Debian Med Imaging packages

Aeskulap è capace di caricare per la loro ispezione una serie di immagini speciali archiviate nel formato DICOM. In aggiunta è capace di interrogare e recuperare immagini DICOM da nodi archivio (chiamati anche PACS) in rete. Aeskulap cerca di diventare un rimpiazzo completamente open source per i visualizzatori DICOM commerciali disponibili.

AMIDE: (Amide's a Medical Imaging Data Examiner). AMIDE è uno strumento per visualizzare e analizzare insiemi di dati di immagini medicali. Tra le sue funzionalità sono incluse: la gestione simultanea di insiemi di dati multipli importati da diversi formati di file, la fusione di immagini, il disegno e l'analisi di regioni 3D di interesse, la resa dei volumi e l'allineamento di corpi rigidi.

Advanced Normalization Tools (ANTS) è una suite basata su ITK di strumenti di normalizzazione, segmentazione e costruzione di modelli per l'analisi morfometrica quantitativa. Molti degli strumenti di registrazione in ANTS sono diffeomorfi, ma sono disponibili trasformazioni di deformazione (elastica e BSpline). Tra le caratteristiche uniche di ANTS: metriche di somiglianza multivariata, guida al landmark, possibilità di usare immagini etichetta per guidare la mappatura, implementazioni dei diffeomorfismi sia greedy sia ottimali in spazio-tempo. La strategia di normalizzazione simmetrica (SyN) fa parte di ANTS in quanto Diretta Manipolazione di Forme libere (Free) di Deformazione (DMFFD).

Questo pacchetto, basato sulla libreria BioSig, fornisce strumenti a riga di comando, come:

• save2gdf: converte tra diversi formati di file inclusi, ma non limitati a, SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF, BDF, CWFB. save2gdf può essere usato anche per caricare o recuperare dati da un server bscs.

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.

Questo software permette di creare, visualizzare e manipolare ricostruzioni di superficie della corteccia cerebrale e cerebellare, di visualizzare volumi e mostrare dati sperimentali sulle superfici e sui volumi. Benché Caret sia principalmente una applicazione GUI, con "caret_command" si ha anche un versatile strumento a riga di comando che permette di accedere ad una sostanziosa porzione delle funzionalità di Caret.

Caret può scaricare e usare atlanti stereotassici (uomo, scimmia, topo e ratto) da un database aperto in rete.

Alcune funzionalità di Caret sono disponibili solamente quando sono presenti alcuni file dati aggiuntivi forniti dal pacchetto caret-data. Tra queste sono incluse:

• mappatura di volumi su superficie attraverso atlante PALS,
• morphing multi-risoluzione,
• proiezione di fuochi con atlas PALS,
• registrazione basata su superficie,
• appiattimento di superfici.

Attualmente il pacchetto caret-data è disponibile solo dal repository NeuroDebian. Per maggiori informazioni vedere http://neuro.debian.net

DICOM è uno standard per la memorizzazione, annotazione e condivisione di immagini. È ampiamente usato in ambito medico. Il software Centrale Test Node (CTN) è un'implementazione di tale standard.

Questo pacchetto comprende il file binario e i file di configurazione di CTN.

CTSim è un simulatore interattivo di tomografia assiale computerizzata. Questa è una tecnica che stima l'interno degli oggetti mediante la misura dell'assorbimento dei raggi X che li attraversano.

Sono disponibili sia un'interfaccia grafica che strumenti da riga di comando. CTSim presenta delle modalità estremamente educative sia per vedere la simulazione della raccolta dati, che per la ricostruzione.

DCMTK è una raccolta di librerie e applicazioni per esaminare, costruire e convertire file immagine DICOM, maneggiare supporti offline, inviare e ricevere immagini tramite connessione di rete, così come esempi di server per archiviazione di immagini e worklist.

Questo pacchetto contiene le applicazioni di utilità di DCMTK.

Nota: questa versione è stata compilata con il supporto per libssl.

Utilità a riga di comando per creare, modificare, fare il dump e convalidare file di attributi DICOM. Supporta la conversione di alcuni formati per immagini medicali proprietari in DICOM. Può gestire dati nel vecchio formato ACR/NEMA e alcune versioni proprietarie di esso come SPI.

Il programma dinifti converte immagini MRI memorizzate in formato DICOM nel formato NIfTI. Quest'ultimo è considerato il nuovo formato standard per le immagini medicali e può essere usato con, per esempio, FSL, AFNI, SPM, Caret o Freesurfer.

dinifti converte file singoli, ma supporta anche la conversione completamente automatica di complete directory dicom. In aggiunta, i file NIfTI convertiti possono essere rinominati in modo appropriato usando le informazioni sulle serie di immagini nei file DICOM.

