Implemented available packages completely in med-imaging(-dev) tasks file
← Revision 55 as of 2009-03-16 03:33:36
converted to 1.6 markup
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|This wiki page is meant to reflect the rather volatile aspects of DebianMedImaging. If you are looking for more information or translations into your own language be sure to visit the [http://www.debian.org/devel/debian-med official Debian-Med website].||This wiki page is meant to reflect the rather volatile aspects of DebianMedImaging. If you are looking for more information or translations into your own language be sure to visit the [[http://www.debian.org/devel/debian-med|official Debian-Med website]].|
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|Med-imaging is a metapackage from the DebianMed CustomDebianDistribution. It contains the software listed on [http://debian-med.alioth.debian.org/tasks/imaging.php the tasks page]. You might also like to notice the [http://debian-med.alioth.debian.org/tasks/imaging-dev.php packages for developing medical imaging applications].||Med-imaging is a metapackage from the DebianMed CustomDebianDistribution. It contains the software listed on [[http://debian-med.alioth.debian.org/tasks/imaging.html|the tasks page]]. You might also like to notice the [[http://debian-med.alioth.debian.org/tasks/imaging-dev.html|packages for developing medical imaging applications]].|
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| * [http://people.debian.org/~igloo/popcon-graphs/index.php?packages=amide+ctn+ctsim+dcmtk+dicomnifti+fsl+fslview+imagej+libinsighttoolkit3.0+libniftiio0+libnifti1+paul+python-nifti+xmedcon&show_installed=on&want_legend=on&beenhere=1 Package popularity statistics]
* [http://qa.debian.org/developer.php?packages=amide+ctn+ctsim+dcmtk+dicomnifti+fsl+fslview+imagej+insighttoolkit+nifticlib+paul+pynifti+vtk+xmedcon Technical summary] (bugs, version information, ...)
| * [[http://people.debian.org/~igloo/popcon-graphs/index.php?packages=amide+ctn+ctsim+dcmtk+dicomnifti+fsl+fslview+imagej+libinsighttoolkit3.0+libniftiio0+libnifti1+paul+python-nifti+xmedcon&show_installed=on&want_legend=on&beenhere=1|Package popularity statistics]]
* [[http://qa.debian.org/developer.php?packages=amide+ctn+ctsim+dcmtk+dicomnifti+fsl+fslview+imagej+insighttoolkit+nifticlib+paul+pynifti+vtk+xmedcon|Technical summary]] (bugs, version information, ...)
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|== Inoffcial and prospective packages ==
||<tablewidth="100%"rowbgcolor="#ffff99">''Name'' ||''Description'' ||''Licence'' ||''ITP'' ||''Upstream website'' ||
||[http://afni.nimh.nih.gov/afni/ afni] ||AFNI (which might be an acronym for Analyis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes. ||GPL ||[http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=409849 #409849] ||[http://afni.nimh.nih.gov/afni/ link] ||
||[http://apsy.gse.uni-magdeburg.de/main/index.psp?sec=1&page=hanke/debian&lang=en caret] || Computerized Anatomical Reconstruction and Editing Toolkit. 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. || GPL ||[http://bugs.debian.org/421703 #421703] ||[http://brainmap.wustl.edu/caret/ link] ||
||[http://apsy.gse.uni-magdeburg.de/main/index.psp?sec=1&page=hanke/debian&lang=en mni-autoreg] || completely automatic multi-resolution fitting method to transform anatomical brain images into the Talairach stereotaxic coordinate system. Packages for not-yet-packaged dependencies are provided as well (mni-autoreg-model, libmni-perllib-perl and libgetopt-tabular-perl). ||non-free (deps: free) ||None ||[http://www.bic.mni.mcgill.ca/software/mni_autoreg/ link] ||
||[http://apsy.gse.uni-magdeburg.de/main/index.psp?sec=1&page=hanke/debian&lang=en mni-n3] ||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. Package for not-yet-packaged dependency is provided as well (libebtks-dev). ||BSDish ||None ||[http://www.bic.mni.mcgill.ca/software/N3/ link] ||
||[http://od1n.sourceforge.net/ odin] || C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms ||GPL ||[http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=410318 RFP:#410318] ||[http://od1n.sourceforge.net/ link] ||
||[http://www.rumba.rutgers.edu/soft/index.php rumba] ||RUMBA (Rutgers University Mind Brain Analysis) toolkit was developed for the analysis of MRI anatomical and functional datasets. The toolkit provides means to perform I/O, registration, motion correction, filtering, PCA, ICA, GLM, and visualization. To take advantage of speedy C++ written I/O and processing routines, bindings to high level programming (python) or computational (R) environments are available. ||Artistic ||none ||[http://www.rumba.rutgers.edu/soft/index.php link] ||
There might be [http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=med-imaging;firstname.lastname@example.org additional ITP bugs] tagged as ''med-imaging'' in the Debian bug tracking system (BTS).
