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
Registration: http://www.fmrib.ox.ac.uk/fsldownloads/
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: python-nitime
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: dicomscope

Depends: pixelmed-java

Depends: vmtk

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 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.
 .
 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: 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 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.

Depends: afni
Homepage: http://afni.nimh.nih.gov/
WNPP: 409849
Responsible: NeuroDebian Team <team@neuro.debian.net>
License: GPL
Pkg-URL: http://neuro.debian.net/pkgs/afni.html
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: 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/).

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: NeuroDebian Team <team@neuro.debian.net>
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: NeuroDebian Team <team@neuro.debian.net>
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 develop a system
 that is an ensemble 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: 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: NeuroDebian Team <team@neuro.debian.net>
WNPP: 556552
Pkg-URL: http://neuro.debian.net/pkgs/openelectrophy.html
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.

Depends: invesalius
Homepage: http://svn.softwarepublico.gov.br/trac/invesalius
License: GPL-2
X-Screenshot: http://dl.dropbox.com/u/4053278/invesalius_trac/screenshots/invesalius3_promed_0446_bone.png
WNPP: 584920
Pkg-URL: http://svn.softwarepublico.gov.br/trac/invesalius/wiki/downloads/3.0-beta-1#GNULinux
Pkg-Description: 3D medical imaging reconstruction
 InVesalius generates 3D medical imaging reconstruction based on a
 sequence of 2D DICOM files acquired with CT or MRI equipments.
 InVesalius is internationalized (currently available in English,
 Portuguese, French and Spanish), multi-platform (GNU Linux, Windows
 and MacOS) and provides several tools:
  * DICOM-support including:
     * ACR-NEMA version 1 and 2
     * DICOM version 3.0 (including various encodings of JPEG -lossless and lossy-, RLE)
  * Image manipulation facilities (zoom, pan, rotation, brightness/contrast, etc)
  * Segmentation based on 2D slices
  * Pre-defined threshold ranges according to tissue of interest
  * Edition tools (similar to Paint Brush) based on 2D slices
  * 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)

Depends: loci-bio-formats
Homepage: http://www.loci.wisc.edu/software/bio-formats
License: GPL
Language: Java
Pkg-Description: a standalone Java library for reading and writing life sciences image file formats
 Bio-Formats is a standalone Java library for reading and writing life
 sciences image file formats. It is capable of parsing both pixels and
 metadata for a large number of formats, as well as writing to several
 formats.  The software includes a visualisation tool VisBio and it also
 works with ImageJ.
 .
 Currentla Bio-Formats supports 75 formats including the most very
 frequently used in biological and medical research.
Remark: This library would enhance the package imagej


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


Depends: mricron
Published-Title: Improving lesion-symptom mapping
Published-Authors: Chris Rorden, Hans-Otto Karnath, Leonardo Bonilha
Published-In: Journal of Cognitive Neuroscience, 19: 1081-1088
Published-Year: 2007
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/17583985


Depends: voxbo
Registration: http://voxbo.org/usage.html


Depends: mrtrix
Published-Title: Robust determination of the fibre orientation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical deconvolution
Published-Authors: J-Donald Tournier, Fernando Calamantea, Alan Connelly
Published-In: NeuroImage, 35: 1459-1472
Published-Year: 2007
Published-DOI: 10.1016/j.neuroimage.2007.02.016


Depends: ants
Published-Title: The optimal template effect in hippocampus studies of diseased populations
Published-Authors: Brian B. Avants, Paul Yushkevich, John Pluta, David Minkoff, Marc Korczykowski, John Detre and James C. Gee
Published-In: NeuroImage, 49: 2457-2466
Published-Year: 2010
Published-DOI: 10.1016/j.neuroimage.2009.09.062
X-Institution: UCLA Center for Computation Biology


Depends: itksnap
Published-Title: User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability
Published-Authors: Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig
Published-In: Neuroimage, 31: 1116-1128
Published-Year: 2006
Published-DOI: 10.1016/j.neuroimage.2006.01.015


