Debian Med Imaging packages

Aeskulap er i stand til at indlæse en serie af specielle billeder gemt i DICOM-formatet, så de kan gennemses. Derudover er programmet i stand til at hente og sætte billeder fra DICOM i kø fra arkivknuder (også kaldt PACS) over netværket. Aeskulap forsøger at blive en fuldt open source-erstatning for kommercielt tilgængelige DICOM-fremvisere.

AMIDE: (Amide's a Medical Imaging Data Examiner, på dansk: Amides er et dataundersøgelsesværktøj til medicinsk billedbehandling) AMIDE er et værktøj til at fremvise og analysere medicinske billeder af datasæt. Dets egenskaber inkluderer simultan håndtering af adskillige datasæt, importeret fra en vifte af filformater, billedfusion, optegning og analyse for områder af interesse i 3D, optegnelse af volumen, og justering af stive legemer.

Advanced Normalization Tools (ANTS) is an ITK-based suite of normalization, segmentation and template-building tools for quantitative morphometric analysis. Many of the ANTS registration tools are diffeomorphic, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD).

Baseret på BioSig-biblioteket tilbyder denne pakke værktøjer for kommandolinjen, såsom:

• save2gdf: Konverteringsprogram mellem forskellige filformater, inklusive men ikke begrænset til SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF, BDF, CWFB. save2gdf kan også bruges til at overføre eller hente data fra en bscs-server.

CamiTK helps researchers and clinicians to easily and rapidly collaborate in order to prototype CAMI applications, that feature medical images, surgical navigation and biomechanical simulations.

imp is the CamiTK flagship application.

Denne software gør det muligt at skabe, vise og manipulere overfladiske rekonstruktioner af storhjernen og hjernebarken, vise volumener, samt til at vise eksperimentelle data fra overflader og volumener. Selv om Caret primært er en applikation med en grafisk brugerflade, så er der også et fleksibelt kommandolinjeværktøj, der tillader adgang til en stor del af Carets egenskaber.

Caret kan hente og anvende stereotaktiske atlasser (menneske, abe, mus og rotte) fra en åben online-database.

Nogle af Carets egenskaber er kun tilgængelig når ekstra datafiler, der tilbydes af pakken caret-data, er tilgængelige. Dette inkluderer:

• Kortvolumener til overflader via PALS-atlas
• Morfing i flere opløsninger
• Projektion af foci via PALS-atlas
• Overfladebaseret registrering
• Udjævning af overflade

På nuværende tidspunkt er pakken caret-data kun tilgængelig fra arkivet NeuroDebian. Se venligst http://neuro.debian.net for mere information.

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 inkluderer en samling af biblioteker og applikationer til at undersøge, konstruere og konvertere DICOM-billedfiler, håndtere medier uden forbindelse, sende og modtage billeder over en netværksforbindelse, såvel som demonstrative servere til billedlagring og arbejdslister (»worklist«).

Denne pakke indeholder DCMTK-redskabsprogrammerne.

Bemærk: Denne version blev kompileret med libssl-understøttelse.

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.

dinifti-programmet konverterer MRI-billeder gemt i DICOM-formatet til NIfTI-formatet. NIfTI-formatet er tænkt som det nye standardbilledformat for medicinske billeder og kan bruges for eksempel med FSL, AFNI, SPM, Caret eller Freesurfer.

dinifti konverterer enkeltfiler, men understøter også fulde batchkonverteringer af fulde dicom-mapper. Derudover kan konverterede NIfTI- filer navngives korrekt, med brug af billedserieinformation fra DICOM- filerne.

DICOMscope er en fri DICOM-fremviser som kan vise ukomprimerede monochrome DICOM-billeder fra alle modaliteter og som understøtter kalibrering af skærm jævnfør DICOM part 14 samt præsentationstilstande.

DICOMscope tilbyder en udskrivningsklient (DICOM Basic Grayscale Print Management) som også implementerer den valgfrie Presentation LUT SOP- klasse.

Udviklingen af denne prototype blev igangsat af »Committee for the Advancement of DICOM« og fremvist på European Congress of Radiology ECR 1999. En forbedret udgave blev udviklet for »DICOM Display Consistency Demonstration« på RSNA InfoRAD 1999.