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 has been demonstrated at ECR 2001 and contains numerous extensions, including a print server, support for encrypted DICOM communication, digital signatures and structured reporting.

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 fornisce una soluzione completa per visualizzatore DICOM con capacità avanzate e gestione di estensioni.

• Interfaccia facile e personalizzabile attraverso profili.
• Visualizzazione completa di immagini DICOM.
• Insieme completo di strumenti (misuratori, marcatori, testo, ...).
• Gestione di più modalità (neurologica, radiologica, dermatologica, oftalmologica, ultrasuoni, endoscopia, ...).
• Gestione della trasformazione in DICOM di JPEG, PNG, GIF e TIFF.
• Gestione dell'integrazione EMH completa: flussi di lavoro standard HL7 e conformi con IHE.
• Workstation PACS (C-FIND, C-MOVE, C-STORE, ...).
• Estensibile tramite estensioni personalizzate:
• composizione di mosaici di immagini retinali;
• diagnostica automatica di analisi retinali;
• diagnostica automatica di psoriasi.

Gli obiettivi principali di GoFigure2 sono di fornire:

• interazione/visualizzazione/navigazione in bioimmagini in 4D multi-canale;
• salvare/recuperare informazioni collegate all'elaborazione di immagini, risultati di analisi;
• estrarre oggetti da bioimmagini (ad esempio: nuclei, membrane cellulari, ...);
• tracciare strutture subcellulari, cellule;
• rilevare e tracciare la divisione cellulare nel tempo;
• generare e visualizzare la discendenza cellulare.

Gwyddion è un programma modulare per la visualizzazione e l'analisi di dati ottenuti con microscopia a scansione di sonda (SPM, Scanning Probe Microscopy). È pensato principalmente per l'analisi dei dati del campo altezza ottenuti d tecniche di microscopia quali

• AFM (Atomic Force Microscopy),
• MFM (Magnetic Force Microscopy),
• STM (Scanning Tunneling Microscopy),
• SNOM o NSOM (Near-field Scanning Optical Microscopy) e altri. Può essere tuttavia usato per analisi di immagini e campi altezza arbitrari.

Questo pacchetto contiene l'applicazione principale ed i suoi moduli. Contiene anche un creatore di miniature per GNOME, e Xfce, che crea anteprime per tutti i tipi di file gestiti da Gwyddion.

È inclusa anche l'interfaccia per script Python per Gwyddion.

Può visualizzare, modificare, analizzare, processare, salvare e stampare immagini a 8, 16 e 32 bit. Può leggere molti formati immagine inclusi TIFF, GIF, JPEG, BMP, DICOM, FITS e "raw". Supporta "stack": una serie di immagini che condividono un'unica finestra.

Può calcolare statistiche su valori di area e pixel di selezioni definite dall'utente. Può misurare distanze ed angoli. Può creare istogrammi di densità e grafici con linee di contorno. Supporta le funzioni standard di elaborazione delle immagini come manipolazione del contrasto, sharpening, sfumatura, rilevamento dei bordi e filtri mediani.

La calibrazione spaziale è disponibile per fornire misure dimensionali nel mondo reale in unità quali i millimetri. È anche disponibile la calibrazione della densità o della scala di grigi.

ImageJ è sviluppato da Wayne Rasband (wayne@codon.nih.gov) al Research Services Branch del National Institute of Mental Health di Bethesda nel Maryland, USA.

ImageVis3D è un'applicazione per il rendering volumetrico progettata specificamente per grandi quantità di dati. Questo è ottenuto suddividendo l'insieme dei dati in più LoD (levels of detail, livelli di dettaglio), con ogni livello a sua volta scomposto in più blocchetti (primitive di rendering atomiche). Le interazioni avvengono sul LoD più grezzo, di cui può essere fatto il rendering istantaneamente su quasi tutti i sistemi moderni. Dopo un ritardo configurabile, ImageVis3D farà successivamente il rendering di livelli di dettaglio più precisi, fino a che i dati saranno visibili alla loro risoluzione nativa.

