Differences between revisions 1 and 42 (spanning 41 versions)
Revision 1 as of 2006-11-30 19:46:25
Size: 7657
Editor: MichaelHanke
Comment: Inital draft: Wiki version of the software list for Debian-med imaging software
Revision 42 as of 2008-03-19 13:48:01
Size: 7362
Editor: AndreasTille
Comment: Bioimagesuite and blox just are on the tasks page
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
= Debian-Med: Medical Imaging =
The list below includes various imaging-
related software projects which are of some interest to the Debian-Med 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 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.
Line 4: Line 3:
||||||||<tablestyle="width: 100%" #CCFF99 ( >'''Packages in Debian'''||
||''Name''||''Description''||''Licence''||''Homepage''||
||[http://packages.debian.org/unstable/source/ctn ctn]||The Central Test Node (CTN) software is a DICOM implementation which was designed to be used at the RSNA (Radiological Society of North America) annual meetings to foster cooperative demonstrations by the medical imaging vendors. The goal was to provide a centralized implementation that facilitated vendor participation based on the evolving DICOM standard.||DFSG-free||[http://www.erl.wustl.edu/DICOM/ctn.html link]||
||[http://packages.debian.org/unstable/source/ctsim ctsim]||CTSim provides an interactive computed tomography simulator. Computed tomography is the technique of estimating the interior of an object by on measuring x-ray absorption through an object. It has both command-line tools as well as a graphical user interface. CTSim has very education trace modes for viewing the data collection simulation as well as the reconstruction.||GPL||[http://www.ctsim.org/ link]||
||[http://packages.debian.org/unstable/source/dcmtk dcmtk]||DCMTK is a collection of libraries and applications implementing large parts the DICOM standard for medical image communication. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstration image storage and worklist servers. DCMTK is written in a mixture of ANSI C and C++.||BSD||[http://dicom.offis.de/dcmtk.php.en link]||
||[http://packages.debian.org/unstable/source/dicomnifti dicomnifti]||The dinifti program converts MRI images stored in DICOM format to NIfTI format. Files in the NIfTI format can be used with the programs FSL, AFNI and SPM. Dinifti converts single files, but also supports batch conversions of complete directories.||GPL||[https://www.cbi.nyu.edu/public/software/dinifti/ link]||
||[http://packages.debian.org/unstable/source/nifticlib nifticlib]||Niftilib is a set of i/o libraries for reading and writing files in the NIfTI-1 data format. NIfTI-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images.||public domain||[http://niftilib.sourceforge.net link]||
||[http://packages.debian.org/unstable/source/paul paul]||Paul = Program zur Auswertung und Umwandlung von Laserbildern (for non German speakers: Program to evaluate and convert laser images). Especially designed to work with gray scaled image sequences but may be useful for any image. The use of imlib gives great flexibility of file formats and is fast. Features: move images until they match; cut images precisely; create clickable HTML maps; 2D-FFT; operations onto single image or set of images.||GPL||[http://www.physik.uni-halle.de/~e2od5/debian/paul.html link]||
||[http://packages.debian.org/unstable/source/xmedcon (x)medcon]||The project name stands for Medical Image Conversion. It provides a flexible command-line utility (for batch conversion) and a neat graphical front-end using the Gtk+ toolkit. The supported formats are: Acr/Nema 2.0, Analyze (SPM), Concorde, DICOM 3.0 (incl. Siemens "mosaic" format), Ecat/Matrix 6.4, InterFile3.3, Gif87a/89a and raw/binary data. The library (libmdc) can be used by other programs for import and export (see e.g. AMIDE) and is extendable for other formats.||(L)GPL||[http://xmedcon.sourceforge.net/ link]||
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].
Line 14: Line 5:
[http://people.debian.org/~igloo/popcon-graphs/index.php?packages=ctn+ctsim+dcmtk+dicomnifti+libniftiio0+paul+xmedcon&show_installed=on&want_legend=on&beenhere=1 Popularity stats]
[http://qa.debian.org/developer.php?packages=ctn+ctsim+dcmtk+dicomnifti+nifticlib+paul+xmedcon Technical summary]
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].
Line 17: Line 7:
||||||||||<tablestyle="width: 100%" #FFFF99 ( >'''Inoffcial and prospective packages'''||
||''Name''||''Description''||''Licence''||''ITP''||''Homepage''||
||[http://apsy.gse.uni-magdeburg.de/fsl fsl]||FSL is a comprehensive library of image analysis and statistical tools for fMRI, MRI, and DTI brain imaging data.||non-free||[http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=332666 #332666]||[http://www.fmrib.ox.ac.uk/fsl/ link]||
== Popcon data and technical summary of mediacl imaging packages Debian ==
Debian provides various information about each package. Most interesting might be:
Line 21: Line 10:
||||||||||<tablestyle="width: 100%" #FFCC99 ( >'''Unpackaged software'''||
||''Name''
||''Description''||''Licence''||
||[http://amide.sourceforge.net/ amide]||AMIDE ("AMIDE's a Medical Image Data Examiner") is a completely free tool for viewing, analyzing, and registering volumetric medical imaging data sets.||GPL||
||[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://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://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://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://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, ...)

There might be [http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=med-imaging;users=debian-med@lists.debian.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://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] ||

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 [http://www.debian.org/devel/debian-med official Debian-Med website].

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].

Popcon data and technical summary of mediacl imaging packages Debian

Debian provides various information about each package. Most interesting might be:

There might be [http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=med-imaging;users=debian-med@lists.debian.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.

Name

Description

Licence

[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]