Den aktuelle version 3.5.1 er blevet demonstreret på ECR 2001 og indeholder mange udvidelser, inklusiv en udskrivningsserver, understøttelse af krypteret DICOM-kommunikation, digitale underskriftere og struktureret rapportering.

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.

Ginkgo CADx tilbyder en komplet løsning til DICOM-fremvisning, der har avancerede egenskaber og understøtter udvidelsesmoduler.

• Nem grænseflade som kan tilpasses gennem profiler.
• Visualisering af DICOM-billeder med fuld funktionalitet.
• Komplet værktøjssæt (måling, markører, tekst, ...).
• Understøttelse af flere modaliteter (neurologisk, radiologisk, dermatologisk, oftalmologisk, ultralyd, endoskopi, ...).
• Understøttelse af dikomisering fra JPEG, PNG, GIF og TIFF.
• Understøttelse af fuld EMH-integration: HL7-standardiserede og IHE-kompatible arbejdsgange.
• PACS-arbejdsstation (C-FIND, C-MOVE, C-STORE, ...).
• Kan udvides gennem tilpassede udvidelsesmoduler.
• Mosaik-komposition af retina-billeder.
• Automatisk diagnostik af retina-analyse.
• Automatisk psoriasis-diagnostik.

Hovedformålet med GoFigure2 er at tilbyde

• interaktion/visualisering/navigering i 4D flerkanals biobilleder
• gem/hent information relateret til billedbehandlingen, analyseresultater
• udtrække objekter fra biobilleder (f.eks. nucleii, cellemembraner ...)
• spore undercellular struktur, celler
• detektere og spore celleopdeling igennem tid
• oprette og visualisere cellelinjeværk

Gwyddion er et modulopbygget program for skanning (Skanning Probe Mikroskopi, SPM), samt visualisering og analyse af data. Det er primært beregnet til analyse af højdefeltdata indhentet via mikroskopiteknikker som

• Atomar Force Mikroskopi (AFM),
• Magnetisk Force Mikroskopi (MFM),
• Skanning Tunneling Mikroskopi (STM),
• Nær-felt Skanning Optisk Mikroskopi (SNOM eller NSOM) og andet. Det kan dog bruges til vilkårlige højdefelter og til billedanalyse.

Denne pakke indeholder det primære program og dets moduler. Den indeholder også en GNOME (og Xfce) miniaturefremstiller som opretter forhåndsvisninger af alle kendte filtyper til Gwyddion.

Gwyddions grænseflade til Python-skripting, Pygwy er også inkluderet.

Det kan vise, redigere, analysere, behandle, gemme og udskrive 8-bit, 16- bit og 32-bit billeder. Det kan læse mange billedformater inklusive TIFF, GIF, JPEG, BMP, DICOM, FITS og »raw«. Det understøtter »stakke«, en serie af billeder som deler et enkelt vinude.

Den kan udarbejde værdistatistikker for områder og billedepunkter fra brugerdefinerede markeringer. Det kan måle afstande og vinkler. Det kan oprette histogrammer over tæthed og plotte linjeprofiler. Det understøtter standardfunktioner til billedbehandling såsom manipulation af kontrast, øget skarphed, udjævning, kantdetektering og median-filtrering.

Rumlig kalibrering er tilgængelig for at tilbyde målinger af dimensioner fra den virkelige verden i enheder som milimeter. Tætheds- eller gråskala- kalibrering er også tilgængelig.

ImageJ er udviklet af Wayne Rasband (wayne@codon.nih.gov), der er ved: the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.

ImageVis3D is a volume rendering application specifically designed to render large data. This is achieved by splitting the dataset into multiple levels of detail (LoD), with each level itself decomposed into multiple bricks (atomic rendering primitive). Interaction occurs at the coarsest LoD, which can be rendered instantaneously on almost all modern systems. After a configurable delay, ImageVis3D will successively render finer levels of detail, until the data are visible at their native resolution.

Development of ImageVis3D is sponsored by the NIH/NCRR Center for Integrative Biomedical Computing (CIBC), and the DOE Visualization And Analytics Center for Enabling Technologies (VACET).