Lo sviluppo di ImageVis3D è sponsorizzato dal NIH/NCRR Center for Integrative Biomedical Computing (CIBC) e dal 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 provides semi-automatic segmentation of structures in medical images (e.g. magnetic resonance images of the brain) using active contour methods, as well as manual delineation and image navigation. Noteworthy features are:

• Linked cursor for seamless 3D navigation
• Manual segmentation in three orthogonal planes at once
• Support for many different 3D image formats, including NIfTI
• Support for concurrent, linked viewing and segmentation of multiple images
• Limited support for color images (e.g., diffusion tensor maps)
• 3D cut-plane tool for fast post-processing of segmentation results

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 è una libreria C++ per file medicali DICOM. È inglobata automaticamente in Python/C#/Java (tramite swig). Gestisce RAW, JPEG (con e senza perdita di dati), J2K, JPEG-LS, RLE e deflated.

Installare questo pacchetto per i programmi: 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.

Questo progetto riguarda la conversione di immagini medicali. È rilasciato sotto licenza (L)GPL e viene fornito con il completo codice sorgente in C della libreria, una flessibile utilità a riga di comando e una bella interfaccia grafica che usa il toolkit GTK+. I formati attualmente gestiti sono: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 e PNG.

Può anche leggere file non supportati senza compressione, visualizzare i valori dei pixel estrarre/riordinare le immagini specificate. È possibile recuperare i vettori grezzi delle immagini in formato binario o ASCII produrre immagini PNG per le applicazioni desktop.

Questo è lo strumento a riga di comando per l'elaborazione di massa.

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.

Questo pacchetto contiene strumenti per manipolare file MINC.

Il formato di file Minc è un formato per immagini medicali altamente flessibile costruito sulla base del formato dati generalizzato NetCDF. Il formato è semplice, auto-descrittivo, estensibile, portabile e a N dimensioni, con interfacce di programmazione sia per accesso di basso livello ai dati, sia per manipolazione di volumi ad alto livello. Sopra alle librerie è costruita una suite di strumenti generici per la manipolazione di file immagine. Il formato, le librerie e gli strumenti sono pensati per l'uso in ambienti di ricerca sulle immagini medicali: sono semplici e potenti e non cercano in alcun modo di fornire una bella interfaccia per gli utenti.

MRIConvert è un'utilità di conversione per file di immagini medicali che converte i file DICOM nei formati di volumi NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager e MetaImage.

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 è un insieme di librerie di I/O per la lettura e la scrittura di file dati nel formato NIfTI-1. NIfTI-1 è un formato binario per l'archiviazione di immagini mediche, tipo risonanza magnetica (RMN) o immagini cerebrali da RMN funzionale (fRMN).

Questo pacchetto comprende gli strumenti forniti con la libreria (nifti_tool, nifti_stats e 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 è una libreria C che fornisce una semplice interfaccia per leggere immagini di whole-slide, anche conosciute come slide virtuali.

Le immagini whole-slide, conosciute anche come slide virtuali, occupano molto spazio, sono immagini ad alta risoluzione usate in patologia digitale. Leggere queste immagini tramite strumenti o librerie per immagini standard è problematico, poiché questi strumenti sono tipicamente progettati per immagini che possono essere comodamente decompresse in RAM o in un file swap. Le immagini whole-slide di norma eccedono la dimensione della RAM, occupando spesso decine di gigabyte quando sono decompresse. In aggiunta, le immagini whole-slide sono tipicamente a multi-risoluzione e solo una piccola quantità di dati delle immagini può essere necessaria ad una determinata risoluzione.

Questa libreria attualmente gestisce:

• Trestle (.tif),
• Hamamatsu (.vms, .vmu),
• Aperio (.svs, .tif),
• MIRAX (.mrxs),
• TIFF generiche con tile (.tif).

Questo pacchetto contiene gli strumenti a riga di comando per la manipolazione di file.

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.

Questo è un toolkit DICOM autonomo che implementa il codice per leggere e creare dati DICOM, la rete e la gestione di file DICOM, un database di oggetti DICOM, la gestione per la visualizzazione di cartelle, immagini, rapporti e spettri, e la validazione di oggetti DICOM.

Plastimatch è un software open source per registratura di immagini deformabili. È progettato per registrature volumetriche ad alte prestazioni di immagini medicali, come tomografie computerizzate (CT) ai raggi X, tomografie a risonanza magnetica (MRI) e tomografie a emissione di positroni (PET). Le caratteristiche del software includono:

• metodo B-spline per la registratura deformabile di immagini (con accelerazione GPU e multiprocessore);
• metodo Demons per la registratura deformabile di immagini (con accelerazione GPU);
• algoritmi basati su ITK per registratura a traslazione, rigide, affini, demons e B-spline;
• infrastruttura di registratura con pipe, multi-stadio con conversione perfetta tra la maggior parte degli algoritmi e i tipi di trasformazione;
• registratura deformabile basata su punti di confine usando spline thin-plate per la registratura globale;
• registratura deformabile basata su punti di confine usando funzioni a base radiale per correzioni locali;
• ampia gestione di formati di file per immagini 3D (usando ITK) inclusi DICOM, Nifti, NRRD, MetaImage e Analyze;
• importazione ed esportazione DICOM e DICOM-RT;
• importazione ed esportazione XiO;

