Debian Med Imaging packages

Aeskulap is able to load a series of special images stored in the DICOM format for review. Additionally it is able to query and fetch DICOM images from archive nodes (also called PACS) over the network. Aeskulap tries to achieve a full open source replacement for commercially available DICOM viewers.

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.

This software allows for creating, viewing and manipulating surface reconstructions of the cerebral and cerebellar cortex, viewing volumes and for displaying experimental data on the surfaces and volumes. While Caret is primarily a GUI application with 'caret_command' there is also a versatile command line tool, that allows access to a substantial proportion of Caret's functionality.

Caret can download and use stereotaxic atlases (human, monkey, mouse and rat) from an open online database.

Reference:

 Van Essen, D.C., Dickson, J., Harwell, J., Hanlon, D., Anderson, C.H. and
 Drury, H.A. 2001. An Integrated Software System for Surface-based Analyses of
 Cerebral Cortex. Journal of American Medical Informatics Association, 8(5),
 443-459.

DICOM is the standard for image storage, annotation, and networking. It is used widely for medical imaging. The Central Test Node software (CTN) provides an implementation of this standard.

This package includes the binary and run-time configuration files for CTN.

CTSim provides an interactive computed tomography simulator. Computed tomography is the technique of estimating the interior of an object by measuring x-ray absorption through that object.

CTSim has both command-line tools and a graphical user interface. CTSim has very educational trace modes for viewing the data collection simulation as well as the reconstruction.

DCMTK includes a collection of libraries and applications for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.

This package contains the DCMTK utility applications.

Note: This version was compiled with libssl support.

Command line utilities for creating, modifying, dumping and validating files of DICOM attributes. Support conversion of some proprietary medical image formats to DICOM. Can handle older ACR/NEMA format data, and some proprietary versions of that such as SPI.

The dinifti program converts MRI images stored in DICOM format to NIfTI format. The NIfTI format is thought to be the new standard image format for medical imaging and can be used with for example with FSL, AFNI, SPM, Caret or Freesurfer.

dinifti converts single files, but also supports fully automatic batch conversions of complete dicomdirs. Additionally, converted NIfTI files can be properly named, using image series information from the DICOM files.

This package provides 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.

Gwyddion is a modular program for Scanning Probe Microscopy (SPM) data visualization and analysis. It is primarily intended for analysis of height field data obtained by microscopy techniques like Atomic Force Microscopy (AFM), Magnetic Force Microscopy (MFM), Scanning Tunneling Microscopy (STM), Near-field Scanning Optical Microscopy (SNOM or NSOM) and others. However, it can be used for arbitrary height field and image analysis.

This package contains the main application and its modules. It also contains a GNOME (and Xfce) thumbnailer which creates previews for all file types known to Gwyddion.

Gwyddion's Python scripting interface Pygwy is also included.

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". It supports "stacks", a series of images that share a single window.

It can calculate area and pixel value statistics of user-defined selections. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering.

Spatial calibration is available to provide real world dimensional measurements in units such as millimeters. Density or gray scale calibration is also available.

ImageJ is developed by Wayne Rasband (wayne@codon.nih.gov), is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.

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.

Install this package for the gdcmanon, gdcmconv, gdcmdump, gdcmgendir, gdcmimg, gdcminfo, gdcmpdf, gdcmraw, gdcmscanner, gdcmtar programs.

Leipzig Image Processing and Statistical Inference Algorithms (LIPSIA)

This is a software package for the data processing and evaluation of functional magnetic resonance images. The analysis of fMRI data comprises various aspects including filtering, spatial transformation, statistical evaluation as well as segmentation and visualization. All these aspects are covered by LIPSIA. For the statistical evaluation, a number of well established and peer-reviewed algorithms were implemented in LIPSIA that allow an effcient and user-friendly processing of fMRI data sets. As the amount of data that must be handled is enormous, an important aspect in the development LIPSIA was the efficiency of the software implementation.

LIPSIA operates exclusively on data in the VISTA data format. However, the package contains converters for medical image data in iBruker, ANALYZE and NIfTI format -- converting VISTA images into NIfTI files is also supported.

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.

The program also allows to read unsupported files without compression, to print pixel values or to extract/reorder specified images. It is possible to retrieve the raw binary/ascii image arrays or to write PNG for desktop applications.

This is the command line tool for batch processing.

This package contains tools to manipulate MINC files.

The Minc file format is a highly flexible medical image file format built on top of the NetCDF generalized data format. 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 tools that are shipped with the library (nifti_tool, nifti_stats and nifti1_test).

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.

Using PyNIfTI one can easily read and write NIfTI and ANALYZE images from within Python. The NiftiImage class provides Python-style access to the full header information. Image data is made available via NumPy arrays.

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).