InVesalius generates 3D medical imaging reconstructions based on a sequence of 2D DICOM files acquired with CT or MRI equipments. InVesalius is internationalized (currently available in English, Portuguese, French, German, Spanish, Greek and Chinese) and provides several tools:

• DICOM support including: (a) ACR-NEMA version 1 and 2; (b) DICOM version 3.0 (including various encodings of JPEG -lossless and lossy-, RLE)
• Image manipulation features (zoom, pan, rotation, brightness/contrast, etc)
• Segmentation based on 2D slices
• Pre-defined threshold ranges according to tissue of interest
• Edition tools (similar to Paint Brush) based on 2D slices
• 3D surface creation
• 3D surface connectivity tools
• 3D surface exportation (including: binary STL, OBJ, VRML, Inventor)
• High-quality volume rendering projection
• Pre-defined volume rendering presets
• Volume rendering crop plane
• Picture exportation (including: BMP, TIFF, JPG, PostScript, POV-Ray)

SNAP tilbyder semiautomatisk segmentering af strukturer i medicinske billeder (f.eks. magnetisk ressonansbilleder af hjernen) med brug af aktiv konturmetoder, samt som manuel skitsetegning og billednavigering. Funktioner værd at nævne er:

• Lænket markør for let 3D-navigering
• Manuel segmentering i tre ortogonale planer på en gang
• Understøttelse af mange forskellige 3D-billedformater, inklusiv NIfTI
• Understøttelse af sammenfaldende, lænket visning og segmentering af flere billeder
• Begrænset understøttelse af farvebilleder (f.eks. diffusion tensor-kort)
• 3D-skæringsværktøj for hurtig efterbehandling af segmenteringsresultater

KiNG (Kinemage, Next Generation) is an interactive system for three-dimensional vector graphics. It supports a set of graphics primitives that make it suitable for many types of graphs, plots, and other illustrations; although its first use was to display macromolecular structures for biophysical research. KiNG builds on Mage, JavaMage, and the "kinemage" (kinetic image) concept to deliver a full-featured Java application with a user-friendly interface and integrated editing features. The KiNG jar file can be used within a web page as a Java applet or Java object to promote easy access to kinemages or coordinate files from a web browser.

Grassroots DICOM er et C++-bibliotek for DICOm-medicinske filer. Den omsluttes automatisk om python/C#/Java (med swig). Den understøtter RAW,JPEG (med og uden kvalitetstab),J2K,JPEG-LS, RLE og deflated.

Installer denne pakke for programmerne gdcmanon, gdcmconv, gdcmdiff, gdcmdump, gdcmgendir, gdcmimg, gdcminfo, gdcmpdf, gdcmraw, gdcmscanner, gdcmscu, gdcmtar.

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 efficient 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 of 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.

Command lines tools to run general purpose image processing tasks on 2D and 3D gray scale images, and basic operations on triangular meshes. Supported image processing algorithms are image filtering, combining, image registration, motion compensation for image series, and the estimation of various statiistics over images.

This tool provides a simple 3D renderer that can visualize surfaces directly from 3D volumes and can be used to set 3D landmarks. It is best suited for CT data sets.

Denne pakke indeholder værktøjer til at manipulere MINC-filer.

Minc-filformatet er et stærkt fleksibelt medicinsk billedfilformat bygget oven på det NetCDF-generaliserede dataformat. Formatet er simpelt, selvbeskrivende, kan udvides, flytbart og n-dimensionelt med programmeringsgrænseflader for dataadgang på lavt niveau og manipulering af diskenhed (volume) på højt niveau. Oven på bibliotekerne er en programpakke af generiske manipulationsværktøjer for billedfiler. Formatet, biblioteket og værktøjer er designet for brug i forskningsmiljøer for medicinsk billedfremstilling: De er simple og funktionsrige og gør intet for at vise en pæn brugerflade for brugerne.

MRIConvert er et redskab til konvertering af medicinske billedfiler, der konverterer DICOM-filer til volumen-formaterne NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager og MetaImage volume.

This is a GUI-based visualization and analysis tool for (functional) magnetic resonance imaging. MRIcron can be used to create 2D or 3D renderings of statistical overlay maps on brain anatomy images. Moreover, it aids drawing anatomical regions-of-interest (ROI), or lesion mapping, as well as basic analysis of functional timeseries (e.g. creating plots of peristimulus signal-change).

In addition to 'mricron', this package also provides 'dcm2nii' that supports converting DICOM and PAR/REC images into the NIfTI format, and 'npm' for non-parametric data analysis.

