Debian Med Project
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Summary
Imaging
pacchetti Debian Med per elaborazione e visualizzazione di immagini

Questo metapacchetto installa i pacchetti Debian che possono essere utili nell'elaborazione e nella visualizzazione di immagini medicali.

Da un lato installa svariati pacchetti che gestiscono vari formati di file immagine e gestioni di immagini come DICOM (Digital Imaging and Communications in Medicine), che è lo standard di fatto per la gestione di immagini medicali, e NIFTI. Dall'altro fornisce una varietà di pacchetti software che possono essere utilizzati per la visualizzazione e per l'elaborazione di immagini, da un'interfaccia utente grafica, la riga di comando o implementati in flussi di lavoro.

Description

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

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

Links to other tasks

Debian Med Imaging packages

Official Debian packages with high relevance

amide
software per immagini medicali
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fieldmedicine, medicine:imaging
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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.

Amide importa la maggior parte dei file DICOM clinici (usando la libreria DCMTK).

Please cite: Andreas Markus Loening and Sanjiv Sam Gambhir: AMIDE: A Free Software Tool for Multimodality Medical Image Analysis. (PubMed) Molecular Imaging 2(3):131-7 (2003)
Other screenshots of package amide
VersionURL
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17677/simage/large-8f7aaa9529343865541ebc968e464c74.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17676/simage/large-6cc9cfe18a76cd3b247214d8ae0339b6.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17675/simage/large-d5d4f705acb3ff24758ea101b026c05b.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17674/simage/large-7756276dad8ba12ceeacc79f2df9fa3e.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17673/simage/large-7640f62c8ac17498b7e825bdc3e3be71.png
1.0.5-12+b1https://screenshots.debian.net/shrine/screenshot/17678/simage/large-deeb0fc832965282d8e7bd9a43b6065e.png
0.9.1-2https://screenshots.debian.net/shrine/screenshot/356/simage/large-a3b9d7e99aafc8e159ad1288d6031445.png
Screenshots of package amide
ants
strumento avanzato di normalizzazione per analisi mentali e di immagini
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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 fornisce la configurazione di moduli di ambiente. Usare "module load ants" per rendere tutti gli strumenti a riga di comando disponibili nella propria shell.

Screenshots of package ants
bart
strumenti per immagini di risonanza magnetica computazionale
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Berkeley Advanced Reconstruction Toolbox (BART) è un'infrastruttura libera e open source per la ricostruzione di immagini di risonanza magnetica computazionale (Computational Magnetic Resonance Imaging). Consiste di una libreria di programmazione e di un toolbox di programmi a riga di comando. La libreria fornisce operazioni comuni su array multidimensionali, trasformazioni di Fourier e wavelet, e anche implementazioni generiche di algoritmi di ottimizzazione iterativa. Gli strumenti a riga di comando forniscono accesso diretto alle operazioni di base su array multidimensionali e anche implementazioni efficienti di molti algoritmi di ricostruzione e calibrazione per acquisizione parallela, compressed sensing e apprendimento macchina.

Please cite: Martin Uecker, Sebastian Rosenzweig, H. Christian M. Holme, Moritz Blumenthal, Zhengguo Tan, Xiaoqing Wang, Jonathan I. Tamir and Michael Lustig: BART Toolbox for Computational Magnetic Resonance Imaging.
bart-view
visualizzatore per dati multidimensionali a valori complessi
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Berkeley Advanced Reconstruction Toolbox (BART) è un'infrastruttura libera e open source per la ricostruzione di immagini di risonanza magnetica computazionale (Computational Magnetic Resonance Imaging).

Questo pacchetto fornisce un visualizzatore di immagini come componente opzionale dell'infrastruttura BART. Il visualizzatore è progettato per dati multidimensionali a valori complessi.

Screenshots of package bart-view
biosig-tools
strumenti di conversione di formato per formati di dati biomedici
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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;
  • biosig2gdf: converte file di dati biosig in GDF, per semplificare l'analisi e il caricamento da parte di linguaggi di scripting (es. loadgdf.{py,r});
  • rec2bin, bin2rec, heka2itx, save2aecg, save2scp: diversi strumenti di conversione basati su save2gdf;
  • biosig_fhir: impacchetta dati biosignal in file modello HL7/FHIR binari;
  • physicalunits: convertitore per codifica e decodifica di unità di misura fisiche secondo la ISO 11073-10101.
Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
camitk-imp
applicazione workbench per la libreria CamiTK
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CamiTK aiuta i ricercatori e i clinici a collaborare semplicemente e velocemente allo scopo di creare prototipi di applicazioni CAMI che hanno immagini medicali, navigazione chirurgica e simulazioni biomediche.

camitk-imp è l'applicazione workbench di CamiTK con cui si possono provare tutte le estensioni disponibili per fare prototipazione. Fornisce un accesso facile e interattivo a tutti i dati disponibili e tutti i parametri degli algoritmi, inclusi quelli che sono creati dall'utente usando l'SDK CamiTK.

camitk-imp può, ad esempio, visualizzare immagini medicali da moltissimi diversi formati (standard), offre algoritmi di elaborazione e segmentazione di immagini per ricostruire una geometria a griglie ed eseguire una simulazione biomeccanica.

Please cite: Céline Fouard, Aurélien Deram, Yannick Keraval and Emmanuel Promayon: CamiTK: a Modular Framework Integrating Visualization, Image Processing and Biomechanical Modeling. :323-354 (2012)
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caret
??? missing short description for package caret :-(
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Please cite: David C. Van Essen, Heather A. Drury, James Dickson, John Harwell, Donna Hanlon and Charles H. Anderson: An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex. (PubMed,eprint) Journal of American Medical Informatics Association 8(5):443-459 (2001)
ctn
Central Test Node, un'implementazione per immagini mediche DICOM
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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.

Please cite: S.M. Moore, S.A. Hoffman and D.E. Beecher: DICOM Shareware: A Public Implementation of the DICOM Standard 2165:772–781 (1994)
ctsim
simulatore di tomografia computerizzata
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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.

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dcm2niix
convertitore di prossima generazione da DICOM a NIfTI
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dcm2niix è il successore di dcm2nii, un popolare strumento per la conversione di immagini dai complicati formati utilizzati dai produttori di scanner (DICOM, PAR/REC) al più semplice formato NIfTI utilizzato da molti strumenti scientifici. Funziona per tutte le modalità (CT, MRI, PET, SPECT) e i tipi di sequenza.

dcmtk
programmi a riga di comando del toolkit OFFIS DICOM
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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.