== Unpackaged software ==
This is either ''free'' or at least ''open-source'' imaging-related software which is not yet packaged for Debian. If you are looking for something to do, this might be a source of inspiration. If you decide to package something, please follow the [http://www.debian.org/doc/developers-reference/ch-pkgs.en.html regular procedure] by filing an ITP bug and tagging it with ''med-imaging'' as described [http://people.debian.org/~tille/debian-med/talks/paper-cdd/debian-cdd.html/ap-bts.en.html#s-howto_itp here].
If you think there is some software missing in this list, feel free to add it.
||<tablewidth="100%"rowbgcolor="#ffcc99">''Name'' ||''Description'' ||''Licence'' ||
||[http://www.bioimagesuite.org BioImage Suite] ||BioImage Suite is an integrated image analysis software suite developed at Yale University. It 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. ||GPLv2 ||
||[http://pni.med.jhu.edu/blox/ blox] ||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. ||GPL ||
||[http://brainvisa.info/ brainvisa] ||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. ||Free? (CeCill License) ||
||[http://www.xs4all.nl/~ingenium/dicom.html ConQuest DICOM server] ||A full featured DICOM server that has been developed based on and heavily extending the public domain UCDMC DICOM code. ||Free ||
||[http://sourceforge.net/projects/dcm4che/ dcm4che] ||dcm4che is an implementation of DICOM in Java. The sample applications may be useful on their own. It also includes an IHE compliant Image Archive application, based on J2EE. ||LGPL ||
||[http://dicom.offis.de/dscope.php.en DICOMScope] ||DICOMScope is a free DICOM viewer which can display uncompressed, monochrome DICOM images of all modalities and supports a calibration of the monitor according to DICOM part 14 as well as the new Presentation States. DICOMScope offers a print client (DICOM Basic Grayscale Print Management) which also implements the optional Presentation LUT SOP Class. The current release 3.5.1 contains numerous extensions, including a print server, support for encrypted DICOM communication, digital signatures and structured reporting. ||Unknown ||
||[http://www.dclunie.com/dicom3tools.html Dicom3tools] ||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. ||Unknown ||
||[http://www.cardiothink.com/downloads/ ecg2png] ||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. ||GPL ||
||[http://www.orcero.org/irbis/kradview/ kradview] ||kradview is a viewer of images obtained from some different sources: X-ray, NMR, and all DICOM-compatible imaging devices. Its aim is to be a complete platform for medical imaging and image processing. ||GPL ||
||[http://maris.homelinux.org/ MARiS] ||«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.» ||Free ||
||[http://www.mirthproject.org Mirth] ||«Mirth is an open source cross-platform HL7 interface engine that enables bi-directional sending of HL7 messages between systems and applications over multiple transports. By utilizing an enterprise service bus framework and a channel-based architecture, Mirth allows messages to be filtered, transformed, and routed based on user-defined rules. Creating HL7 interfaces for existing systems becomes easy using the web-based interface and channel creation wizard which associates applications with Mirth engine components.» ||Free ||
||[http://mbi.dkfz-heidelberg.de/mbi/software/ piano] ||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. ||BSD ||
||[http://neuroimaging.scipy.org/ nipy] ||Python-based development platform for neuroimaging research. Please see [https://cirl.berkeley.edu/view/Grants/BrainPySummary here] for a description of the various subprojects. ||Free ||
||[http://www.pixelmed.com/index.html#PixelMedJavaDICOMToolkit 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. ||Free ||
||[http://www.slicer.org/ slicer] ||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. ||[http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl non-free] ||
|There might be [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=med-imaging;email@example.com|additional ITP bugs]] tagged as ''med-imaging'' in the Debian bug tracking system (BTS).|
This page contains lists of various imaging-related software projects which are of some interest to the DebianMed Project. Currently, only a few of them are available as Debian packages. However, it is the goal of Debian-med, to include all software which can sensibly add to a high quality Custom Debian Distribution.
This wiki page is meant to reflect the rather volatile aspects of DebianMedImaging. If you are looking for more information or translations into your own language be sure to visit the official Debian-Med website.
Med-imaging is a metapackage from the DebianMed CustomDebianDistribution. It contains the software listed on the tasks page. You might also like to notice the packages for developing medical imaging applications.
Popcon data and technical summary of mediacl imaging packages Debian
Debian provides various information about each package. Most interesting might be:
There might be additional ITP bugs tagged as med-imaging in the Debian bug tracking system (BTS).