Task: Imaging
Description: Debian Med imaging packages
 This meta package will install Debian packages which might be useful in medical
 image processing.
 .
 It installs several packages supporting DICOM (Digital Imaging and
 Communications in Medicine) which is the de-facto standard for medical
 image management. The standard defines data structures and services for
 the exchange of medical images and related information. The latest release
 has been published in 2004 and consists of 18 parts.
 .
 For more information, you can visit the NEMA homepage http://medical.nema.org/
 or download the current DICOM standard as PDF files from
 http://www.dclunie.com/dicom-status/status.html .

Depends: amide, ctsim, ctn, dicomnifti, imagej, minc-tools, medcon, python-nifti, xmedcon, dcmtk

Suggests: imagemagick, pngquant, imview

Depends: nifti-bin, dicomnifti, libvolpack1

Depends: aeskulap

Depends: fslview, fsl

Depends: bioimagesuite
Homepage: http://www.bioimagesuite.org/
License: GPL
Pkg-Description: integrated image analysis software suite
 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 intergrated 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.
 .
 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

Depends: drjekyll
Homepage: http://drjekyll.sourceforge.net
License: GPL
Pkg-Description: interactive voxel editor for viewing and editing three-dimensional images
 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.
Why: Hint given by Petter Reinholdtsen

Depends: libvista2
Homepage: http://mia.sourceforge.net/
License: GPL
Pkg-Description: software environment for computer vision research
 Vista is a software environment for computer vision research. It is
 designed to support not only images, but also edge sets, camera models,
 and more complex  data structures. Vista includes libraries of common
 computer vision and image  processing algorithms. It is written in
 ANSI C, for UNIX platforms running X Windows, and it is freely available.
 The original development was done  at University of British Columbia
 (http://www.cs.ubc.ca/nest/lci/vista/vista.html).
 .
 Because the development was stalled by the original authors the
 development continued in the "Tools for Medical Image Analysis"
 framework (http://mia.sourceforge.net/) which is maintained by
 Max Planck Institute of Cognitive Neuroscience
 (http://www.cns.mpg.de/).

Depends: dcm4che
Homepage: http://www.dcm4che.org/
License: LGPL, MPL, Apache, other (also non-free)
Pkg-Description: collection of open source applications and utilities healthcare enterprise
 At the core of the dcm4che project is a robust implementation of the
 DICOM standard. The dcm4che-1.x DICOM toolkit is used in many production
 applications across the world, while the current (2.x) version of the
 toolkit has been re-architected for high performance and flexibility.
 .
 Also 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.

Depends: gwyddion

Depends: piano
Homepage: http://mbi.dkfz-heidelberg.de/mbi/software/
License: BSD
Pkg-Description: medical image processing library for surgical planning
 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.

Depends: pixelmed
Homepage: http://www.pixelmed.com/index.html#PixelMedJavaDICOMToolkit
License: Free
Pkg-Description: PixelMed Java DICOM Toolkit
 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.

Depends: slicer
Homepage: http://www.slicer.org/
License: BSD like
Pkg-Description: visualization, registration, segmentation, and quantification of medical data
 The 3D Slicer is freely available, open-source software for visualization,
 registration, segmentation, and quantification of medical data. The slicer
 source seems to be available via CVS only.
 .
 The license statement can be seen at
 http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl

Depends: sofa
Homepage: http://www.sofa-framework.org/
License: LGPL
Pkg-Description: Simulation Open Framework Architecture
 SOFA (Simulation Open Framework Architecture) is an Open Source framework
 primarily targeted at real-time simulation, with an emphasis on medical
 simulation. It is mostly intended for the research community to help develop
 newer algorithms, but can also be used as an efficient prototyping tool.
 Based on an advanced software architecture, it allows to:
  * create complex and evolving simulations by combining new algorithms
    with algorithms already included in SOFA
  * modify most parameters of the simulation - deformable behavior, surface
    representation, solver, constraints, collision algorithm, etc. - by
    simply editing an XML file
  * build complex models from simpler ones using a scene-graph description
  * efficiently simulate the dynamics of interacting objects using abstract
    equation solvers
  * reuse and easily compare a variety of available methods
 SOFA version 1.0 beta 1 was released during the Medicine Meets Virtual
 Reality 2007 conference in Long Beach, California.

Depends: mesa-test-tools
Homepage: http://ihedoc.wustl.edu/mesasoftware/
License: free
Pkg-Description: IHE Test Software for Radiology
 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."