• plugin verso 3D Slicer. Plastimatch ha anche due utili strumenti che non sono direttamente correlati con la registratura di immagini:

• ricostruzione di CT con fascio a cono FDK (con accelerazione GPU e multiprocessore);

• generazione di radiografie ricostruite digitalmente (DRR) (con accelerazione GPU e multiprocessore).

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 facilita le analisi di classificazione di grandi insiemi di dati, con un accento sulle neuroimmagini. Fornisce un'astrazione di alto livello per i tipici passi di elaborazione (es., preparazione dei dati, classificazione, selezione di caratteristiche, test delle generalizzazioni), diverse implementazioni di alcuni algoritmi usati comunemente (es., kNN, GNB, regressione ridge, regressione logistica multinomiale sparsa) e collegamenti per librerie esterne per l'apprendimento automatico (libsvm, shogun).

Benché non limitato ai dati di immagini neurologiche (es., fMRI o EEG), è adatto principalmente per questo tipo di insiemi di dati.

Usando PyNIfTI si possono leggere e scrivere facilmente immagini NIfTI e ANALYZE dall'interno di Python. La classe NiftiImage fornisce un accesso in stile Python alle complete informazioni nell'header. I dati immagini sono resi disponibili attraverso array NumPy.

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 interfaccia Python con altri pacchetti per neuroimmagini e crea un'API per specificare una completa catena di elaborazione dati per analisi in Python. Attualmente ha interfacce per SPM, FSL, AFNI, Freesurfer, ma potrebbe essere estesa ad altri pacchetti (come 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 è un'infrastruttura Open Source mirata principalmente alla simulazione in tempo reale, in particolare alla simulazione medica. È rivolta soprattutto alla comunità della ricerca per aiutare nello sviluppo di nuovi algoritmi, ma può anche essere usata come efficiente strumento per costruire prototipi.

Questo pacchetto contiene l'applicazione principale di SOFA.

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 contains some simple command-line tools which provide fast and easy access to the functionality in the various libraries.

È gestito solo un sottoinsieme della specifica TIFF, per lo più senza compressione e con compressione senza perdita di dati con interi a 1-32 bit, così come immagini a 32 e 64 bit in virgola mobile che sono comunemente usate nelle immagini scientifiche.

Questo strumento è implementato per gestire i TIFF con estensioni personalizzate e cioè:

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

Attualmente vengono letti solo i record di informazione primari per i formati immagine STK, FluoView e NIH.

VIA è una suite di analisi di immagini volumetriche per immagini (medicali) funzionali e strutturali. La suite comprende diversi strumenti che vanno dalla semplice manipolazione passando per la visualizzazione fino alla trasformazione complessa di immagini.

Tutti gli strumenti operano su dati in formato VISTA. Il pacchetto contiene numerosi convertitori da es. PNG, PGM o PNM a questo formato e viceversa.

VolView è un sistema intuitivo e interattivo per la visualizzazione di volumi che permette ai ricercatori di esplorare e analizzare velocemente dati 3D complessi, medici o scientifici, su computer Windows, Mac e Linux. Gli utenti possono facilmente caricare e esplorare interattivamente insiemi di dati usando strumenti e metodi di visualizzazione 2D e 3D. Gli strumenti 3D includono il rendering di volumi, proiezioni di massima intensità e riformattazione obliqua. La capacità di salvare un'intera sessione di visualizzazione permette agli utenti di fermare e avviare facilmente le sessioni. Gli utenti avanzati possono effettuare elaborazioni personalizzate dei dati usando una semplice API a plugin.

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.

Questo progetto riguarda la conversione di immagini medicali. È rilasciato sotto licenza (L)GPL e viene fornito con il completo codice sorgente in C della libreria, una flessibile utilità a riga di comando e una bella interfaccia grafica che usa il toolkit GTK+. I formati attualmente gestiti sono: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 e PNG.

Può anche leggere file non supportati senza compressione, visualizzare i valori dei pixel estrarre/riordinare le immagini specificate. È possibile recuperare i vettori grezzi delle immagini in formato binario o ASCII produrre immagini PNG per le applicazioni desktop.

