Debian Med Project
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Summary
Imaging development
Debian Med packages for medical image development

This metapackage will install Debian packages which might be useful for developing applications for medical image processing.

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The list to the right includes various software projects which are of some interest to the Debian Med Project. Currently, only a few of them are available as Debian packages. It is our goal, however, to include all software in Debian Med which can sensibly add to a high quality Debian Pure Blend.

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

Links to other tasks
Index of all tasks

Debian Med Imaging development packages

Official Debian packages

Cimg-dev
powerful image processing library
Homepage not available
Version: 1.2.0.1
License: DFSG free
Official Debian package -
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The CImg Library is a C++ toolkit providing simple classes and functions to load, save, process and display images in your own C++ code. It consists only of a single header file CImg.h that must be included in your program source. It contains useful image processing algorithms for loading/saving, resizing/rotating, filtering, object drawing (text, lines, faces, ellipses, 
 ...), etc.
Images are instancied by a class able to represent images up to 4-dimension wide (from 1-D scalar signals to 3-D volumes of vector-valued pixels), with template pixel types. It depends on a minimal number of libraries : you can compile it with only standard C libraries. No need for exotic libraries and complex dependencies.
Ctn-dev
Development files for Central Test Node, a DICOM implementation 		Version: 3.0.6
License: DFSG free
Official Debian package -
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DICOM is the standard for image storage, annotation, and networking. It is used widely for medical imaging.
This package includes the header files and static library used for creating programs that use the CTN library.
Libigstk3-dev
Toolkit for image-guided surgery applications 		Version: 3.0.0~cvs20080716
License: DFSG free
Official Debian package -
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This package contains the development files needed to build your own IGSTK applications.
Libinsighttoolkit3-dev
Image processing toolkit for registration and segmentation - development 		Version: 3.8.0
License: DFSG free
Official Debian package -
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ITK is an open-source software toolkit for performing registration and segmentation. Segmentation is the process of identifying and classifying data found in a digitally sampled representation. Typically the sampled representation is an image acquired from such medical instrumentation as CT or MRI scanners. Registration is the task of aligning or developing correspondences between data. For example, in the medical environment, a CT scan may be aligned with a MRI scan in order to combine the information contained in both.
This package contains the development files needed to build your own ITK applications.
Libmdc2-dev
Medical Image (DICOM, ECAT, ...) conversion tool 		Version: 0.10.4
License: DFSG free
Official Debian package -
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This project stands for Medical Image Conversion. Released under the (L)GPL, it comes with the full C-source code of the library, a flexible command line utility and a neat graphical front-end using the GTK+ toolkit. The currently supported formats are: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 and PNG.
Static library, include files and documentation for developers.
Libminc-dev
MNI medical image format development environment 		Version: 2.0.16
License: DFSG free
Official Debian package -
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This package contains the library and headers for libminc2 and libvolume_io2.
The Minc file format is a highly flexible medical image file format. Minc version 1 is built on top of the NetCDF generalized data format. Minc version 2 is built on top of the HDF data format. This library handles both formats. In each case the format is simple, self-describing, extensible, portable and N-dimensional, with programming interfaces for both low-level data access and high-level volume manipulation. On top of the libraries is a suite of generic image-file manipulation tools. The format, libraries and tools are designed for use in a medical-imaging research environment : they are simple and powerful and make no attempt to provide a pretty interface to users.
Libnifti1-dev
IO libraries for the NIfTI-1 data format
Maintainer: Michael Hanke
 Version: 1.1.0
License: DFSG free
Official Debian package -
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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.
This package provides the header files and static libraries of libniftiio, znzlib, libnifticdf and the high-level libfslio.
Libvolpack1-dev
fast volume rendering library 		Version: 1.0b3
License: DFSG free
Official Debian package -
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VolPack is a software library for fast, high-quality volume rendering with this features: 
 * Renders data sampled on a regular, three-dimensional grid.
 * Supports user-specified transfer functions for both opacity and color.
 * Provides a shading model with directional light sources, multiple material
   types with different reflective properties, depth cueing, and shadows.
 * Produces color (24 bits/pixel) or grayscale (8 bits/pixel) renderings,
   with or without an alpha channel.
 * Supports arbitrary affine view transformations.
 * Supports a flexible data format that allows an arbitrary C structure to be
   associated with each voxel.
This is the development package.
Python-mvpa
multivariate pattern analysis with Python
Maintainer: Michael Hanke
 Version: 0.4.0
License: DFSG free
Official Debian package -
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Python module to ease pattern classification analyses of large datasets. It provides high-level abstraction of typical processing steps (e.g. data preparation, classification, feature selection, generalization testing), a number of implementations of some popular algorithms (e.g. kNN, Ridge Regressions, Sparse Multinomial Logistic Regression), and bindings to external machine learning libraries (libsvm, shogun).
While it is not limited to neuroimaging data (e.g. fMRI, or EEG) it is eminently suited for such datasets.