Depends: gdcm
Homepage: http://sourceforge.net/project/showfiles.php?group_id=137895
License: BSD
Pkg-URL: http://sourceforge.net/project/showfiles.php?group_id=137895&package_id=197047
Why: Real Address is http://sourceforge.net/project/showfiles.php?group_id=137895&package_id=197047, but update-tasks is buggy
Pkg-Description: Grass Root DICOM
 GDCM is yet another C++ library dedicated to reading/parsing and writing
 DICOM medical files. GDCM stands as a short for "Grass roots DiCoM".
 Supports currently RAW,JPEG,J2K,JPEG lossless,RLE, deflate(zlib) but
 not JPEG-LS,MPEG for now.

Depends: dicom4j
Homepage: http://dicom4j.sourceforge.net/
License: GPL
Pkg-Description: Java framework for Dicom
 Java framework for Dicom

Depends: opendicom.net
Homepage: http://opendicom.sourceforge.net/
License: LGPL
Responsible: Albert Gnandt <agnandt@users.sourceforge.net>
Pkg-URL: http://ubuntu.mi.hs-heilbronn.de/other/opendicom
Pkg-Description: API to DICOM in C# for Mono
 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 Assocation (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 Libary, 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.

Depends: afni
Homepage: http://afni.nimh.nih.gov/
WNPP: 409849
Responsible: Michael Hanke <michael.hanke@gmail.com>
License: GPL
Pkg-URL: http://sourceforge.net/project/showfiles.php?group_id=61662&package_id=60298
Pkg-Description: environment for processing and displaying functional MRI data
 AFNI is an environment for processing and displaying functional
 MRI data. It provides a complete analysis toolchain, including
 3D cortical surface models, and mapping of volumetric data (SUMA).
 In addition to its own format AFNI understands the NIfTI format and is
 therefore easily usable in combination with FSL and Freesurfer.

Depends: blox
Homepage: http://sourceforge.net/projects/blox/
License: GPL
Pkg-Description: medical imaging and visualization program
 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).

Depends: conquest-dicom-server
Homepage: http://www.xs4all.nl/~ingenium/dicom.html
License: Public domain
Pkg-Description: full featured DICOM server
 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 automatic image forwarding and (de)compression
  * DICOM caching and archive merging 

Depends: dicomscope
Homepage: http://dicom.offis.de/dscope.php.en
License: Has to be clarified
Pkg-Description:
 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 3.5.1 has
 been demonstrated at ECR 2001 and contains numerous extensions,
 including a print server, support for encrypted DICOM communication,
 digital signatures and structured reporting.
 .
 DICOMscope is not meant as a competition for commercial DICOM
 viewers. The application is rather a feasibility study for DICOM
 presentation states. The program is not appropriate to be used in a
 clinical environment, e.g. for reporting.

Depends: dicom3tools
Homepage: http://www.dclunie.com/dicom3tools.html
License: BSD
Pkg-Description: handling offline files of DICOM 3 attributes
 Tools and libraries for handling offline files of DICOM 3 attributes,
 and conversion of proprietary formats to DICOM 3. Can handle older
 ACR/NEMA format data, and some proprietary versions of that such as
 SPI.
 .
 It has extremely limited X display capability and no networking
 code that is why this is not a complete DICOM implementation. 

Depends: ecg2png
X-Homepage-old: http://www.cardiothink.com/downloads
License: GPL
Pkg-Description: convert scanned electrocardiograms into PNG format
 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: 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/ .

Depends: kradview
Homepage: http://www.orcero.org/irbis/kradview/
License: GPLv3
Pkg-Description: the free DICOM viewer for Linux
 Kradview is a GPLed viewer of images obtained for some different
 sources: X-ray, NMR and DICOM-compatible imaging devices that runs on
 free operating systems. 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.
 .
 Kradview as been developed in C and C++ using KDE libraries. The
 parsing, rendering, and processing routines has been developed in C,
 and the graphical interface has been developed in C++ and includes
 the former routines with "extern C" for fast use.

Depends: opensourcepacs
Homepage: http://www.mii.ucla.edu/index.php/MainSite:OpenSourcePacsHome
License: GPL
Pkg-Description: medical image referral, archiving, routing and viewing system
 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/).

Depends: pixelmed-dicom-toolkit
Homepage: http://www.pixelmed.com/index.html#PixelMedJavaDICOMToolkit
License: BSD
Pkg-Description:
 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.
 .
 The toolkit is a completely new implementation, which does not depend
 on any other DICOM tools, commercial or free. It does make use of
 other freely available pure Java tools for compression and XML and
 database support.