Slicer is an application for computer scientists and clinical researchers. The platform provides functionality for segmentation, registration and three-dimensional visualization of multi-modal image data, as well as advanced image analysis algorithms for diffusion tensor imaging, functional magnetic resonance imaging and image-guided therapy. Standard image file formats are supported, and the application integrates interface capabilities to biomedical research software and image informatics frameworks.

3D Slicer main application.

SOFA is an Open Source framework primarily targeted at real-time simulation, with an emphasis on medical simulation. It is mostly intended for the research community to help develop newer algorithms, but can also be used as an efficient prototyping tool.

This package contains the SOFA main application.

VIA is a volumetric image analysis suite for functional and structural (medical) images. The suite consists of different tools ranging from simple data handling over viewers to complex image transformation.

All tools operate on data in VISTA format. The package contains several converters from e.g. PNG, PGM or PNM to this data format and back.

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.

The program also allows to read unsupported files without compression, to print pixel values or to extract/reorder specified images. It is possible to retrieve the raw binary/ascii image arrays or to write PNG for desktop applications.

This is the program version for X based on GTK+. Processes only one file at a time.

ImageMagick is a software suite to create, edit, and compose bitmap images. It can read, convert and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to translate, flip, mirror, rotate, scale, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves. All manipulations can be achieved through shell commands as well as through an X11 graphical interface (display).

Imview is an application which

• Displays a large number of image formats.
• Displays 2D or 3D (as slices) images with a very good zoom and pan feature.
• Works with multi-spectral, time series or multi-page documents (e.g.: Satellite images, TIFF stacks, animated GIFs and heterogeneous multi-component files).
• Displays all pixel types (1-bit to 64-bit data, integer or floating point).
• Arbitrary 1-D profile of 2-D images (or of 2-D slices of 3-D images) can be displayed.
• Has support for arbitrary colourmaps for all pixel types (i.e.: false colour display).
• Has standard image manipulation facilities (brightness/contrast, gamma, zoom, crop, rotation, etc).
• Can be controlled remotely via sockets and text commands (for easy integration into various image analysis systems).
• Images can be uploaded into Imview via sockets or shared memory.
• And much more!

pngquant is a command-line conversion utility to quantize and dither truecolor PNG images, especially those with a full alpha channel, down to 8-bit (or smaller) RGBA-palette PNGs. Such images are usually two to four times smaller than the full 32-bit versions, and partial transparency is preserved quite nicely. This makes pngquant especially useful both for Web sites and for PlayStation 2 development, where one of the texture formats is RGBA-palette-based (though not PNG-compressed). This is the same technique used for many of the images on the Miscellaneous Transparent PNGs page (http://www.libpng.org/pub/png/pngs-img.html), and the results are often indistinguishable from the original, truecolor PNG images.

Optimizers (like pngcrush and optipng) optimize the compression, usually losslessly, while pngquant quantizes colors down to 256 (or fewer) distinct RGBA combinations, which is lossy.

FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data.

FSL provides an easy to use GUI.

FSL interoperates well with other brain imaging related software. This includes Caret, FreeSurfer (cortical flattening and modelling).

DICOMscope is a free DICOM viewer which can display uncompressed, monochrome DICOM images from all modalities and which supports monitor calibration according to DICOM part 14 as well as presentation states. DICOMscope offers a print client (DICOM Basic Grayscale Print Management) which also implements the optional Presentation LUT SOP Class. The development of this prototype was commissioned by the "Committee for the Advancement of DICOM" and demonstrated at the European Congress of Radiology ECR 1999. An enhanced version was developed for the "DICOM Display Consistency Demonstration" at RSNA InfoRAD 1999. The current release 3.5.1 has been demonstrated at ECR 2001 and contains numerous extensions, including a print server, support for encrypted DICOM communication, digital signatures and structured reporting.

DICOMscope is not meant as a competition for commercial DICOM viewers. The application is rather a feasibility study for DICOM presentation states. The program is not appropriate to be used in a clinical environment, e.g. for reporting.

Kradview is a GPLed viewer of images obtained for some different sources: X-ray, NMR and DICOM-compatible imaging devices that runs on free operating systems. Its aim is a easy to use DICOM viewer with instant rendering of images, no matter the size and the zoom of the DICOM image. It covers the "let's see the the X-ray image" need of the medical professional.

Kradview as been developed in C and C++ using KDE libraries. The parsing, rendering, and processing routines has been developed in C, and the graphical interface has been developed in C++ and includes the former routines with "extern C" for fast use.

AFNI is an environment for processing and displaying functional MRI data. It provides a complete analysis toolchain, including 3D cortical surface models, and mapping of volumetric data (SUMA). In addition to its own format AFNI understands the NIfTI format and is therefore easily usable in combination with FSL and Freesurfer.

Web based PACS (Picture Archiving and Communication System) to access DICOM studies images, in an easy and quick manner.

