Debian Med Imaging development packages

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 instantiated 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.

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.

This package contains the header files and static library needed to compile applications that use OpenCV (Open Computer Vision).

The Open Computer Vision Library is a collection of algorithms and sample code for various computer vision problems. The library is compatible with IPL (Intel's Image Processing Library) and, if available, can use IPP (Intel's Integrated Performance Primitives) for better performance.

OpenCV provides low level portable data types and operators, and a set of high level functionalities for video acquisition, image processing and analysis, structural analysis, motion analysis and object tracking, object recognition, camera calibration and 3D reconstruction.

Grassroots DiCoM is a C++ library for DICOM medical files. It is automatically wrapped to python/C#/Java (using swig). It supports RAW,JPEG (lossy/lossless),J2K,JPEG-LS, RLE and deflated.

Headers and static libraries for libgdcm. These are not needed to use GDCM, but are needed to build plugins or programs that link against libgdcm.

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.

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.

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.

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 and libnifticdf.

Teem is a coordinated group of libraries for representing, processing, and visualizing scientific raster data. Teem includes command-line tools that permit the library functions to be quickly applied to files and streams, without having to write any code. The most important and useful libraries in Teem are:

• Nrrd (and the unu command-line tool on top of it) supports a range of operations for transforming N-dimensional raster data (resample, crop, slice, project, histogram, etc.), as well as the NRRD file format for storing arrays and their meta-information.
• Gage: fast convolution-based measurements at arbitrary point locations in volume datasets (scalar, vector, tensor, etc.)
• Mite: a multi-threaded ray-casting volume render with transfer functions based on any quantity Gage can measure
• Ten: for estimating, processing, and visualizing diffusion tensor fields, including fiber tractography methods.

This package provides the Teem header files required to compile C++ programs that use Teem to do 3D visualisation.

VIA is a volumetric image analysis suite. The included libraries provide about 70 image analysis functions.

This package provides the header files and static libraries of vialib, vxlib and viaio.

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.

VXL (the Vision-something-Libraries) is a collection of C++ libraries designed for computer vision research and implementation. It was created from TargetJr and the IUE with the aim of making a light, fast and consistent system. VXL is written in ANSI/ISO C++ and is designed to be portable over many platforms.

This package contains the development files needed to build your own VXL applications.

ODIN is a framework for magnetic resonance imaging (MRI). It covers the whole toolchain of MRI, from low-level data acquisition to image reconstruction. In particular, it aims at rapid prototyping of MRI sequences. The sequences can be programmed using a high-level, object oriented, C++ programming interface. It provides advanced sequence analysis tools, such as interactive plotting of k-space trajectories, a user interface for a fast compile-link-test cycle and a powerful MRI simulator which supports different virtual samples. For fast and flexible image reconstruction, ODIN contains a highly customizable, multi-threaded data-processing framework.

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.

NiPy is a Python-based framework for the analysis of structural and functional neuroimaging data. It currently has a full system for general linear modeling of functional magnetic resonance imaging (fMRI).

The Image-Guided Surgery Toolkit (IGstk: pronounced IGStick) is a high-level component-based framework providing common functionality for image-guided surgery applications.

This software framework consists of a set of high-level components integrated with other low-level open source software libraries and application programming interfaces (API) from hardware vendors.

The cornerstone of IGstk is robustness. IGstk provides the following high-level functionality: Ability to read and display medical images including CT and MRI in DICOM format. An interface to common tracking hardware (e.g. AURORA from Northern Digital Inc.). A graphical user interface and visualization capability including a four-quadrant view (axial, sagittal, coronal, and 3D) as well as a multi-slice axial view (from 1 by 1 to many by many such as 10 by 10).

Registration: point based registration and a means for selecting these points. Robust common internal software services for logging, exception-handling and problem resolution.

This package contains examples from the IGstk source.

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.

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.

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.

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.

Collection of various Perl module used by other MNI software packages.

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.

This project aims at defining a script language (G'MIC) dedicated to image processing. The interpreter of this minimal but powerful language is distributed as open-source modules/libraries embeddable in third-party applications. G'MIC can be used to define complex image processing pipelines for converting, manipulating, filtering and visualizing generic 1D/2D/3D multi-spectral image datasets. Of course, it is able to manage color images, but also more complex data as image sequences or 3D volumetric data.

G'MIC is an open framework : it is possible to extend the proposed default language with custom G'MIC-written commands, defining thus new image filters. By the way, it already contains a substantial set of pre-defined image processing algorithms.

A Gimp plugin gmic_gimp is available as well.

G'MIC has been designed with portability in mind and runs on different platforms. It can be easily re-used in any other free software, as an external library. It is developed in the Image Team of the GREYC laboratory, in Caen/France, by permanent researchers working in the image processing field.

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.