Set of tools to perform diffusion-weighted MRI white matter tractography of the brain in the presence of crossing fibres, using Constrained Spherical Deconvolution, and a probabilisitic streamlines algorithm. Magnetic resonance images in DICOM, ANALYZE, or uncompressed NIfTI format are supported.

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.

OpenMEEG consists of state-of-the art solvers for forward problems in the field of MEG and EEG. Solvers are based on the symmetric Boundary Element method [Kybic et al, 2005], providing excellent accuracy, particularly for superficial cortical sources. OpenMEEG can compute four types of lead fields (EEG, MEG, Internal Potential and Electrical Impedence Tomography).

This package provides command line interface to openmeeg functionality.

OpenSlide er et C-bibliotek, som tilbyder en simpel grænseflade til at læse whole-slide-billeder også kendt som virtuelle dias.

Whole-slide-billeder, også kendt som virtuelle dias, er store, højopløste billeder brugt i digital patologi. Læsning af disse billeder med normale billedværktøjer eller biblioteker er en udfordring, da disse værktøjer typisk er designet for billeder som komfortabelt kan udpakkes i RAM eller en swap-fil. Whole-slide-billeder overgår normalt RAM-størrelsen og fylder ofte en masse gigabyte, når de er udpakket. Derudover er whole-slide typisk i flere opløsninger, og kun en lille mængde af billeddata er krævet ved en bestemt opløsning.

Dette bibliotek understøtter aktuelt:

 -Trestle (.tif)
 -Hamamatsu (.vms, .vmu)
 -Aperio (.svs, .tif)
 -MIRAX (.mrxs)
 -Generic tiled TIFF (.tif)

Denne pakke indeholder kommandolinjeværktøjer for filmanipulering.

Orthanc aims at providing a simple, yet powerful standalone DICOM server. Orthanc can turn any computer running Windows or Linux into a DICOM store (in other words, a mini-PACS system). Its architecture is lightweight, meaning that no complex database administration is required, nor the installation of third-party dependencies.

What makes Orthanc unique is the fact that it provides a RESTful API. Thanks to this major feature, it is possible to drive Orthanc from any computer language. The DICOM tags of the stored medical images can be downloaded in the JSON file format. Furthermore, standard PNG images can be generated on-the-fly from the DICOM instances by Orthanc.

Orthanc lets its users focus on the content of the DICOM files, hiding the complexity of the DICOM format and of the DICOM protocol.

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.

Plastimatch is an open source software for deformable image registration. It is designed for high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). Software features include:

• B-spline method for deformable image registration (GPU and multicore accelerated)
• Demons method for deformable image registration (GPU accelerated)
• ITK-based algorithms for translation, rigid, affine, demons, and B-spline registration
• Pipelined, multi-stage registration framework with seamless conversion between most algorithms and transform types
• Landmark-based deformable registration using thin- plate splines for global registration
• Landmark-based deformable registration using radial basis functions for local corrections
• Broad support for 3D image file formats (using ITK), including DICOM, Nifti, NRRD, MetaImage, and Analyze
• DICOM and DICOM-RT import and export
• XiO import and export

• Plugin to 3D Slicer Plastimatch also features two handy utilities which are not directly related to image registration:

• FDK cone-beam CT reconstruction (GPU and multicore accelerated)

• Digitally reconstructed radiograph (DRR) generation (GPU and multicore accelerated)

Dipy is a toolbox for the analysis of diffusion magnetic resonance imaging data. It features:

• Reconstruction algorithms, e.g. GQI, DTI
• Tractography generation algorithms, e.g. EuDX
• Intelligent downsampling of tracks
• Ultra fast tractography clustering
• Resampling datasets with anisotropic voxels to isotropic
• Visualizing multiple brains simultaneously
• Finding track correspondence between different brains
• Warping tractographies into another space, e.g. MNI space
• Reading many different file formats, e.g. Trackvis or NIfTI
• Dealing with huge tractographies without memory restrictions
• Playing with datasets interactively without storing

PyMVPA eases pattern classification analyses of large datasets, with an accent on neuroimaging. 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, GNB, 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 provides functionality for

• General linear model (GLM) statistical analysis
• Combined slice time correction and motion correction
• General image registration routines with flexible cost functions, optimizers and re-sampling schemes
• Image segmentation
• Basic visualization of results in 2D and 3D
• Basic time series diagnostics
• Clustering and activation pattern analysis across subjects
• Reproducibility analysis for group studies

Nipype interfaces Python to other neuroimaging packages and creates an API for specifying a full analysis pipeline in Python. Currently, it has interfaces for SPM, FSL, AFNI, Freesurfer, but could be extended for other packages (such as lipsia).

