-2+
Debian package not available
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Version: 2.0-1

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

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

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

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

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

Cellprofiler
quantitatively measure phenotypes from images automatically
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License: GPL-2
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Version: 3.0.0-1

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

Crea
base library of the creaTools medical image processing suite
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License: CeCILL-B
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Version: 0.0.20131107-1

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

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

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

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

Freesurfer
analysis and visualization of functional brain imaging data
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Version: 5.1.0+dev+cvs20120104-1

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

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

This package depends upon the latest version of freesurfer.

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

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

Insightapplications
InsightToolKit (ITK) based medical imaging applications
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License: BSD
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Version: 3.20.0-1.1

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

Jist
Java Image Science Toolkit
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License: free
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Version: 2.0.20100907.dfsg1-1

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

Kradview
medical image viewer for DICOM images
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License: GPL-3+
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Version: 1.1.0-2

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

Libdcm4che-java
Clinical Image and Object Management
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Dcm4che is a collection of open source applications and utilities for the healthcare enterprise.

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

Remark of Debian Med team: Needs jai_imageio as prerequsite

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

Mayam
Cross-platform DICOM Viewer
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Version: 0.8-1

A Cross-platform DICOM viewer using the dcm4che toolkit.

The current features are:

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

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

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

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

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

Mipav
quantitative analysis and visualization of medical images
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License: non-free
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Version: 5.0.0.20100907-2

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

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

Mni-colin27-nifti
Talairach stereotaxic space template
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License: free
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Version: 1.1-2

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

This package provides the template in NIfTI format.

Openelectrophy
data analysis GUI for intra- and extra-cellular recordings
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License: free
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Version: 0.0.svn143

This package provides the startup script for the OpenElectrophy GUI.

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

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

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

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

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

Xnat
platform for data management and productivity tasks in neuroimaging
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License: XNAT_SLA
Debian package not available
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Version: 1.7.5.1-1

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

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

Unofficial packages built by somebody else

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

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

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

Fiji is a project aiming at simplifying:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

No known packages available

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

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

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

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

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

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

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

Java framework for Dicom

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

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

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

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

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

licensing terms.

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

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

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

Remark of Debian Med team: Homepage vanished

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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