Task: Imaging
Description: Debian Med imaging packages
 This metapackage 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 2008 and consists of 18 parts.
 .
 For more information, you can visit the NEMA homepage
 http://medical.nema.org/ .
 .
 The status of the official DICOM base standard plus all the
 supplements and correction items are summarized at David Clunie's webpage:
 http://www.dclunie.com/dicom-status/status.html
 where you'll find direct links to the most recent yearly edition
 ftp://medical.nema.org/medical/dicom/2008/ .

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

Suggests: imagemagick, pngquant, imview

Depends: nifti-bin

Depends: aeskulap

Depends: fsl
Published-Title: Advances in functional and structural MR image analysis and implementation as FSL
Published-Authors: 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, P.M. Matthews
Published-In: NeuroImage, 23:208-219
Published-Year: 2004
Published-DOI: 10.1016/j.neuroimage.2004.07.051

Depends: fslview
Published-Title: Advances in functional and structural MR image analysis and implementation as FSL
Published-Authors: 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, P.M. Matthews
Published-In: NeuroImage, 23:208-219
Published-Year: 2004
Published-DOI: 10.1016/j.neuroimage.2004.07.051

Depends: via-bin

Depends: gwyddion

Depends: sofa-apps

Depends: python-mvpa
Why: Suggested by maintainer Michael Hanke <michael.hanke@gmail.com>
Published-Title: PyMVPA: a unifying approach to the analysis of neuroscientific data
Published-Authors: Michael Hanke, Yaroslav O. Halchenko, Per B. Sederberg, Emanuele Olivetti, Ingo Fründ, Jochem W. Rieger, Christoph S. Herrmann, James V. Haxby, Stephen José Hanson, Stefan Pollmann
Published-In: Frontiers in Neuroinformatics, 3:3
Published-Year: 2009
Published-URL: http://www.frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/003.2009/
Published-DOI: 10.3389/neuro.11.003.2009


Depends: python-nipy
Why: Although listed in -dev task, it also has a strong focus on interactive
 data analysis.

Depends: python-nipype
Why: Although listed in -dev task, it also has a strong focus on interactive
 data analysis.

Depends: caret
Registration: http://brainmap.wustl.edu/register.html
Published-Title: An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex
Published-Authors: David C. Van Essen, Heather A. Drury, James Dickson, John Harwell, Donna Hanlon, Charles H. Anderson
Published-In: Journal of American Medical Informatics Association, 8(5): 443-459
Published-Year: 2001
Published-URL: http://www.pubmedcentral.nih.gov/articlerender.fcgi?pubmedid=11522765

Depends: libgdcm-tools

Depends: slicer

Depends: lipsia
Published-Title: Lipsia—a new software system for the evaluation of functional magnetic resonance images of the human brain
Published-Authors: Gabriele Lohmann, Karsten Müller, Volker Bosch, Heiko Mentzel, Sven Hessler, Lin Chen, S. Zysset, D. Yves von Cramon
Published-In: Computerized Medical Imaging and Graphics, 25: 449-457
Published-Year: 2001
Published-URL: http://www.medicalimagingandgraphics.com/article/S0895-6111(01)00008-8
Published-DOI: 10.1016/S0895-6111(01)00008-8

Depends: dicom3tools

Depends: odin
Published-Title: ODIN: Object-oriented development interface for NMR
Published-Authors: Thies H. Jochimsen, Michael von Mengershausen
Published-In: Journal of Magnetic Resonance 170:67-78
Published-Year: 2004
Published-URL: http://od1n.sourceforge.net/odin.pdf

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/).
Remark: With libvia an alternative implementation is already part of Debian.

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: 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: 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: devide
Homepage: http://code.google.com/p/devide/
License: BSD
WNPP: 509110
Responsible: Mathieu Malaterre <mathieu.malaterre@gmail.com>
Pkg-Description: Delft Visualization and Image processing Development Environment
 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

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.
Published-Title: AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages
Published-Authors: Robert W. Cox
Published-In: Computers and Biomedical Research, 29:162-173
Published-Year: 1996
Published-URL: http://afni.nimh.nih.gov/pub/dist/doc/papers/afni_paper1.pdf

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: OFFIS
WNPP: 508990
Responsible: Mathieu Malaterre <mathieu.malaterre@gmail.com>
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/dicomscope/trunk
Pkg-Description: DICOMscope - DICOM Viewer
 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: ecg2png
X-Homepage-old: http://www.cardiothink.com/downloads
Homepage: http://www.freshports.org/graphics/ecg2png/
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: 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/ .

Depends: kradview
Homepage: http://www.orcero.org/irbis/kradview/
License: GPLv3
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/kradview/trunk
Responsible: Andreas Tille <tille@debian.org>
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
WNPP: 509113
Responsible: Mathieu Malaterre <mathieu.malaterre@gmail.com>
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: 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: There was some previous work on this software which is stalled currently
 Michael Hanke agreed to take over his stuff from mentors
 http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=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: There was some previous work on this software which is stalled currently
 Michael Hanke agreed to take over his stuff from mentors
 http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=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: micromanager
Homepage: http://www.micro-manager.org/
License: free, but some nonfree parts with NDA
Responsible: Johan Henriksson <johan.henriksson@ki.se>
Pkg-URL: http://mahogny.areta.org/temp/debs/
Pkg-Description: imaging and control of automated microscopes, shutters, cameras etc.
 µManager is an Open Source software package for imaging and control
 of automated microscopes. Together with ImageJ, a popular image processing
 package, μManager provides a comprehensive imaging solution – comparable to
 commercially available ones.
 .
 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.

Suggests: mrisim
Homepage: http://packages.bic.mni.mcgill.ca/tgz/
License: BSD-like
Pkg-Description: simulator for magnetic resonance imaging data
 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.

Depends: fiji
Homepage: http://pacific.mpi-cbg.de/
Responsible: Mark Longair <mark-debianlists@longair.net>
Pkg-URL: http://pacific.mpi-cbg.de/wiki/index.php/Downloads
Pkg-Description: The Fiji image processing suite (based on ImageJ)
 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: 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.

Depends: pixelmed
Homepage: http://www.pixelmed.com/
License: BSD
Language: Java
Responsible: Mathieu Malaterre <mathieu.malaterre@gmail.com>
WNPP: 547184
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.
 .
 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.

Depends: cdmedicpacs
Homepage: http://cdmedicpacsweb.sourceforge.net/
License: GPL2
Pkg-URL: http://sourceforge.net/projects/cdmedicpacsweb/files/
Pkg-Description: web interface to PACS to access DICOM study images
 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

Depends: stir
Homepage: http://stir.sourceforge.net/
License: GPL
Pkg-Description: Software for Tomographic Image Reconstruction
 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: Even if this is GPLed software the download requires registration.

Depends: openelectrophy
Homepage: http://neuralensemble.org/trac/OpenElectrophy
License: Cecill v2 (GPL-compatible)
Language: Python
Responsible: Michael Hanke <michael.hanke@gmail.com>
WNPP: 556552
Published-In: Frontiers in Neuroinformatics, 3:14
Published-Year: 2009
Published-DOI: 10.3389/neuro.11.014.2009
Pkg-Description: data analysis framework for intra- and extra-cellular recordings
 This package provide a library und GUI for analyzing electrophysiological
 data. The data handling and storage uses a MySQL-server. The package is written
 in pure Python.

Comment: Several related R packages are listed at CRAN:
         http://cran.r-project.org/web/views/MedicalImaging.html