Nitime is a Python module for time-series analysis of data from neuroscience experiments. It contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code.

This is a Python package for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi’s powerful visualization engine with a high-level interface for working with MRI and MEG data.

PySurfer offers both a command-line interface designed to broadly replicate Freesurfer’s Tksurfer program as well as a Python library for writing scripts to efficiently explore complex datasets.

SigViewer is a viewing and scoring software for biomedical signal data. It relies on biosig4c++ library which supports a number of data formats (including EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro, TMS32). The complete list of supported file formats is available at http://pub.ist.ac.at/~schloegl/biosig/TESTED .

Besides displaying biosignals, SigViewer supports creating annotations to select artifacts or specific events.

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 (»Simulation Open Framework Architecture«) er et open souce- rammeværktøj primært målrettet mod realtidssimulering, med vægt på medicinsk simulering. Det er hovedsagelig rettet mod forskningssamfundet til at hjælpe med at udvikle nye algoritmer, men kan også bruges som et effektivt værktøj for prototyper.

Denne pakke indeholder hovedprogrammet for SOFA.

Only a subset of the TIFF specification is supported, mainly uncompressed and losslessly compressed 1-32 bit integer as well as 32 and 64-bit float images, which are commonly used in scientific imaging.

This tool is implemented to support TIFF with custom extensions, namely:

• STK (MetaMorph)
• LSM (Carl Zeiss MicroImaging)

Currently only primary info records are read for STK, FluoView, and NIH image formats.

VIA er en programpakke for billedanalyser af volumer for funktionel og strukturel (medicinske) billeder. Programpakken består af forskellige værktøjer fra simpel datahåndtering over fremvisere til komplekse billedtransformationer.

Alle værktøjer opererer på data i VISTA-format. Pakken indeholder flere muligheder for omdannelser f.eks. fra PNG, PGM eller PNM til dette dataformat og tilbage igen.

VolView is an intuitive, interactive system for volume visualization that allows researchers to quickly explore and analyze complex 3D medical or scientific data on Windows, Mac and Linux computers. Users can easily load and interactively explore datasets using 2D and 3D display methods and tools. 3D tools include volume rendering, maximum intensity projections, and oblique reformatting. The ability to save an entire visualization session allows users to easily stop and start sessions. Advanced users can perform custom data processing using a simple plug-in API.

This is a toolkit for analysis of functional neuroimaging (chiefly fMRI) experiments and voxel-based lesion-behavior mapping. VoxBo supports the modified GLM (for autocorrelated data), as well as the standard GLM for non-autocorrelated data. The toolkit is designed to be interoperable with AFNI, FSL, SPM and others.

Dette projekt står for Medical Image Conversion, dvs. et medicinsk billedkonverteringsværktøj. Programmet er udgivet under (L)GPL. Den fulde C-kildekode fra biblioteket følger med. Det er et fleksibelt kommandolinjeredskab med en pæn grafisk grænseflade, som anvender GTK+- værktøjssættet. Formater som aktuelt understøttes er: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 og PNG.

Programmet tillader også indlæsning af ukomprimerede filer, som ikke understøttes, udskrivning af billedpunktværdier eller udtræk/ændring af rækkefølge for angivne billeder. Det er muligt at hente de rå binære/ascii- billedtabeller eller at skrive PNG til skrivebordsprogrammer.

Dette er programversionen til X baseret på GTK+. Behandler kun én fil ad gangen.

A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O.

The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear regression).

Fremviseren, »The Connectome Viewer« er et udvideligt, skriptbart, pythonisk forskningsmiljø for visualisering og (netværks-)analyse i neurobilledbehandling og »connectomics«.

Med brug af formatet »Connectone File Format«, bliver forskellige datatyper såsom netværk, overflader, volume, spor og metadata håndteret og integreret. Fremviseren »The Connectome Viewer« er en del af værktøjssættet »MR Connectome Toolkit«.

