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||[http://packages.debian.org/unstable/source/imagej ImageJ]||ImageJ is a Java image processing program inspired by NIH Image. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw".||public domain||[http://rsb.info.nih.gov/ij/ link]||

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].

Packages in Debian

The following table contains a list of software that is already available in Debian. Debian provides various information about each package. Most interesting might be:




Upstream website

[http://packages.debian.org/unstable/graphics/amide amide]

AMIDE: (Amide's a Medical Imaging Data Examiner) AMIDE is a tool for viewing and analyzing medical image data sets. It's capabilities include the simultaneous handling of multiple data sets imported from a variety of file formats, image fusion, 3D region of interest drawing and analysis, volume rendering, and rigid body alignments.


[http://amide.sourceforge.net/ link]

[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 compliant

[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.


[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++.


[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.


[https://www.cbi.nyu.edu/public/software/dinifti/ link]

[http://packages.debian.org/unstable/source/fslview fslview]

FSLView is a viewer for 3d and 4d MRI data as well as DTI images. FSLView is able to display ANALYZE and NIFTI files. The viewer supports multiple 2d viewing modes (orthogonal, lightbox or single slices), but also 3d volume rendering. Additionally FSLView is able to visualize timeseries and can overlay metrical and stereotaxic atlas data. FSLView is part of FSL.


[http://www.fmrib.ox.ac.uk/fsl/fslview link]

[http://packages.debian.org/unstable/source/imagej ImageJ]

ImageJ is a Java image processing program inspired by NIH Image. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw".

public domain

[http://rsb.info.nih.gov/ij/ 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.


[http://www.physik.uni-halle.de/~e2od5/debian/paul.html link]

[http://packages.debian.org/unstable/source/pynifti pynifti]

Python interface to the NIfTI I/O libraries


[http://apsy.gse.uni-magdeburg.de/main/index.psp?page=hanke/pynifti&lang=en 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.


[http://xmedcon.sourceforge.net/ link]

Inoffcial and prospective packages





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.


[http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=409849 #409849]

[http://afni.nimh.nih.gov/afni/ link]


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.


[http://bugs.debian.org/421703 #421703]

[http://brainmap.wustl.edu/caret/ link]

[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.


[http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=332666 #332666]

[http://www.fmrib.ox.ac.uk/fsl/ 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)


[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).



[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


[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.



[http://www.rumba.rutgers.edu/soft/index.php link]

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.




[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.


[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.


[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.


[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.


[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.


[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.


[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.


[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.


[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.


[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.


[http://www.slicer.org/ slicer]

The 3D Slicer is freely available, open-source software for visualization, registration, segmentation, and quantification of medical data. Please note that slicer depends on ITK which is currently not available as a Debian package. Update there is a package for [http://packages.debian.org/testing/libs/libinsighttoolkit3.0 ITK] now. The slicer source seems to be available via CVS only.

[http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl non-free]