Depends: mriconvert
Homepage: http://lcni.uoregon.edu/~jolinda/MRIConvert/
License: GPL
Responsible: Steve M. Robbins <smr@debian.org>
WNPP: 599880
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mriconvert/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mriconvert/trunk/
Pkg-Description: converts DICOM files to other formats
 MRIConvert is a medical image file conversion utility that converts
 DICOM files to NIfTI 1.1, Analyze 7.5 , SPM99/Analyze, BrainVoyager,
 and MetaImage volume formats.


Depends: connectomeviewer
Homepage: http://www.connectomics.org/viewer
License: GPL-3
Responsible: NeuroDebian Team <team@neuro.debian.net>
WNPP: 565431
Registration: http://www.connectomeviewer.org/users/register
Pkg-Description: visualization and analysis of structural neuroimaging data
 The ConnectomeViewer application was developed to meet the needs of basic and
 clinical neuroscientists, as well as complex network scientists, providing an
 integrative, extensible platform to visualize and analyze Connectomics
 data. It provides
 .
  * Support of the connectome and generic neuroimaging file formats:
    metadata in XML, networks (NetworkX), surfaces (GIfTI), volumes (NIfTI),
    fiber tracks (TrackVis)
  * Interactive data manipulation and scripting capabilities with Python
  * Integration of the neuroanatomy knowledge-base ConnectomeWiki
  * Storage and retrieval of datasets from the ConnectomeDatabase
Published-Title: Mapping the Structural Core of Human Cerebral Cortex
Published-Authors: Patric Hagmann, Leila Cammoun, Xavier Gigandet, Reto Meuli, Christopher J. Honey, Van J. Wedeen, Olaf Sporns
Published-In: PLoS Biology 6: e159
Published-Year: 2008
Published-DOI: 10.1371/journal.pbio.0060159

Depends: sigviewer
License: GPL
Responsible: NeuroDebian Team <team@neuro.debian.net>
WNPP: 585535
Homepage: http://sigviewer.sourceforge.net
Vcs-Git: git://git.debian.org/pkg-exppsy/sigviewer.git
Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/sigviewer.git;a=summary
Pkg-Description: GUI viewer for biosignals such as EEG, EMG, and ECG
 SigViewer is a viewing and scoring software for biomedical signal
 data.  It relies on biosig4c++ library which supports a number of
 data formats (including EDF, BDF, GDF, BrainVision, BCI2000, CFWB,
 HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI,
 EEG1100, FAMOS, SigmaPLpro, TMS32). The complete list of supported
 file formats is available at
 http://hci.tugraz.at/schloegl/biosig/TESTED .


Depends: mni-icbm152-nlin-2009
Homepage: http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
License: custom, DFSG-compliant
Responsible: NeuroDebian Team <team@neuro.debian.net>
Pkg-Description: MNI stereotaxic space human brain template
 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.
Published-Authors: V.S. Fonov, A.C. Evans, R.C. McKinstry, C.R. Almli and D.L. Collins
Published-Title: Unbiased nonlinear average age-appropriate brain templates from birth to adulthood.
Published-In: NeuroImage, 47, Supplement 1: 102
Published-Year: 2009
Remark: This package is waiting for the Debian data package archive to become available.


Depends: mni-colin27-nifti
Homepage: http://packages.bic.mni.mcgill.ca/tgz/
License: custom, DFSG-compliant
Responsible: NeuroDebian Team <team@neuro.debian.net>
Pkg-URL: http://neuro.debian.net/pkgs/mni-colin27-nifti.html
Pkg-Description: Talairach stereotaxic space template
 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.
Published-Authors: C.J. Holmes, R. Hoge, L. Collins, R. Woods, A.W. Toga, A.C. Evans
Published-Title: Enhancement of MR images using registration for signal averaging.
Published-In: J Comput Assist Tomogr, 22: 324-333
Published-Year: 1998
Remark: This package is waiting for the Debian data package archive to become available.