Billedregistrering baseret på den velkendte Insight Segmentation and Registration Toolkit (ITK). Programmet består af en samling af algoritmer, som ofte bruges til at løse (medicinske) billedregistreringsproblemer. Det modulære design i elastix lader brugeren hurtigt konfigurere, teste og sammenligne forskellige registreringsmetoder for et specifik program. En kommandolinjegrænseflade aktiverer automatiseret behandling af et stort antal datasæt, ved hjælp af skripter.

ImageMagick er en programpakke til at oprette, redigere og komponere bitmap-billeder. Det kan læse, konvertere og skrive billeder i en række formater (over 100), inklusive DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG og TIFF. Brug ImageMagick til at oversætte, vende, spejle, rotere, skalere, trapezere og transformere billeder, justere billeder, farver, anvende forskellige specialeffekter eller tegne tekst, linjer, polygoner, ellipser og Bézier-kurver.

Imview er et program som

• Viser et stort antal billedformater
• Viser 2D- eller 3D-billeder (som dias) med en udbygget zoom- og panoreringsfunktion.
• Virker med flerspektral, tidsserier eller flersidedokumenter (f.eks.: satellitbilleder, TIFF-stakke, animerede GIF'er og heterogene flerkomponentfiler).
• Viser alle billedpunktstyper (1-bit til 64-bit data, heltal eller kommatal.
• Arbitrær 1-D-profil af 2-D-billeder (eller af 2-D-dias af 3-D-billeder) kan vises.
• Har understøttelse for arbitrære farvekort for alle billedpunktstyper (dvs.: falsk farvevisning).
• Har standardfaciliteter for billedmanipulering (lysstyrke/kontrast, gamma, zoon, beskær, rotation etc.).
• Kan kontrolleres eksternt via sokler og tekstkommandoer (for nem integrering i forskellige analysesystemer for billeder).
• Billeder kan overføres til Imvies via sokler eller delt hukommelse.
• Og meget mere!

OpenWalnut is a tool for multi-modal medical and brain data visualization. Its universality allows it to be easily extended and used in a large variety of application cases. It is both, a tool for the scientific user and a powerful framework for the visualization researcher. Besides others, it is able to load NIfTI data, VTK line data and RIFF-format CNT/AVR-files. OpenWalnut provides many standard visualization tools like line integral convolution (LIC), isosurface-extraction, glyph-rendering or interactive fiber-data exploration. The powerful framework of OpenWalnut allows researchers and power-users to easily extend the functionality to their specific needs.

This package contains the QT4 GUI for OpenWalnut.

ParaView is an open-source, multi-platform application designed to visualize data sets of size varying from small to very large. The goals of the ParaView project include the following:

* Develop an open-source, multi-platform visualization application.
* Support distributed computation models to process large data sets.
* Create an open, flexible, and intuitive user interface.
* Develop an extensible architecture based on open standards.

ParaView runs on distributed and shared memory parallel as well as single processor systems and has been successfully tested on Windows, Mac OS X, Linux and various Unix workstations, clusters and supercomputers. Under the hood, ParaView uses the Visualization Toolkit as the data processing and rendering engine and has a user interface written using Qt.

pngquant er et kommandolinjekonverteringsredskab til at kvantisere og farvereducere truecolor PNG-billeder, specielt dem med en fuld alfakanal, ned til 8-bit (eller mindre) RGBA-palet PNG'er. Sådanne billeder er normalt to til fire gange mindre end de fulde 32-bit versioner, og delvis gennemsigtighed bevares ret så godt. Dette gør pngquant specielt nyttigt for internetsider og for PlayStation 2-udvikling, hvor et af teksturformaterne er RGBA-palet-baseret (dog ikke PNG-komprimeret). Dette er den samme teknik brugt for mange af billederne på siden for Miscellaneous Transparent PNG'er (http://www.libpng.org/pub/png/pngs- img.html), og der kan ofte ikke ses forskel til den originale fil i truecolor PNG.

Optimeringsprogrammer (såsom pngcrush og optipgn) optimerer komprimeringen, normalt uden kvalitetstab, mens pngquant kvantiserer farver ned til 256 (eller færre) distinkte RGBA-kombinationer, hvilket giver kvalitetstab.

pyxid is a Python library for interfacing with Cedrus XID (eXperiment Interface Device) and StimTracker devices. XID devices are used in software such as SuperLab, Presentation, and ePrime for receiving input as part of stimulus/response testing experiments.

pyxid handles all of the low level device handling for XID devices in Python projects.