Please cite: Chung-Yueh Lien, Michael Onken, Marco Eichelberg, Tsair Kao and Andreas Hein: Open Source Tools for Standardized Privacy Protection of Medical Images. (eprint) Progress in Biomedical Optics and Imaging - Proceedings of SPIE 7967:79670M-79670M (2011)
dicom3tools
strumenti di manipolazione e conversione di file di immagini medicali DICOM
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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.

dicomscope
visualizzatore OFFIS DICOM
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DICOMscope è un visualizzatore DICOM libero che può mostrare immagini DICOM non compresse, monocrome da tutte le modalità e che gestisce la calibrazione del monitor in accordo a DICOM parte 14 oltre agli stati di presentazione.

DICOMscope offre un client per stampa (DICOM Basic Grayscale Print Management) che implementa anche la classe opzionale Presentation LUT SOP.

Lo sviluppo di questo prototipo è stato commissionato dal "Committee for the Advancement of DICOM" e dimostrato all'European Congress of Radiology ECR 1999. Una versione migliorata è stata sviluppata per la "DICOM Display Consistency Demonstration" al RSNA InfoRAD 1999.

Il rilascio attuale è stato dimostrato all'ECR 2001 e contiene numerose estensioni, incluso un server di stampa, la gestione di comunicazioni DICOM cifrate, firme digitali e rapporti strutturati.

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fslview
??? missing short description for package fslview :-(
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Please cite: S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady and P.M. Matthews: Advances in functional and structural MR image analysis and implementation as FSL. (PubMed) NeuroImage 23:208-219 (2004)
Remark of Debian Med team: fslview was removed from Debian (see #647810)

The bug log (http://bugs.debian.org/647810) explains the reasons for the removal. The maintainers did never respond whether they plan to bring back a more recent version of this package

gdf-tools
libreria di IO per GDF - strumenti ausiliari
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GDF (General Dataformat for Biosignals, formato di dati generico per biosegnali) è pensato per fornire un'archiviazione generica per segnali biologici come EEG, ECG, MEG, ecc.

Questo pacchetto fornisce lo strumento incluso con la libreria (gdf_merger).

Please cite: Alois Schlögl: GDF – A general dataformat for BIOSIGNALS. The Computing Research Repository abs/cs/0608052 (2006)
ginkgocadx
software per immagini medicali e visualizzatore di DICOM completo
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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.
gwyddion
strumento per visualizzazione ed analisi con microscopia a scansione di sonda
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Gwyddion è un programma modulare per la visualizzazione e l'analisi di dati ottenuti con microscopia a sonda a scansione (SPM, Scanning Probe Microscopy). È principalmente pensato per l'analisi di dati nel campo dell'altezza ottenuti con tecniche di microscopia quali:

  • microscopia a forza atomica (AFM);
  • microscopia a forza magnetica (MFM);
  • microscopia a scansione per effetto tunnel (STM);
  • microscopia ottica a scansione in campo prossimo (SNOM o NSOM) e altri. Tuttavia può essere 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.

Please cite: David Nečas and Petr Klapetek: Gwyddion: an open-source software for SPM data analysis. (eprint) Central European Journal of Physics 10(1):181-188 (2012)
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heudiconv
DICOM converter with support for structure heuristics
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This is a flexible dicom converter for organizing brain imaging data into structured directory layouts. It allows for flexible directory layouts and naming schemes through customizable heuristics implementations. It only converts the necessary dicoms, not everything in a directory. It tracks the provenance of the conversion from dicom to nifti in w3c prov format.

imagej
programma di elaborazione delle immagini pensato per immagini di microscopia
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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". Gestisce "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. Gestisce 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.

Please cite: Caroline A Schneider, Wayne S Rasband and Kevin W Eliceiri: NIH Image to ImageJ: 25 years of image analysis. (PubMed,eprint) Nature methods 9:671-675 (2012)
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imagevis3d
applicazione desktop per il rendering volumetrico di grandi quantità di dati
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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
software di ricostruzione 3D per immagini medicali
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InVesalius genera ricostruzioni 3D per immagini medicali basate su una sequenza di file 2D DICOM acquisiti con apparecchiature TC o RM. InVesalius è internazionalizzato (attualmente disponibile in inglese, portoghese, francese, spagnolo, turco, italiano, ceco, giapponese, catalano, coreano, romeno e tedesco) e fornisce diversi strumenti:

  • compatibilità DICOM che include: (a) ACR-NEMA versione 1 e 2; (b) DICOM versione 3.0 (incluse varie codifiche di JPEG, senza perdita e con perdita, RLE),
  • funzionalità di manipolazione immagini (zoom, panoramica, rotazione, luminosità/contrasto, ecc.),
  • segmentazione basata su fette 2D,
  • gamme di soglie predefinite secondo il tessuto di interesse,
  • segmentazione basata su spartiacque,
  • segmentazioni di regioni crescenti,
  • strumenti di modifica (simili a Paint Brush) basati su fette 2D,
  • segmentazione semi-automatica basata su Watershed,
  • creazione di superfici 3D,
  • strumenti di connessione di superfici 3D,
  • esportazione di superfici 3D (include: STL binario, OBJ, VRML, Inventor),
  • proiezione di rendering volumetrico di alta qualità,
  • preimpostazioni predefinite per il rendering volumetrico,
  • piano di taglio del rendering volumetrico,
  • esportazione di immagini (incluse: BMP, TIFF, JPG, PostScript, POV-Ray),
  • visualizzazioni di proiezioni di intensità minima, massima o media, Maximum Intensity Difference Accumulation e basate sui contorni.
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ismrmrd-tools
strumenti a riga di comando per ISMRMRD
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Il formato ISMRMRD combina una miscela di strutture dati flessibili (intestazioni XML) e strutture fisse (equivalenti alle struct del C) per rappresentare dati MRI.

Inoltre, il formato ISMRMRD specifica anche un'intestazione per le immagini per memorizzare le immagini ricostruite e la libreria C++ di accompagnamento fornisce un modo comodo per scrivere tali immagini in file HDF5 insieme ad array generici per memorizzare strutture dati definite meno bene, es. mappe di sensibilità degli avvolgimenti o altri dati di calibrazione.