Depends: gofigure2
Homepage: http://gofigure2.sf.net
License: BSD
Language: C++
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gofigure2/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gofigure2/trunk/
WNPP: 587051
Responsible: Mathieu Malaterre <mathieu.malaterre@gmail.com>
Pkg-Description: Cross-platform for visualizing, processing and analysing of bioimages
 GoFigure2 is an open-source, cross-platform application for
 visualizing, processing and analyzing of multidimensional microscopy
 data. Users can visualize, segment and track cells through time,
 detect cell-division and ultimately generate lineages.


Depends: mipav
Homepage: http://mipav.cit.nih.gov/
License: custom, non-free, closed-source (DFSG-compliant version promised)
Responsible: NeuroDebian Team <team@neuro.debian.net>
WNPP: 587645
Pkg-URL: http://neuro.debian.net/pkgs/mipav.html
Pkg-Description: quantitative analysis and visualization of medical images
 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.
Published-Authors: M.J. McAuliffe, F.M Lalonde, D. McGarry, W. Gandler,  K. Csaky, B.L Trus
Published-Title: Medical Image Processing, Analysis & Visualization In Clinical Research
Published-In: IEEE Computer-based Medical Systems (CBMS)
Published-Year: 2001


Depends: jist
Homepage: http://www.nitrc.org/projects/jist/
License: LGPL
Responsible: NeuroDebian Team <team@neuro.debian.net>
WNPP: 587820
Pkg-URL: http://neuro.debian.net/pkgs/jist.html
Pkg-Description: Java Image Science Toolkit
 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.
Published-Authors: B.C. Lucas, J.A. Bogovic, A. Carass, P.-L. Bazin, J.L. Prince, D. Pham, B.A. Landman
Published-Title: The Java Image Science Toolkit (JIST) for Rapid Prototyping and Publishing of Neuroimaging Software.
Published-In: Neuroinformatics 8, 5-17
Published-Year: 2010


Depends: openmeeg-tools
License: CeCILL-B
Published-Title: OpenMEEG: opensource software for quasistatic bioelectromagnetics
Published-Authors: Alexandre Gramfort, Théodore Papadopoulo, Emmanuel Olivi, Maureen Clerc
Published-In: Preprint
Published-URL: http://hal.archives-ouvertes.fr/inria-00467061/en/


Depends: jemris
License: GPL-2+
Responsible: NeuroDebian Team <team@neuro.debian.net>
WNPP: 590469
Homepage: http://www.jemris.org/
Pkg-Description: high performance computing MRI simulator
 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.
Published-Authors: Tony Stöcker, Kaveh Vahedipour, Daniel Pflugfelder, N. Jon Shah
Published-Title: High-performance computing MRI simulations
Published-In: Magnetic Resonance in Medicine
Published-Year: 2010
Published-DOI: 10.1002/mrm.22406

Depends: insightapplications
Homepage: http://itk.org/ITK/resources/applications.html
License: BSD
WNPP: 598556
Responsible: Steve M. Robbins <smr@debian.org>
Language: C++, Python, Tcl
Pkg-Description: InsightToolKit (ITK) based medical imaging applications
 A variety of applications providing segmentation, registration, and
 other medical image processing algorithms such as MRI bias field
 correction.

Depends: tempo
Homepage: http://code.google.com/p/tempo/
License: BSD
Language: C++, Qt
Pkg-Description: 3D visualization of brain electrical activity
 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: Packaged for OpenSuSE http://en.opensuse.org/TEMPO

Depends: dti-query
Homepage: http://graphics.stanford.edu/projects/dti/software/index.html
License: MIT
Language: C++
Pkg-Description: dynamic queries of the white matter brain pathways
 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: Depends on RAPID library that is available under non-commercial
 licensing terms.