• Easy configuration of PACS nodes (AE,IP,Port) , status, statistics of storage form web interface.
• Dynamic web page generation from DICOM data +- prospective preparation when system is idle.
• Automatic video(mp4/gif) generation from Heart MRI at Patient’s heart bit frame rate and XA at 15 fps.
• Still images in jpeg with Window/Level from DICOM header when present or with Histogram algorithm.
• Possibility on large Studies of still images to make a single mp4 for Series instead of a bunch of jpeg.
• Easy web deletion of Series/Studies and auto deletion (Study date/DB insertion) for temporal PACS.
• Good DICOM interaction with Diagnostic Modalities and commercial DICOM Viewers/Work Stations.
• Good DICOM interaction with free DICOM Viewers Aeskulap

Fiji is a project aiming at simplifying:

• the installation of ImageJ
• the usage of ImageJ
• the usage of specific, powerful ImageJ plugins
• the development of plugins using ImageJ

µManager is an Open Source software package for imaging and control of automated microscopes. Together with ImageJ, a popular image processing package, μManager provides a comprehensive imaging solution – comparable to commercially available ones.

Unfortunately there is a pile of dirty licenses involved so I'm not sure this is ready for Debian yet. Some of the code cannot be given out and some drivers require kernel modules to be built. You have to sign NDAs to get access to all the code.

This package provides a version of the MNI Average Brain (an average of 305 T1-weighted MRI scans, linearly transformed to Talairach space) specially adapted for use with the MNI Linear Registration Package.

• average_305.mnc - a version of the average MRI that covers the whole brain (unlike the original Talairach atlas), sampled with 1mm cubic voxels
• average_305_mask.mnc - a mask of the brain in average_305.mnc
• average_305_headmask.mnc - another mask, required for nonlinear mode

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. Two packages are provided:

• mni-n3 - provides 'nu_correct'
• libebtks-dev - MNI support library with numerical types and algorithms

The openDICOM.NET project implements a new approach towards DICOM (Digital Imaging and Communications in Medicine) libraries. DICOM is a worldwide standard in Medical IT and is provided by the National Electrical Manufacturers Assocation (NEMA). This standard specifies the way medical images and meta data like study or patient related data is stored and communicated over different digital medias. Thus, DICOM is a binary protocol and data format.

The openDICOM# Class Libary, main part of the openDICOM.NET project, provides an API to DICOM in C# for Mono and the .NET Framework. It is a completely new implementation of DICOM. In contrast to other similar libraries the intention of this implementation is to provide a clean classification with support of unidirectional DICOM data streaming. Another implemented goal is the support of DICOM as XML. This is not standard conform but very use- and powerful within software development, storage and manipulation. Currently, full read support of DICOM output stream and full write support to XML is supposed to be provided. The entire DICOM content can be accessed as sequence or as tree of class instances. Latter is the default representation of DICOM content by the library.

The openDICOM.NET Utils are a collection of console tools for working with the needed data dictionaries in different data formats (binary and textual), query of ACR-NEMA (prior DICOM standard) and DICOM files and transcoding them into image formats like JPEG and XML files. These utils are written in C# for Mono and the .NET Framework and are using the openDICOM# API for processing.

The openDICOM.NET Navigator recapitulates the openDICOM.NET Utils in form of a GTK# GUI. It provides different views with focus on DICOM data sets and visualization. Connectivity to GIMP is also given for single image processing purpose as well as the possibility to run through multi-frame images like a movie.

The openDICOM.NET Beagle Filter Plugin increases the usability of ACR-NEMA and DICOM query within your desktop. It makes DICOM content overall indexable for retrieval. The Beagle search engine relies on Mono/.NET and works in the background of your system, but is able to detect content changes in realtime (depending on your configuration).

All GUI applications focus the popular GNOME desktop, but are 100% platform independent by relying on Mono.

DeVIDE, or the Delft Visualization and Image processing Development Environment, is a Python-based dataflow application builder that enables the rapid prototyping of medical visualization and image processing applications via visual programming. In other words, by visually connecting functional blocks (think Yahoo pipes), you can create cool visualizations.

See the DeVIDE website at http://visualisation.tudelft.nl/Projects/DeVIDE

This package provide a library und GUI for analyzing electrophysiological data. The data handling and storage uses a MySQL-server. The package is written in pure Python.

OpenSourcePACS is a free, open source image referral, archiving, routing and viewing system. It adds functionality beyond conventional PACS by integrating wet read functions, implemented through DICOM Presentation State and Structured Reporting standards.

In its first release, OpenSourcePACS delivers a complete wet read system, enabling an imaging clinic or hospital to offer its services over the web to physicians within or outside the institution. In future releases, we hope to incorporate more RIS (dictation, transcription, and reporting) functionality.