Questo pacchetto fornisce gli strumenti a riga di comando.

itksnap
segmentazione semiautomatica di strutture in immagini 3D
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SNAP fornisce la segmentazione semiautomatica di strutture in immagini medicali (es. immagini di risonanza magnetica del cervello) usando metodi di contorno attivo e delineazione manuale e navigazione di immagini. Funzionalità notevoli sono:

  • cursore collegato per navigazione 3D senza interruzioni;
  • segmentazione manuale in 3 piani ortogonali contemporaneamente;
  • gestione di molti formati differenti di immagini 3D, incluso NIfTI;
  • gestione di visualizzazioni collegate concorrenti e segmentazione di immagini multiple;
  • gestione limitata di immagini a colori (es. mappe di tensori di diffusione);
  • strumento di taglio di piani 3D per post-elaborazione veloce dei risultati della segmentazione.
Please cite: Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee and Guido Gerig: User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability. Neuroimage 31:1116-1128 (2006)
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king
sistema interattivo per grafica vettoriale tridimensionale
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KiNG (Kinemage, Next Generation) è un sistema interattivo per grafica vettoriale tridimensionale. Gestisce un insieme di primitive grafiche che lo rendono adatto per molti tipi di grafi, disegni e altre illustrazioni, anche se il suo uso primario era la visualizzazione di strutture macromolecolari per la ricerca biofisica. KiNG si basa su Mage, JavaMage e il concetto "kinemage" (immagine cinetica) per fornire un'applicazione Java completa con un'interfaccia utente facile da usare e funzionalità di modifica integrate. Il file jar di KiNG può essere usato in una pagina web come applet Java oppure oggetto Java per promuovere un facile accesso alle "kinemage" o ai file di coordinate da un browser web.

libgdcm-tools
strumenti e utilità per Grassroots DiCoM
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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, gdcmclean, gdcmconv, gdcmdiff, gdcmdump, gdcmpap3, gdcmgendir, gdcmimg, gdcminfo, gdcmpdf, gdcmraw, gdcmscanner, gdcmscu, gdcmtar, gdcmxml.

Please cite: David Rodríguez González, Trevor Carpenter, Jano I. van Hemert and Joanna Wardlaw: An open source toolkit for medical imaging de-identification. (PubMed,eprint) European Radiology 20(8):1896-1904 (2010)
medcon
strumento di conversione di immagini medicali (DICOM, ECAT...)
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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 o estrarre/riordinare le immagini specificate. È possibile recuperare i vettori grezzi delle immagini in formato binario o ASCII o produrre immagini PNG per le applicazioni desktop.

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

mia-tools
strumenti a riga di comando per elaborazioni di immagini in scala di grigi
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Strumenti a riga di comando per eseguire compiti generici di elaborazione di immagini in scala di grigi a 2D e 3D, e operazioni basilari su reticoli triangolari. Gli algoritmi di elaborazione di immagine gestiti sono: filtraggi di immagine, combinazione, registrazione di immagine, compensazione del movimento per serie di immagini e la stima di diverse statistiche relative alle immagini. Questo pacchetto contiene anche le interfacce nipype per tali strumenti a riga di comando.

The package is enhanced by the following packages: mia-tools-doc
Please cite: Gert Wollny, Jean-Jaques Hublin, Maria-J Ledesma-Carbayo, Matthew M. Skinner, Peter Kellman and Thomas Hierl: MIA - A Free and Open Source Software for Gray Scale Medical Image Analysis. (eprint) Source Code for Biology and Medicine 8:20 (2013)
mia-viewit
programma visualizzatore per insiemi di dati 3D creati usando MIA
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Il programma visualizzatore di MIA per la visualizzazione di insiemi di dati 3D. Le interfacce e i tipi di dati gestiti si concentrano sui risultati che possono essere ottenuti eseguendo programmi dal pacchetto mia-tools.

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mialmpick
strumenti per scelta di punti di riferimento in insiemi di dati di volumi 3D
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Questo strumento fornisce un semplice strumento per rendering 3D che può visualizzare superfici direttamente a partire da volumi 3D e può essere usato per impostare punti di riferimento 3D. È particolarmente adatto per insiemi di dati di tomografia computerizzata.

Please cite: Gert Wollny, Fritjhof Kruggel, Thomas Hierl and Jörg Hendricks: Assessment, validation, and visualisation of bony changes in crano-facial surgery (eprint) :459-464 (2004)
minc-tools
strumenti per immagini medicali in formato MNI
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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.

mricron
conversione, visualizzazione e analisi di immagini di risonanza magnetica
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Questo è uno strumento di visualizzazione e analisi basato su GUI per immagini di risonanza magnetica (funzionale). MRIcron può essere usato per creare rendering 2D o 3D di mappe statistiche sovrapposte su immagini dell'anatomia del cervello. Inoltre aiuta a disegnare le ROI (regions-of-interest) anatomiche o la mappatura delle lesioni, e l'analisi di base delle serie temporali funzionali (es. creando grafici dei cambiamenti di segnali peristimolo).

Oltre a "mricron", questo pacchetto fornisce anche "dcm2nii", che gestisce la conversione di immagini DICOM e PAR/REC nel formato NIfTI, e "npm", per l'analisi di dati non parametrici.

Please cite: Chris Rorden, Hans-Otto Karnath and Leonardo Bonilha: Improving lesion-symptom mapping. (PubMed) Journal of Cognitive Neuroscience 19(7):1081-1088 (2007)
mrtrix3
trattografia MRI pesata in diffusione della materia bianca
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Insieme di strumenti per effettuare trattografia MRI pesata in diffusione della materia bianca del cervello in presenza di fibre incrociate usando CSD (Constrained Spherical Deconvolution) e un algoritmo streamline probabilistico. Sono gestite le immagini di risonanza magnetica nei formati DICOM, ANALYZE o NIfTI non compresso.

Please cite: Donald Tournier, Robert Smith amd David Raffelt, Rami Tabbara, Thijs Dhollander, Maximilian Pietsch, Daan Christiaens, Ben Jeurissene, Chun-Hung Yeh and Alan Connelly: MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage 202:116137 (2019)
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nifti-bin
strumenti forniti con la libreria NIfTI
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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).

odil
libreria C++11 per lo standard DICOM (applicazione)
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Odil sfrutta i costrutti C++ per fornire un'API facile da usare per le diverse parti dello standard DICOM. In Odil sono inclusi: gestione di errori basata su eccezioni, accesso generico a elementi di insiemi di dati, rappresentazione standard JSON e XML di insiemi di dati, implementazione generica di messaggi, client e server per i vari protocolli DICOM.