Questa è la versione per X del programma, basata su GTK+. Elabora un solo file alla volta.

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).

The Connectome Viewer is a extensible, scriptable, pythonic research environment for visualization and (network) analysis in neuroimaging and connectomics.

Employing the Connectome File Format, diverse data types such as networks, surfaces, volumes, tracks and metadata are handled and integrated. The Connectome Viewer is part of the MR Connectome Toolkit.

Registrazione di immagini basata sul ben conosciuto ITK (Insight Segmentation and Registration Toolkit). Il software consiste in una raccolta di algoritmi che sono usati comunemente per risolvere problemi di registrazione di immagini (medicali). Il progetto modulare di elastix permette all'utente di configurare, testare e confrontare velocemente diversi metodi di registrazione per un'applicazione specifica. Un'interfaccia a riga di comando abilita l'elaborazione automatica di un gran numero di insiemi di dati, grazie a script.

ImageMagick è una suite di programmi per creare, modificare e comporre immagini bitmap. Può leggere, convertire e scrivere immagini in moltissimi formati (oltre 100) tra i quali DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, PostScript, SVG e TIFF. Usare ImageMagick per traslare, capovolgere, riflettere, ruotare, scalare, ritagliare e trasformare le immagini, per correggere i colori, per applicare vari effetti speciali oppure per disegnare testi, linee, poligoni, ellissi e curve Bézier. Tutte le operazioni possono essere eseguite sia da riga di comando che attraverso un'interfaccia grafica (display).

Imview è un'applicazione che:

• visualizza immagini in un gran numero di formati;
• visualizza immagini 2D e 3D (come fette) con un ottimo ingrandimento e scorrimento;
• accetta serie temporali e multi-spettrali, o documenti con più pagine (per esempio immagini da satellite, pile TIFF, GIF animate e file con più componenti eterogenei);
• visualizza pixel di ogni tipo (dati da 1 a 64 bit, interi o virgola mobile);
• mostra profili 1D di immagini 2D (oppure fette 2D di immagini 3D);
• supporta mappe di colore arbitrarie per tutti i tipi di pixel (per esempio la visualizzazione in falsi colori);
• dispone delle funzioni standard di manipolazione (luminosità/contrasto, gamma, ingrandimento, ritaglio, rotazione, ecc.);
• può essere controllato da remoto via socket e comandi testuali (per essere facilmente integrato in diversi sistemi di analisi delle immagini);
• le immagini possono essere caricate in Imview via socket o memoria condivisa;
• e molto altro!

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 è un'applicazione multipiattaforma e open source progettata per visualizzare insiemi di dati di dimensioni variabili da piccole a molto grandi. Tra gli scopi del progetto ParaView sono inclusi i seguenti:

• sviluppare un'applicazione di visualizzazione open source e multipiattaforma;
• gestire modelli di calcolo distribuito per elaborare grandi insiemi di dati;
• creare un'interfaccia utente aperta, flessibile e intuitiva;
• sviluppare un'architettura estensibile basata su standard aperti.

ParaView gira su sistemi paralleli a memoria distribuita e condivisa così come con processori singoli ed è stata testata con successo su Windows, Mac OS X, Linux e varie workstation Unix, cluster e supercomputer. Sotto il cofano, ParaView usa il Visualization Toolkit come motore di elaborazione e rendering dei dati ed ha un'interfaccia utente scritta usando Qt.

pngquant è un'utilità di conversione a riga di comando per la quantizzazione e la retinatura di immagini PNG truecolor, specialmente quelle con un canale alfa completo, fino a ottenere immagini PNG con tavolozza RGBA a 8 bit (o meno). Queste immagini sono solitamente da due a quattro volte più piccole che le versioni a 32 bit, e la trasparenza parziale è mantenuta abbastanza bene. Questo rende pngquant particolarmente utile sia per siti web che per lo sviluppo per la PlayStation 2, dove uno dei formati di texture è bastato su tavolozze RGBA (ma senza la compressione PNG). Questa è la stessa tecnica usata da molte delle immagini nella pagina "Miscellaneous Transparent PNGs" (http://www.libpng.org/pub/png/pngs-img.html) e i risultati sono spesso indistinguibili dalle immagini PNG originali in truecolor.

Gli ottimizzatori (come pngcrush e optipng) ottimizzano la compressione, solitamente senza degrado, mentre pngquant quantizza i colori a 256 (o meno) combinazioni distinte RGBA, il che comporta un degrado.

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

MIA viewer program vor the visualization of 3D data sets. The interfaces and supported data types focus on the results that can be obtained by running programs from the mia-tools package.

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.