OpenSourcePACS is a product of the UCLA Medical Imaging Informatics group (http://www.mii.ucla.edu/).

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.

The toolkit is a completely new implementation, which does not depend on any other DICOM tools, commercial or free. It does make use of other freely available pure Java tools for compression and XML and database support.

VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes.

VisIt was designed to handle very large data set sizes in the terascale range and yet can also handle small data sets in the kilobyte range.

BioImage Suite 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 intergrated with other biomedical image processing software, such as FSL and SPM. This site provides information, downloads, documentation, and other resources for users of the software.

BioImage Suite was developed at Yale University and has been extensively used at different labs at Yale since 2004.

There is a forum at BioImage Suite site for discussion of compiling it from source and packaging issues at http://research.yale.edu/bioimagesuite/forum/index.php?board=12.0

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://pni.med.jhu.edu/methods/morph.htm).

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.

A full featured DICOM server that has been developed based on and heavily extending the public domain UCDMC DICOM code. Some possible applications of the Conquest DICOM software are:

• DICOM training and testing
• Demonstration and research image archives
• Image format conversion from a scanner with DICOM network access
• DICOM image viewing and slide making
• DICOM image selection, (limited) editing, and splitting and merging of series
• Advanced automatic image forwarding and (de)compression
• DICOM caching and archive merging

At the core of the dcm4che project is a robust implementation of the DICOM standard. The dcm4che-1.x DICOM toolkit is used in many production applications across the world, while the current (2.x) version of the toolkit has been re-architected for high performance and flexibility.

Also contained within the dcm4che project is dcm4chee (the extra 'e' stands for 'enterprise'). dcm4chee is an Image Manager/Image Archive (according to IHE). The application contains the DICOM, HL7 services and interfaces that are required to provide storage, retrieval, and workflow to a healthcare environment. dcm4chee is pre-packaged and deployed within the JBoss application server. By taking advantage of many JBoss features (JMS, EJB, Servlet Engine, etc.), and assuming the role of several IHE actors for the sake of interoperability, the application provides many robust and scalable services.

Java framework for Dicom

It is specifically aimed at postprocessing of segmented datasets, but offers some functionality for raw data as well. Voxel elements (=voxels) and pixel ("picture element") are viewed as data sets and can be processed by this program as kind of a final polishing process.

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.

The problems this program is designed to solve are (1) an ECG scanned at relatively high resolution (300 to 600 dots per inch) imposes a substantial load on the web browser because it contains about 6 million pixels which may require 18 to 24 MB of RAM to store for display. Also, (2) typical scanners convert a clean paper ECG into a multitude of colors, include green and blue. The resulting file cannot be compressed efficiently because it does not contain as much redundancy, and thus takes more time to transmit over low-speed network connections.

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/).

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.

The MESA software release which is available at http://ihedoc.wustl.edu/mesasoftware/10.15.0/dist/ provides several tools that might cover a wide range of applications for Integrating the Healthcare Enterprise (IHE) testing.

Another important element of the IHE testing process is the set of software tools HIMSS and RSNA have commissioned. Developed by the Electronic Radiology Laboratory at the Mallinckrodt Institute of Radiology, Washington University of St. Louis, the MESA tools are designed for use by participating companies in implementing IHE capabilities in their systems and preparing for the Connectathon. Their purpose is to provide communication partners, test data and test plans to allow organizations to provide a baseline level of testing as they implement the IHE Technical Framework. These tools are made available to participants during the period of an IHE demonstration year and are then released into the public domain at the end of that cycle. The latest version of the MESA Test Tools available in the public domain can be found here.

This kind of software is definitively valuable for information systems vendors and imaging systems vendors.

Because the CTN Debian package is based on an upstream dead project these tools should have a high priority for packaging because the CTN homepage http://erl.wustl.edu/research/dicom/ctn.html says: "The CTN software is also embedded within the MESA tools. The version of CTN software in those tools does not have a separate release number but is more current than version 3.0.6."

mrisim is a simple Magnetic Resonance Imaging (MRI) simulation program which produces MINC volumes from a segmented and labelled brain phantom. It allows intrinsic tissue parameters (T1, T2...) and pulse sequence parameters (TR, TE ...) to be specified and then produces simulated images with noise. Currently, no artifacts are implemented.

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.

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.

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.

The toolkit is a completely new implementation, which does not depend on any other DICOM tools, commercial or free. It does make use of other freely available pure Java tools for compression and XML and database support.

STIR is Open Source software for use in tomographic imaging. Its aim is to provide a Multi-Platform Object-Oriented framework for all data manipulations in tomographic imaging. Currently, the emphasis is on (iterative) image reconstruction in PET, but other application areas and imaging modalities can and might be added.

STIR is the successor of the PARAPET software library which was the result of a (European Union funded) collaboration between 6 different partners, the PARAPET project..