Questo pacchetto contiene l'applicazione a riga di comando.

odin
sviluppa, simula ed esegue sequenze di risonanza magnetica
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ODIN è un'infrastruttura per immagini da risonanza magnetica (MRI). Copre l'intera catena di strumenti di MRI, dall'acquisizione di dati a basso livello alla ricostruzione dell'immagine. In particolare, ha l'obiettivo di una rapida prototipazione di sequenze MRI. Le sequenze possono essere programmate usando un'interfaccia di programmazione C++, orientata agli oggetti, di alto livello. Fornisce strumenti avanzati di analisi delle sequenze, come il disegno interattivo di traiettorie nello spazio k, un'interfaccia utente per un ciclo compilazione-link-test veloce e un potente simulatore di MRI che gestisce differenti campioni virtuali. Per una ricostruzione dell'immagine veloce e flessibile, ODIN contiene un'infrastruttura di elaborazione dati molto personalizzabile e multi-thread.

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openslide-tools
strumenti di manipolazione e conversione per OpenSlide
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OpenSlide è una libreria C che fornisce una semplice interfaccia per leggere immagini 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:

  • Aperio (.svs, .tif),
  • Hamamatsu (.vms, .vmu, .ndpi),
  • Leica (.scn),
  • MIRAX (.mrxs),
  • Sakura (.svslide),
  • Trestle (.tif),
  • TIFF generiche affiancate (.tif).

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

orthanc
server DICOM leggero e RESTful per immagini medicali
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Orthanc mira a fornire un server DICOM, semplice ma potente per le immagini medicali. Orthanc può trasformare qualsiasi computer con in esecuzione Windows o Linux in un archivio indipendente dal produttore (VNA) (in altre parole un sistema mini-PACS). La sua architettura è leggera e ciò significa che non è necessaria alcuna amministrazione di database complessa, né l'installazione di dipendenze di terze parti.

Ciò che rende unico Orthanc è il fatto che fornisce un'API RESTful. Grazie a questa fondamentale funzionalità, è possibile pilotare Orthanc da qualsiasi linguaggio per computer. Le etichette DICOM delle immagini medicali memorizzate possono essere scaricate in formato di file JSON. Inoltre Orthanc può generare al volo immagini PNG standard a partire da istanze DICOM.

Orthanc permette ai propri utenti di concentrarsi sul contenuto dei file DICOM, nascondendo la complessità del formato DICOM e del protocollo DICOM.

Please cite: Sébastien Jodogne: The Orthanc Ecosystem for Medical Imaging. (PubMed,eprint) Journal of Digital Imaging 31(3):341–352 (2018)
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orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)
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Orthanc-WSI brings support of whole-slide imaging for digital pathology into Orthanc, the lightweight, RESTful Vendor Neutral Archive for medical imaging.

This package contains two command-line tools to convert whole-slide images to and from DICOM. Support for proprietary file formats is available through OpenSlide. The package also contains an Orthanc plugin to display such DICOM images by any standard Web browser. The implementation follows DICOM Supplement 145.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
pixelmed-apps
implementazione DICOM contenente un visualizzatore di immagini e di ECG - cli
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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.

Fornisce applicazioni a riga di comando per usare pixelmed.

plastimatch
ricostruzione e registratura di immagini medicali
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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), inclusa la gestione di maschere per le immagini, penalità per punti di confine e regolarizzazione;
  • metodo Demons per la registratura deformabile di immagini (con accelerazione GPU);
  • segmentazione multi-atlante;
  • algoritmi basati su ITK per registratura a traslazione, rigide, affini, diversi metodi 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;
  • toolchain esaustiva per la ricerca radioterapica, inclusa la gestione per i formati di file DICOM, DICOM-RT, DICOM SRO, XiO, l'analisi della gamma, la manipolazione dei contorni, l'analisi della sovrapposizione dei contorni e l'analisi vettoriale dei campi. 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).
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python3-dipy
Python library for the analysis of diffusion MRI datasets
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DIPY is a software project for computational neuroanatomy. It focuses on diffusion magnetic resonance imaging (dMRI) analysis and tractography but also contains implementations of other computational imaging methods such as denoising and registration that are applicable to the greater medical imaging and image processing communities. Additionally, DIPY is an international project which brings together scientists across labs and countries to share their state-of-the-art code and expertise in the same codebase, accelerating scientific research in medical imaging.

Here are some of the highlights:

  • Reconstruction algorithms: CSD, DSI, GQI, DTI, DKI, QBI, SHORE and MAPMRI
  • Fiber tracking algorithms: deterministic and probabilistic
  • Native linear and nonlinear registration of images
  • Fast operations on streamlines (selection, resampling, registration)
  • Tractography segmentation and clustering
  • Many image operations, e.g., reslicing or denoising with NLMEANS
  • Estimation of distances/correspondences between streamlines and connectivity matrices
  • Interactive visualization of streamlines in the space of images

This package contains the Python 3 version.

Please cite: Eleftherios Garyfallidis, Matthew Brett, Vassilis Tsiaras, George Vogiatzis and Ian Nimmo-Smith: Identification of corresponding tracks in diffusion MRI tractographies. (eprint) Proc. Intl. Soc. Mag. Reson. Med. 18 (2010)
python3-nibabel
collegamenti Python 3 a vari formati di dati per neuroimmagini
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NiBabel fornisce accesso in lettura e scrittura ad alcuni formati di file comuni per neuroimmagini e file medicali, inclusi: ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC, così come PAR/REC. Le varie classi per formato per immagini danno accesso pieno o selettivo alle informazioni delle intestazioni (metainformazioni) e l'accesso ai dati dell'immagine è reso disponibile attraverso matrici NumPy. NiBabel è il successore di PyNIfTI.

python3-nipy
Analysis of structural and functional neuroimaging data
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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
Please cite: K. Jarrod Millman and Matthew Brett: Analysis of functional magnetic resonance imaging in Python (eprint) Computing in Science & Engineering 9(3):52-55 (2007)
python3-nipype
catena di elaborazione dati per l'analisi di neuroimmagini in Python 3
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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).

Please cite: SS Ghosh, C Burns, D Clark, K Gorgolewski, YO Halchenko, C Madison, R Tungaraza and KJ Millman: Nipype: Opensource platform for unified and replicable interaction with existing neuroimaging tools (eprint) 16th Annual Meeting of the Organization for Human Brain Mapping :106 (2010)
python3-nitime
timeseries analysis for neuroscience data (nitime)
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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.

python3-pydicom
lettura e scrittura di file medicali DICOM (Python 3)
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pydicom è un modulo in Python puro per l'analisi di file DICOM. DICOM è uno standard (http://medical.nema.org) per comunicare le immagini medicali e le informazioni relative, come rapporti e oggetti di radioterapia.

pydicom rende facile la lettura di file DICOM in naturali strutture pythoniche per una facile manipolazione. Gli insiemi di dati modificati posso essere nuovamente scritti su file in formato DICOM.