FSL is a comprehensive library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. The suite consists of various command line tools, as well as simple GUIs for its core analysis pipelines. Among others, FSL offers implementations of standard GLM analysis, white matter tractography, tissue segmentation, affine and non-linear co-registration, and independent component analysis.

The Vascular Modeling Toolkit is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

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.

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 integrated 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.

BioImageXD is a multi-purpose post-processing tool for bioimaging. The software can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once. Animations of 3D renderings can be created using flying paths or keyframes. BioImageXD has basic image adjustment operations and a collection of noise reduction methods. Processing methods are accompanied with a selection of segmentation methods. Segmentation results can be analysed for tens of parameters or used for motion tracking. Other quantitative analysis methods include for instance voxel and object colocalization methods and internalization analysis. All processing and analysis methods can be build into pipelines and run for hundreds of datasets at once in batch processor.

CellProfiler is cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

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 scriptable image modification, filtering, forwarding and conversion
• DICOM caching and archive merging
• DICOM web access for viewing and data management (scriptable)

The CreaTools are a suite of medical image processing and visualization software and development tools. They are developed by CREATIS, a research unit with extensive experience in the medical image processing field.

The CreaTools are a set of tools designed to meet both the needs of the end-users (physicians, students or researchers) and of the developers.

This project contains the source code for the core Java Advanced Imaging API reference implementation containing the packages javax.media.jai. and com.sun.media.jai..

This package depends upon the latest version of freesurfer.

A command line utility for anonymizing and sending DICOM data to the XNAT image database at the International Neuroinformatics Coordinating Facility (INCF). This tool is maintained by the INCF NeuroImaging DataSharing (NIDASH) task force.

A variety of applications providing segmentation, registration, and other medical image processing algorithms such as MRI bias field correction.

Java Image Science Toolkit (JIST) provides a native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces.

Kradview is a viewer of images obtained for some different sources: X-ray, NMR and DICOM-compatible imaging devices. 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.

Dcm4che is a collection of open source applications and utilities for the healthcare enterprise. 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.

A Cross-platform DICOM viewer using the dcm4che toolkit.

The current features are:

• DICOM Listener for Q/R
• DICOM Send
• Local DB for storing study information
• Importing DICOM studies from local disk
• Parsing DicomDir from local disk or CD
• Query compressed studies without decompressing them
• Multiple Studies viewer using Layout,Tab view
• Export to JPEG (Study, Series, Instance level). Windowing can be applied to a single instance or series of instance while exporting
• Cine Loop & stack navigation
• Toggle for Text and Annotation Overlay
• Windowing Presets Settings (based on modality)
• Layout Settings (based on modality)
• AE Management
• DICOM Tags Viewer

µManager is a software package for control of automated microscopes. It lets you execute common microscope image acquisition strategies such as time-lapses, multi-channel imaging, z-stacks, and combinations thereof. μManager works with microscopes from all four major manufacturers (Leica, Nikon, Olympus and Zeiss), most scientific-grade cameras and many peripherals (stages, filter wheels, shutters, etc.) used in microscope imaging (check the list of supported hardware). Since μManager runs as a plugin to ImageJ, image analysis routines are available within the application.

Unencumbered code provides a GUI for microscope image acquisition, a hardware interface layer and hardware interfacing for:

• ASI stages, filter wheels and shutters
• Arduino
• Conix filter changer
• Velleman K8055 and K8061 digital IO boards
• Leica DMI microscopes
• Ludl shutters, stages and filter Wheels
• Nikon TE2000 microscope
• Physik Instrumente stages
• Pecon stage incubators
• Prior shutters, stages and filter wheels
• Spectral LMM5 laser controller
• Sutter shutters, filter wheels and DG4
• Vincent Uniblitz shutters
• Yokogawa spinning disk confocal CSU22 and CSUX
• Zeiss microscopes (two 'generations')
• iidc1394 compatible cameras (through libdc1394)

The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders. MIPAV provides an interface for plug-ins and serves as the foundation for other projects (e.g. JIST).

This package provides downloader/installer for non-redistributable closed-source version of MIPAV and a convenience startup wrapper. You will have a choice of reviewing the license and accepting or declining it upon installation.