Official Debian packages (Suggested)

Igstk-examples
Example programs for IGSTK 		Version: 3.0.0~cvs20080716
License: DFSG free
Official Debian package -
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This package contains examples from the IGSTK source.
Insighttoolkit3-examples
Image processing toolkit for registration and segmentation - examples 		Version: 3.8.0
License: DFSG free
Official Debian package -
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ITK is an open-source software toolkit for performing registration and segmentation. Segmentation is the process of identifying and classifying data found in a digitally sampled representation. Typically the sampled representation is an image acquired from such medical instrumentation as CT or MRI scanners. Registration is the task of aligning or developing correspondences between data. For example, in the medical environment, a CT scan may be aligned with a MRI scan in order to combine the information contained in both.
This package contains the source for example programs.
Libnifti-doc
NIfTI library API documentation
Maintainer: Michael Hanke
 Version: 1.1.0
License: DFSG free
Official Debian package -
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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.
This package provides the library API reference documentation.
Libvtk5
Visualization Toolkit - A high level 3D visualization library 		Version: 5.0.4
License: DFSG free
Official Debian package -
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VTK - the Visualization Toolkit is an object oriented, high level library that allows one to easily write C++ programs, Tcl, Python and Java scripts that do 3D visualization. This package provides the shared libraries needed to run C++ programs that use VTK. To compile C++ code that uses VTK you have to install libvtk5-dev.
VTK enables users to concentrate on their work by providing a large number of excellent and feature packed high level functions that do visualization. The library needs OpenGL to render the graphics and for Linux machines Mesa is necessary. The terms/copyright can be read in /usr/share/doc/vtk/README and README.html. VTK-Linux-HOWTO has information about using vtk, getting documentataion or help and instructions on building VTK.
Python-libavg
libavg Ain't Vector Graphics
Maintainer: Torsten Werner
 Version: 0.8.0
License: DFSG free
Official Debian package -
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libavg is a high-level multimedia platform with a focus on interactive installations. It is meant to pick up where Macromedia Director leaves off and gives you high-quality hardware-accelerated visuals as well as easy and flexible authoring, testing and deployment. libavg integrates well with other open-source solutions for sound, networking and hardware device support, resulting in a complete and well-integrated package. It uses an xml-based layout language for screen design and Python as scripting language.

Experimental or unofficial Debian packages, projects with packaging stuff in SVN

Libmni-perllib-perl
The MNI Perl Library
Responsible: Michael Hanke
License: Artistic License
Unofficial Debian package
Collection of various Perl module used by other MNI software packages.
Remark: Michael Hanke agreed to take over his stuff from mentors http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=libmni-perllib-perl to Debian Med svn and start group maintenance.
Rumba
analysis of MRI anatomical and functional datasets
License: Artistic
Unofficial Debian package
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.
Remark: There seems to be a lot of packaging stuff just done by upstream guessed from http://itanix.rutgers.edu/rumba/ and the project homepage.

Debian packages not available

Libvista2-dev
software environment for computer vision research
License: GPL
Debian package not available
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/).
This is the development package.
Nipy
development platform for neuroimaging research
License: Free
Debian package not available
Python-based development platform for neuroimaging research. Please see https://cirl.berkeley.edu/view/Grants/BrainPySummary for a description of the various subprojects.
Odin - wnpp
Object Oriented Development Interface for NMR
License: GPL
Debian package not available
C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms. It is
State-of-the-Art: Contemporary magnetic resonance imaging techniques are available, for example sequence modules for echo-planar imaging and spiral-imaging, parallel imaging with GRAPPA reconstruction, two-dimensional pulses and field-map-based distortion corrections.
Easy-to-Use: All common steps, from compiling your sequence to plotting or simulating it, can be performed within a graphical user interface.
Hardware Independent: ODIN runs on a variety of operating systems and scanners. Once you develop a sequence, it can be executed/simulated on very different hardware, ranging from a real-time sequence controller to your personal workstation.
Truly Object-Oriented: Written in C++ with an object-oriented design, ODIN is very modular, flexible and requires very little code to write: The sequences that come with ODIN are easy to understand and modify.