Questo pacchetto installa il modulo per Python 3.

python3-pyxid
interfaccia per i dispositivi XID e StimTracker di Cedrus
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pyxid è una libreria Python per interfacciarsi con i dispositivi XID (eXperiment Interface Device) e StimTracker di Cedrus. I dispositivi XID sono utilizzati in software come SuperLab, Presentation ed ePrime per ricevere input come parte di esperimenti di test con stimoli/risposte.

pyxid gestisce tutta la parte a basso livello del dispositivo per i dispositivi XID nei progetti Python.

python3-surfer
visualize Freesurfer's data in Python3
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This is a Python3 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
visualizzatore con GUI per segnali biologici come EEG, EMG e ECG
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SigViewer è un software di visualizzazione e valutazione per dati di segnali biomedici. Si basa sulla libreria biosig4c++ che gestisce svariati formati di dati (inclusi EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro, TMS32). L'elenco completo dei formati di file gestiti è disponibile su: http://pub.ist.ac.at/~schloegl/biosig/TESTED .

Oltre a visualizzare i segnali biologici, SigViewer permette la creazione di annotazioni per selezionare artefatti o eventi specifici.

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sofa-apps
GUI per SOFA (Simulation Open Framework Architecture)
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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.

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teem-apps
strumenti per elaborare e visualizzare dati e immagini scientifici - strumenti a riga di comando
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Teem è un gruppo coordinato di librerie per rappresentare, elaborare e visualizzare dati scientifici raster. Teem comprende strumenti a riga di comando che permettono di applicare velocemente le funzioni della libreria a file e flussi, senza dover scrivere codice. Le librerie più importanti e utili in Teem sono:

  • Nrrd (e lo strumento a riga di comando unu che ne fa uso) gestisce una gamma di operazioni per trasformare dati raster a N dimensioni (ricampionamento, ritaglio, estrazione, proiezione, istogramma, ecc.), così come il formato di file NRRD per memorizzare array e le loro meta-informazioni;
  • Gage: veloci misurazioni basate su convoluzione in posizioni di punti arbitrari in insiemi di dati di volume (scalare, vettore, tensore, ecc.);
  • Mite: uno strumento di rendering ray-casting multi-thread con funzioni di trasferimento basate su qualsiasi quantità misurabile da Gage;
  • Ten: per stima, elaborazione e visualizzazione di campi tensoriali di diffusione, compresi metodi di trattografia di fibre.

Questo pacchetto contiene alcuni semplici strumenti a riga di comando che forniscono accesso veloce e facile alle funzionalità nelle varie librerie.

tifffile
legge e scrive dati immagine da e su file TIFF
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Le immagini e i metadati possono essere letti da file TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH, ImageJ, MicroManager, FluoView, SEQ e GEL.

È gestito solo un sottoinsieme della specifica TIFF, per lo più immagini in scala di grigi e RGB(A) senza compressione e con compressione senza perdita di dati con interi a 2**(da 0 a 6) bit e 16, 32, 64 bit in virgola mobile, che sono comunemente usate nelle immagini bio-scientifiche. Nello specifico, non è gestita la lettura di dati immagine JPEG/TIFF compressi o di metadati EXIF/IPTC/GPS/XMP. Solo i record delle informazioni primarie sono letti dai formati immagine STK, FluoView, MicroManager e NIH.

Il formato TIFF (Tagged Image File Format) è sotto il controllo di Adobe Systems. BigTIFF permette di avere file più grandi di 4 GB. STK, LSM, FluoView, SEQ, GEL e OME-TIFF sono estensioni personalizzate definite, rispettivamente, da MetaMorph, Carl Zeiss MicroImaging, Olympus, Media Cybernetics, Molecular Dynamics e il consorzio Open Microscopy Environment.

voxbo
elaborazione, analisi statistica e visualizzazione di dati di immagini del cervello
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Questo è un toolkit per l'analisi di esperimenti di neuroimmagini funzionali (principalmente fMRI) e mappatura lesione-comportamento basata su voxel. VoxBo gestisce GLM modificato (per dati autocorrelati), oltre a GLM standard per dati non autocorrelati. Il toolkit è progettato per poter funzionare insieme a AFNI, FSL, SPM e altri.

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vrrender
DICOM viewer
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Medical image viewer featuring negatoscope, multi-planar reconstruction, and volume rendering.

Many image formats are handled such as DICOM, mhd, inr.gz, vtk, vti,... Segmentations meshes can also be imported from DICOM and vtk formats, and visualized in mixed rendering with images.

Tools are provided to measure distances of structures in the image and to place landmarks.

Last, VRRender can also connect directly to a PACS, and then request, download or upload DICOM files.

vtk-dicom-tools
DICOM per VTK - strumenti
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Questo pacchetto contiene un insieme di classi per gestire file e metadati DICOM dall'interno di VTK, e alcuni programmi di utilità per interrogare e convertire file DICOM.

Strumenti a riga di comando.

xmedcon
strumento di conversione di immagini medicali (DICOM, ECAT...) (GUI)
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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 o estrarre/riordinare le immagini specificate. È possibile recuperare i vettori grezzi delle immagini in formato binario o ASCII o produrre immagini PNG per le applicazioni desktop.

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

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Official Debian packages with lower relevance

cmtk
toolkit per morfometria computazionale
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Un toolkit software per morfometria computazionale di immagini biomediche, CMTK comprende un insieme di strumenti a riga di comando e una libreria backend di uso generale per elaborazione e I/O.

Gli strumenti a riga di comando forniscono principalmente le seguenti funzionalità: registrazione (affine e non-rigida; canale singolo e multiplo; a coppie e a gruppi), correzione di immagini (stima del campo del bias MR; correzione degli artefatti delle immagini interlacciate), elaborazione (filtri; combinazione di segmentazioni tramite voto e STAPLE; media basata sulla forma), statistiche (t-test; regressione lineare generale).

Please cite: T. Rohlfing: User Guide to The Computational Morphometry Toolkit. (eprint) The Insight Journal (2009)
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connectomeviewer
Interactive Analysis and Visualization for MR Connectomics
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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.