Suggests: visit
Homepage: http://www.llnl.gov/visit/
WNPP: 395573
License: 3-clause BSD license with additional disclaimers
Pkg-Description:visualization and graphical analysis tool for viewing scientific data
 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.

Depends: caret
Homepage: http://brainmap.wustl.edu/caret/
WNPP: 421703
License: GPL
Responsible: Michael Hanke <michael.hanke@gmail.com>
Pkg-URL: http://apsy.gse.uni-magdeburg.de/debian/pool/main/c/caret/
Pkg-Description: Computerized Anatomical Reconstruction and Editing
 This software allows for viewing and manipulating surface
 reconstructions of the cerebral and cerebellar cortex, viewing
 volumes and for displaying experimental data on the surfaces and
 volumes.
 .
 Caret can download and use stereotaxic atlases (human, monkey, mouse
 and rat) from an open online database.

Depends: mni-autoreg
Homepage: http://www.bic.mni.mcgill.ca/software/mni_autoreg/
License: no-free, but GPLed parts
Responsible: Michael Hanke <michael.hanke@gmail.com>
Pkg-URL: http://apsy.gse.uni-magdeburg.de/debian/pool/contrib/m/mni-autoreg-model/
Pkg-Description: MNI average brain (305 MRI) stereotaxic registration model
 This package provides a version of the MNI Average Brain (an average of 305
 T1-weighted MRI scans, linearly transformed to Talairach space) specially
 adapted for use with the MNI Linear Registration Package.
 .
  * average_305.mnc - a version of the average MRI that covers the whole brain
    (unlike the original Talairach atlas), sampled with 1mm cubic voxels
  * average_305_mask.mnc - a mask of the brain in average_305.mnc
  * average_305_headmask.mnc - another mask, required for nonlinear mode
 .
 Remark: Michael Hanke agreed to take over his stuff from mentors
 http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg
 and
 http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg-model
 to Debian Med svn and start group maintenance.

Depends: mni-n3
Homepage: http://www.bic.mni.mcgill.ca/software/N3/
License: BSDish
Responsible: Michael Hanke <michael.hanke@gmail.com>
Pkg-URL: http://mentors.debian.net/debian/pool/main/m/mni-n3/
Pkg-Description: MNI Non-parametric Non-uniformity Normalization
 MNI Non-parametric Non-uniformity Normalization (N3). This package provides
 the 'nu_correct' tool for unsupervised correction of radio frequency (RF)
 field inhomogenities in MR volumes. Two packages are provided:
  * mni-n3 - provides 'nu_correct'
  * libebtks-dev - MNI support library with numerical types and algorithms
 .
 Remark: Michael Hanke agreed to take over his stuff from mentors
 http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-n3
 to Debian Med svn and start group maintenance.

Depends: brainvisa
Homepage: http://brainvisa.info/
License: Free? (CeCill License)
Pkg-Description: image processing factory for MR images
 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.

Depends: maris
Homepage: http://maris.homelinux.org/
License: GPL
Pkg-Description: package suite for Radiological Workflow
 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 develope a system
 that is an ensamble of single pieces that cooperate together using
 IHE profiles.

Depends: lipsia
Homepage: http://www.cbs.mpg.de/institute/software/lipsia
License: GPL
Responsible: Felix Botner <botner@cbs.mpg.de>
Pkg-URL: ftp://lipsia.cbs.mpg.de/lipsia
Pkg-Description: Analysis of MRI and fMRI data - binary
 Leipzig Image Processing and Statistical Inference Algorithms
 (LIPSIA)
 .
 The software package LIPSIA was developed by the Max Planck Institute
 of Cognitive Neuroscience, Leipzig, 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
 effcient 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 LIPSIA was the efficiency of the software
 implementation. In LIPSIA, particular emphasis was placed on the
 development of new visualization and segmentation techniques that
 support visualizations of individual brain anatomy so that experts
 can assess the exact location of activation patterns in individual
 brains. LIPSIA is non- commercial. LIPSIA is freely available upon
 request. However, as we don't have suffcient manpower, we can't
 support an unlimited number of LIPSIA users.  Therefore, we plan to
 offer LIPSIA initially on lytoa limited number of cooperation
 partners. Please contact us, if you are interested in becoming a
 LIPSIA cooperation partner.