This template MRI volume was created from 27 T1-weighted MRI scans of a single individual that have been transformed into the Talairach stereotaxic space. The anatomical image is complemented by a brain and a head mask. All images are in 1x1x1 mm resolution.

This package provides the template in NIfTI format.

This package provides the startup script for the OpenElectrophy GUI.

Command-line tools to calculate numerous fMRI scanner stability metrics, based on the FBIRN quality assurance test protocal. Any 4D volumetric timeseries image in NIfTI format is support input. Output is a rich HTML report.

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

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 Association (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 Library, 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

DTI-TK is a spatial normalization & atlas construction toolkit, designed from ground up to support the manipulation of diffusion-tensor images (DTI) with special cares taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. The key features include:

• NIfTI support for scalar, vector and DTI volumes
• tool chains for manipulating DTI volumes: resampling, smoothing, warping, registration & visualization
• pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies
• built-in cluster-computing support
• interoperability with other major DTI tools: AFNI, Camino, DTIStudio & FSL

EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data.

This framework aids access of and conversion between various established neuro-imaging data formats, like Nifti, Analyze, DICOM and VISTA. ISIS is extensible with plugins to add support for additional data formats.

JEMRIS, which stands for "Juelich Extensible MRI Simulator", is a general simulator of MRI (Magnetic Resonance Imaging) data. The general process of simulation consists of preparation by choice or implementation of sequence, sample and coil setup and the invocation of the simulation run itself.

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/).

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.

The primary functionality of XNAT is to provide a place to store and control access to neuroimaging data. This includes sophisticated user control, search and retrieval, and archiving capabilities. As open-source software, XNAT also supports a wide variety of research-based processing pipelines, and is able to link up with supercomputer processing power to dramatically shorten image processing time.

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.

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 application allows neuroscientists to place and interactively manipulate box-shaped regions (or volumes of interest) to selectively display pathways that pass through specific anatomical areas. A simple and extensible query language allows for arbitrary combinations of these queries using Boolean logic operators. Queries can be further restricted by numerical path properties such as length, mean fractional anisotropy, and mean curvature.

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.

GIMIAS is a workflow-oriented environment for solving advanced biomedical image computing and individualized simulation problems, which is extensible through the development of problem-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Physiome community while allowing business-friendly technology transfer and commercial product development.

The Human Imaging Database (HID) is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large.

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 develop a system that is an ensemble of single pieces that cooperate together using IHE profiles.

Photograph, manage, view, compare, document and archive medical photos fully integrated into doctor's practice systems. Take a photo and immediately see how the picture gets archived to your current patient automatically.

• direct support for Olympus E-System cameras
• network support
• fully integrated via GDT interface into many medical software systems
• organise photos by patients effectively
• define your own localisations
• compare photos of healing processes at different times
• work time-optimized and effective, photos automatically get added and archived under the current patient in your system
• easily print selected photos and archive or give them to your patients

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."

MIView features - DICOM files browser - volume rendering - reads DICOM v3, NEMA/ACR, Papyrus, Jpeg, GIF, bitmap, TIFF,

  Analyze 7.5, and Nifti1 files
- can convert to raster (jpeg, bitmap, etc) and Analyze/Nifti1

This is an unbiased standard magnetic resonance imaging template volume for the normal human population. It has been created by the Montreal Neurological Institute (MNI) using anatomical data from the International Consortium for Brain Mapping (ICBM).

The package provides a 1x1x1 mm and 0.5x0.5x0.5 mm resolution templates (hemissphere-symetric and asymetric non-linearily co-registered versions), some including T1w, T2w, PDw modalities, T2 relaxometry, and tissue probability maps. In addition, it contains a lobe atlas, and masks for brain, eyes and face.

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.

OMERO is client-server software for visualisation, management and analysis of biological microscope images.

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.

 PyMEG is a project in Python to do various neuroimaging processing
 with magnetoencephalography (MEG) data. The purpose of this project,
 is to create a suite of functions to do MEG analysis in Python.

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..

TEMPO is open source software for 3D visualization of brain electrical activity. TEMPO accepts EEG file in standard EDF format and creates animated sequence of topographic maps. Topographic maps are generated over 3D head model and user is able to navigate around head and examine maps from different viewpoints. Most mapping parameters are adjustable through appropriate graphical user interface controls. Also, individual topographic maps could be saved in PNG format for future examination or publishing.