Please cite: Gerhard S, Daducci A, Lemkaddem A, Meuli R, Thiran J-P and Hagmann P: The Connectome Viewer Toolkit: An open source framework to manage, analyze, and visualize connectomes. (2011)
elastix
cassetta degli attrezzi per la registrazione rigida e non rigida di immagini
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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.

Please cite: Denis P. Shamonin, Esther E. Bron, Boudewijn P. F. Lelieveldt, Marion Smits, Stefan Klein and Marius Staring: Fast parallel image registration on CPU and GPU for diagnostic classification of Alzheimer's disease. (PubMed,eprint) frontiers in Neuroinformatics 7(50):1-15 (2014)
illustrate
cartoonish representations of large biological molecules
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This package provides a binary to transform PDF-formatted proteins into simplified but instructive graphics. The software has been used for the Protein-of-the-month's biomolecular illustrations for the past 20 years.

Please cite: D.S. Goodsell and A.J. Olson: Molecular Illustration in Black and White. (PubMed) J. Mol. Graphics 10(4):235-240 (1992)
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imagemagick
programmi per la manipolazione di immagini -- binari
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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. Si può 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 di Bézier. Tutte le operazioni possono essere eseguite sia da riga di comando che attraverso un'interfaccia grafica X11 (display).

Questo pacchetto include collegamenti ai binari e alle pagine di manuale specifici per profondità di canale.

Questo è un pacchetto fittizio. Può essere rimosso, anche completamente, senza problemi.

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imview
applicazione per visualizzare e analizzare immagini
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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!
Please cite: Hugues Talbot: ImView: a portable image display application (eprint)
orthanc-dicomweb
plugin per estendere Orthanc con la gestione di WADO e DICOMweb
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Orthanc DICOMweb è un plugin per Orthanc, un archivio per immagini mediche leggero, indipendente dal produttore e basato su REST. Estende il nucleo principale di Orthanc con la gestione degli standard WADO (ora noto come WADO-URI) e DICOMweb (QIDO-RS, STOW-RS, WADO-RS).

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
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orthanc-gdcm
transcodificatore/decodificatore DICOM per Orthanc che usa GDCM (particolarmente per JPEG2k)
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Questo pacchetto installa un plugin per Orthanc, un archivio di immagini medicali leggero, RESTful e indipendente dal produtttore. Il plugin estende Orthanc con un transcodificatore/decodificatore di immagini DICOM che è costruito sopra alla libreria GDCM, mentre il transcodificatore/decodificatore incorporato di Orthanc usa DCMTK.

Questo plugin è in particolare necessario ad Orthanc per poter transcodificare e decodificare sintassi di trasferimento JPEG2k.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
orthanc-imagej
plugin per ImageJ per importare immagini da Orthanc
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Questo plugin per ImageJ permette a ImageJ di sfogliare il contenuto di un server Orthanc e di importare immagini DICOM 2D/3D da Orthanc in ImageJ. Orthanc è un server DICOM RESTful e leggero per ricerche in campo sanitario e medico.

Questo plugin semplifica l'indicizzazione di immagini DICOM quando si usa ImageJ (es. per controllo di qualità delle modalità DICOM o per uso pedagogico). Non c'è nemmeno bisogno di intraprendere una complicata configurazione della rete dal momento che il plugin usa direttamente l'API REST di Orthanc. Ciò rende la sua installazione e il suo uso piuttosto diretti.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
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orthanc-mysql
plugin per usare MySQL o MariaDB come backend di database per Orthanc
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Orthanc MySQL è un insieme di due plugin per Orthanc, un archivio di immagini medicali leggero, RESTful e indipendente dal fornitore. Tali plugin sostituiscono il motore SQLite predefinito di Orthanc con un backend MySQL o MariaDB. Essi portano scalabilità in Orthanc, rendendolo pronto per ambienti professionali.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
orthanc-neuro
plugin per neuroimmagini per Orthanc
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Questo pacchetto installa un plugin per Orthanc, un archivio per immagini medicali leggero e indipendente dal venditore basato su REST. Questo plugin aggiunge la gestione di neuroimmagini in Orthanc, in particolare per convertire facilmente da DICOM a NIfTI.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
orthanc-postgresql
plugin per usare PostgreSQL come backend di database per Orthanc
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Orthanc PostgreSQL è un insieme di due plugin per Orthanc, un archivio per immagini mediche leggero, indipendente dal produttore e basato su REST. Questi plugin sostituiscono il motore SQLite predefinito di Orthanc con un backend PostgreSQL. Essi portano la scalablilità in Orthanc rendendolo pronto per ambienti professionali.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
orthanc-webviewer
visualizzatore web di immagini medicali per Orthanc
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Orthanc Web Viewer è un plugin per Orthanc, un archivio per immagini medicali leggero e indipendente dal venditore basato su REST. Estende Orthanc con un visualizzatore web integrato di immagini DICOM.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)
paraview
applicazione per visualizzazione parallela
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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
utilità di ottimizzazione per immagini PNG (Portable Network Graphics)
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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.

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science-workflow
sistemi di gestione dei flussi di lavoro per ricerca scientifica
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Questo task elenca alcuni pacchetti che forniscono sistemi di gestione dei flussi di lavoro utili per la ricerca scientifica.

trimage
interfaccia GUI e a riga di comando per l'ottimizzazione di immagini
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Trimage è un'interfaccia multipiattaforma con GUI e a riga di comando per l'ottimizzazione di immagini mediante optipng, advpng, pngcrush e jpegoptim, in funzione del tipo di file (attualmente sono gestiti i file PNG e JPG). Tutti i file delle immagini sono compressi senza perdita al livello di compressione massimo disponibile. Trimage fornisce varie funzioni di input per adattarsi al flusso di lavoro dell'utente: un classico dialogo per i file, trascinamento e rilascio e varie opzioni a riga di comando.

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bart-cuda
tools for computational magnetic resonance imaging
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The Berkeley Advanced Reconstruction Toolbox (BART) is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging. It consists of a programming library and a toolbox of command-line programs. The library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms. The command-line tools provide direct access to basic operations on multi-dimensional arrays as well as efficient implementations of many calibration and reconstruction algorithms for parallel imaging, compressed sensing, and machine learning.

This package provides BART with CUDA support.

fsl
transitional dummy package
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The only purpose of this package is to enable upgrades to the new 'fsl-core' package which replaces 'fsl'. This package can safely be removed.

Users aiming to perform a complete FSL installation (including all data components) are advised to install the 'fsl-complete' package from NeuroDebian.

Please cite: Mark Jenkinson, Christian F. Beckmann, Timothy E. J. Behrens, Mark W. Woolrich and Stephen M. Smith: FSL. (PubMed) NeuroImage 62(2):782-790 (2012)
vmtk
the Vascular Modeling Toolkit
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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.

Please cite: < M. Piccinelli, A. Veneziani, D. A. Steinman, A. Remuzzi and L. Antiga: A framework for geometric analysis of vascular structures: application to cerebral aneurysms.. IEEE Trans Med Imaging 28(8):1141-1155 (2009)
Registry entries: SciCrunch 

Packaging has started and developers might try the packaging code in VCS

bioimagesuite
integrated image analysis software suite
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Version: 2.0-1

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.

Please cite: X. Papademetris, M. Jackowski, N. Rajeevan, R. T. Constable and L. Staib: BioImage Suite: An integrated medical image analysis suite. (eprint) Insight Journal (2005)
Remark of Debian Med team: Contact to upstream

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

bioimagexd
Analyzing, processing and visualizing of multi dimensional microscopy images
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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
quantitatively measure phenotypes from images automatically
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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.

crea
base library of the creaTools medical image processing suite
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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.

Please cite: J. F. Carrillo, M. Hernández Hoyos, E. E. Dávila Serrano and M. Orkiszw: Recursive tracking of vascular tree axes in 3D medical images. (eprint) Int J Comput Assisted Radiol Surg 1(6):331-339 (2007)
dicoogle
Java Advanced Imaging API reference implementation
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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..

fiji
"batteries-included" distribution of ImageJ
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Fiji is an image processing package — a "batteries-included" distribution of ImageJ, bundling many plugins which facilitate scientific image analysis for the life sciences.

Remark of Debian Med team: About packaging status the authors said:

See the thread on the Debian Med mailing list at: http://lists.debian.org/debian-med/2009/04/msg00059.html

  • We've been working to get rid of, or replace, any remaining non-DFSG licensed plugins, but there's at least one left. The bug for tracking this is here: http://pacific.mpi-cbg.de/cgi-bin/bugzilla/show_bug.cgi?id=19
  • At the moment Fiji depends on sun-java6 rather than openjdk.
  • The packages are rather large at the moment (about 35MiB). This is mostly due to bundling various components with Fiji that could be satisfied as dependencies in Debian, such as junit, jruby, etc. but I haven't had time to work on separating those out.
  • Fiji uses a modified version of ImageJA (which again is bundled into the fiji package) rather than depending on the imagej Debian package created by people on this list.
  • One of the aims of Fiji was to make Benjamin Schmid's Java3D-based 3D viewer plugin work out-of-the-box, since people often had trouble installing it manually. At the time when I first made these packages there were no java3d packages in Debian, but now that these are in sid we should eventually be able to switch to using those.
freesurfer
analysis and visualization of functional brain imaging data
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FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. It contains a fully automatic structural stream for processing cross sectional and longitudinal data.

FreeSurfer provides many anatomical analysis tools, including: representation of the cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from the rest of the brain, skull stripping, B1 bias field correction, nonlinear registration of the cortical surface of an individual with an sterotaxic atlas, labeling of regions of the cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures, etc.

This package depends upon the latest version of freesurfer.

Please cite: A. M. Dale, B. Fischl and M. I. Sereno: Cortical surface-based analysis. I. Segmentation and surface reconstruction. (PubMed) Neuroimage 9(2):179-94 (1999)
Remark of Debian Med team: The 'tktools' (tkmedit, tksurfer and tkregister2) under the
 CorTechs license are not readily redistributable thus excluded.
 .
 Here you can see a list where Freesurfer was cited
 http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation
incf-nidash-oneclick-clients
utility for pushing DICOM data to the INCF datasharing server
Responsible: NeuroDebian Team
License: BSD
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Language: Python

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.

insightapplications
InsightToolKit (ITK) based medical imaging applications
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A variety of applications providing segmentation, registration, and other medical image processing algorithms such as MRI bias field correction.

jist
Java Image Science Toolkit
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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
medical image viewer for DICOM images
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Version: 1.1.0-2

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.

libdcm4che-java
Clinical Image and Object Management
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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 DICOM toolkit is used in many production applications across the world.

Remark of Debian Med team: Needs jai_imageio as prerequsite

Building the package using the packaging code in SVN works up to a point were jai_imageio.jar is required. For the status of packaging this prerequisite see the Debian Java mailing list at http://lists.debian.org/debian-java/2011/04/msg00045.html

mayam
Cross-platform DICOM Viewer
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Version: 0.8-1

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
micromanager
Microscopy Software
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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)
Remark of Debian Med team: Partially problematic licenses

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

mipav
quantitative analysis and visualization of medical images
Versions of package mipav
ReleaseVersionArchitectures
VCS5.0.0.20100907-2all
Versions and Archs
License: non-free
Git
Version: 5.0.0.20100907-2

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.

mni-colin27-nifti
Talairach stereotaxic space template
Versions of package mni-colin27-nifti
ReleaseVersionArchitectures
VCS1.1-2all
Versions and Archs
License: free
Git
Version: 1.1-2

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.

openelectrophy
data analysis GUI for intra- and extra-cellular recordings
Versions of package openelectrophy
ReleaseVersionArchitectures
VCS0.0.svn143all
Versions and Archs
License: free
Git
Version: 0.0.svn143

This package provides the startup script for the OpenElectrophy GUI.

Please cite: Samuel Garcia and Nicolas Fourcaud-Trocmé: OpenElectrophy: an electrophysiological data- and analysis-sharing framework. Frontiers in Neuroinformatics 3:14 (2009)
openmeeg-tools
openmeeg library -- command line tools
Versions of package openmeeg-tools
ReleaseVersionArchitectures
VCS2.4.2-1all
Versions and Archs
License: CeCILL-B
Debian package not available
Git
Version: 2.4.2-1

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.

Please cite: Alexandre Gramfort, Théodore Papadopoulo, Emmanuel Olivi and Maureen Clerc: OpenMEEG: opensource software for quasistatic bioelectromagnetics. (PubMed,eprint) BioMedical Engineering OnLine 9:45 (2010)
slicer
software package for visualization and image analysis - main application
Versions of package slicer
ReleaseVersionArchitectures
VCS4.10.2-1all
Versions and Archs
License: free
Debian package not available
Git
Version: 4.10.2-1

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.

Remark of Debian Med team: slicer was removed from Debian (see #644352)

The bug log (http://bugs.debian.org/644352) explains the reasons for the removal and the conditions when a new version might be back

stabilitycalc
evaluate fMRI scanner stability
Responsible: NeuroDebian Team
License: BSD
Git
Language: Python

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.

via-bin - wnpp
tools for volumetric image analysis
Versions of package via-bin
ReleaseVersionArchitectures
VCS1.6.0-3.1all
Versions and Archs
License: free
Git
Version: 1.6.0-3.1

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

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

visit - wnpp
interactive parallel visualization and graphical analysis tool
Versions of package visit
ReleaseVersionArchitectures
VCS2.9.1-1all
Versions and Archs
License: free
Debian package not available
Git
Version: 2.9.1-1

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.

xnat
platform for data management and productivity tasks in neuroimaging
Versions of package xnat
ReleaseVersionArchitectures
VCS1.7.5.1-1all
Versions and Archs
License: XNAT_SLA
Debian package not available
Git
Version: 1.7.5.1-1

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.

Please cite: Daniel S. Marcus, Timothy R. Olsen, Mohana Ramaratnam and Randy L. Buckner: The Extensible Neuroimaging Archive Toolkit (XNAT): An informatics platform for managing, exploring, and sharing neuroimaging data.. (PubMed,eprint) Neuroinformatics 5(1):11-34 (2007)

Unofficial packages built by somebody else

cdmedicpacs
web interface to PACS to access DICOM study images
License: GPL2

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
mni-autoreg
MNI average brain (305 MRI) stereotaxic registration model
Responsible: NeuroDebian Team
License: no-free, but GPLed parts

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-n3
MNI Non-parametric Non-uniformity Normalization
Responsible: NeuroDebian Team
License: BSDish

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
opendicom.net
API to DICOM in C# for Mono
Responsible: Albert Gnandt
License: LGPL

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.

No known packages available but some record of interest (WNPP bug)

devide - wnpp
Delft Visualization and Image processing Development Environment
Responsible: Mathieu Malaterre
License: BSD
Debian package not available

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

dtitk - wnpp
DTI spatial normalization and atlas construction toolkit
License: GPL-3+
Debian package not available
Language: C++

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
Please cite: H Zhang, P A Yushkevich, D C Alexander, and J C Gee: Deformable registration of diffusion tensor MR images with explicit orientation optimization. (2006)
eeglab - wnpp
toolbox for processing and visualization of electrophysiological data
Responsible: NeuroDebian Team
License: GPL-2+
Debian package not available
Language: C, Matlab/Octave

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.

Please register by following this link if you are using eeglab.
Please cite: Delorme A and Makeig S: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics (2004)
isis - wnpp
I/O framework for neuroimaging data
Responsible: NeuroDebian Team
License: GPL-2+
Debian package not available
Language: C++

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 - wnpp
high performance computing MRI simulator
Responsible: NeuroDebian Team
License: GPL-2+
Debian package not available

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.

Please cite: Tony Stöcker, Kaveh Vahedipour, Daniel Pflugfelder, N. Jon Shah: High-performance computing MRI simulations. (2010)
opensourcepacs - wnpp
medical image referral, archiving, routing and viewing system
Responsible: Mathieu Malaterre
License: GPL
Debian package not available

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/).

No known packages available

blox
medical imaging and visualization program
License: GPL
Debian package not available

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
image processing factory for MR images
License: Free? (CeCill License)
Debian package not available

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.

dcm4chee
Clinical Image and Object Management (enterprise)
License: LGPL, MPL, Apache, other (also non-free)
Debian package not available

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.

dicom4j
Java framework for Dicom
License: GPL
Debian package not available

Java framework for Dicom

drjekyll
interactive voxel editor for viewing and editing three-dimensional images
License: GPL
Debian package not available

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.

dti-query
dynamic queries of the white matter brain pathways
License: MIT
Debian package not available
Language: C++

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.

Remark of Debian Med team: Depends on RAPID library that is available under non-commercial

licensing terms.

ecg2png
convert scanned electrocardiograms into PNG format
License: GPL
Debian package not available

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.

Remark of Debian Med team: Homepage vanished

The homepage of this project that used to be at http://www.cardiothink.com/downloads/ecg2png/ vanished but the source can be downloaded fro instance from http://www.freshports.org/graphics/ecg2png/ .

gimias
Graphical Interface for Medical Image Analysis and Simulation
License: BSD-like
Debian package not available

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.

hid
database management system for clinical imaging
License: BSD, BIRN
Debian package not available
Language: java

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.

Please register by following this link if you are using hid.
Please cite: Keator, D.B.; Grethe, J.S.; Marcus, D.; Ozyurt, B.; Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.;Notestine, R.; Bockholt, H.J.; Papadopoulos, P.: A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN) (2008)
maris
package suite for Radiological Workflow
License: GPL
Debian package not available

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.

medisnap
photograph, manage, view, compare, document and archive medical photos
License: GPL-3
Debian package not available

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
mesa-test-tools
IHE Test Software for Radiology
License: free
Debian package not available

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
Medical Images viewer and converter
License: GPL-3+
Debian package not available
Language: C++

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
Remark of Debian Med team: At the moment available only for Windows, but author says

there should be no major showstoppers to build it on Linux -- just needs building infrastructure

mni-icbm152-nlin-2009
MNI stereotaxic space human brain template
Responsible: NeuroDebian Team
License: custom, DFSG-compliant
Debian package not available

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.

Please cite: V.S. Fonov, A.C. Evans, R.C. McKinstry, C.R. Almli and D.L. Collins: Unbiased nonlinear average age-appropriate brain templates from birth to adulthood. (2009)
Remark of Debian Med team: This package is waiting for the Debian data package archive to become available.
mrisim
simulator for magnetic resonance imaging data
Responsible: NeuroDebian Team
License: BSD-like
Debian package not available

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
coming standard LIMS for microscopy images
License: GPL
Debian package not available

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

piano
medical image processing library for surgical planning
License: BSD
Debian package not available

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
suite for analysis of magnetoencephalography (MEG) data
License: GPL-3
Debian package not available
Language: Python
 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.
Remark of Debian Med team: Needs DFSG-ification.
       According to the author is not yet ready for the use by
       mortals -- wasn't released yet.
stir
Software for Tomographic Image Reconstruction
License: GPL
Debian package not available

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..

Remark of Debian Med team: Even if this is GPLed software the download requires registration.
tempo
3D visualization of brain electrical activity
License: BSD
Debian package not available
Language: C++, Qt

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.

Remark of Debian Med team: Packaged for OpenSuSE http://en.opensuse.org/TEMPO
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 244547