Osirix Plugins

This pages will list not only my plugins, but internet sites from other plugin programmers as well. If you think a site is missing, write it into the comments and I will add it. Make sure to check out the plugins, which are directly available over the OsiriX plugin manager.

Alexandre Amatohomepagecontact

  • Surface Length 3D … uses surface rendering and creates paths over those surfaces, measuring it. It can also do direct (straight) 3D measures.

Alexandre Martinethomepagecontact

  • Dental 3D Plugin … extends the OsiriX 3D Curved MPR Viewer features to allow the user to perform basic dental implant treatment planning. Features include: basic implants shape polygon ROIs drawing, implant ROI diameter automatic calculation based upon image analysis algorithm, ROIs are associated with each transverse section position, extended zooming in the transverse view, pilot drill volumes for 3D surface rendering and implant numbering

Aurelie Canale – homepage – contact

  • CreateROIMask … convert an Osirix ROI into a binary image in Analyze format.

Brian Hargreaveshomepagecontact

  • RGPhaseCorr … is a plugin implantation for taking I & Q images from a FIESTA acquisition and separating water and fat using phase-sensitive SSFP. This can also be used for 2-point Dixon imaging (Moriguchi et al., Magn Reson Med. 2004 Dec;52(6):1342-50) and probably for phase-sensitive inversion recovery imaging (Kellman et al., Magn Reson Med. 2002 Feb;47(2):372-83).
  • ImageToMatlab … After selecting a series and the 2D/3D viewer, ImageToMatlab.plugin will save a simple image file that you can read into Matlab using read3dfloats.m.
  • MatlabToOsirix … It is quite easy to transfer 3D images from Matlab to Osirix. Here are simple instructions and a simple script, im2osirix.m.

Brian Jensen – homepage – contact

  • Osirix Segmentation Tool … The user interface has support for three standard ITK region growing algorithms: connected threshold, neighborhood connected threshold and confidence connected. A fourth algorithm was developed using the ITK framework, gradient threshold.
  • PetSpectFusion … automatic registration of cardiac PET and SPECT images  based upon the ITK Framework.

Deqiang Qiuhomepage – contact

  • DTIMap … calculates Fractional Anisotropy (FA), Mean diffusivity, radial and axial diffusivity and color coded FA maps from DTI images.
  • Exporter … exports/loads DICOM images to/from nifti image and saves the current view to the database. Intended to be used as an interface between Osirix and many tools developed to work with nifti format, such as FSL.
  • NiftiToDicom … This plugin imports image from nifti file to Osirix database.

Institute for Surgical Technology & Biometrics University Bernhomepagecontact

  • iSix = image Segmentation for OsiriX … allows to perform manual and semi-automatic segmentation using: different size brushes, region growing and livewire segmentation. For MRI studies using Dixon sequences, it incorporates a dedicated module to quantify amount of fat and muscle in the tissues.

Joël Spaltenstein – homepage – contact

  • unImportantNotice … removes the various “Not for Medical Usage” banners and alerts on any OsiriX version before 6.0 . The Source code and binaries are free to download.
  • ProSizeAV … TAVI plugin to ease the sizing process, automate annoying standard steps and generate standardized reports. The plugin is free, but registration is required! No FDA and no CE approval, yet. Created in collaboration with

    Andreas Holzamer.

Konrad Weryshomepage – contact

Kyung Hyun Sunghomepagecontact

  • DCE Tool … allows you to easily analyze dynamic contrast enhanced (DCE) MRI data.
  • B1 Map … allows you to estimate B1 field inhomogeneity using either Bloch-Siegert shift or double angle method.
  • Fusion Tool … allows you to combine two 4D viewers. When combing two viewers, you can limit slice numbers and temporal points for original and dragged viewers.
  • Custom 4D Viewer … allows you to customize the 4D viewer
  • Quality Assessment Tool … allows you to compute RMSE and MSSIM between two images
  • Functional MRU Tool
  • SNR Calculator … allows you to calculate SNR from repeated acquisitions of an image. Simply open the repeated series in the 4D viewer and run the plugin.

Matthew Blackledge – homepage – contact

  • pyOsiriX … provides a Python interface to many of OsiriX’ viewing functions and allows you to use many of the scientific libraries available to Python in your OsiriX workflow. <Paper on this Subject>

Open Source Software University Medicine Manheim

  • UMMPerfusion … An OsiriX plugin for calculation of perfusion parameters on the basis of 4-dimensional datasets. <Paper on this Subject>
  • UMMDiffusion … Advanced Diffusion calculation Plugin (project under construction). The following DWI Models will be supported: standard ADC calculation, IVIM Model, Kurtosis DWI. <Paper on this Subject>
  • UMMRegistration … Image registration plugin for dynamic MRI data (project under construction)

Radiopaedia.orghomepagecontact

  • Case Uploader (by Jarrel Seah, Jennifer Tang and Andrew Dixon) … allows quick upload of DICOM cases from Mac to Radiopaedia. Source code is available on GitHub.

René Laqua homepagecontact

Thomas Stefani – homepage – contact

  • Cranial Nerves …provides assistance in locating cranial nerves’ nuclei.

More plugins:

  • dianeXu … Open Source Automated Left Atrial Fibrosis Quantization on the OsiriX Platform. Source Code Available.
  • SIVIC … an open-source, standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.
  • Fovia’s High Definition Volume Rendering® (HDVR®) … Research Version for Non-Commercial Use … also take a look at the gallery
  • inTag …software to calculate, display and analyze myocardial strains and intra-myocardial mechanics from cardiac MR images with a tagging pattern.
  • Spectroscopic Imaging Visualization and Computing (SIVIC) … visualizing and processing DICOM MR spectroscopy data
  • iPAD … annotation tool, to make the semantic content (the meaning and other key metadata) explicit and machine-accessible. iPAD, implements the AIM standard (Annotation and Image Markup) of the caBIG project.
  • Mia Lite … ultra-fast level set based segmentation in 3D. Free for academic use. Available OsiriX plugin and standalone application for Mac, Linux and Windows.
  • Harmonic Phase Flow … MRI tagging for regional assessment of the heart function. This technique produces a grid-like pattern of saturated magnetization over the myocardium that deforms by the underlying motion of the heart. This enables visualization of transmural deformation.

36 Responses to Osirix Plugins

  1. A generic Open Source MRI perfusion analysis tool for quantitative parameter mapping to be used in a clinical workflow and methods for quality management of perfusion data.

    http://ikrsrv1.medma.uni-heidelberg.de/redmine/projects/ummperfusion

  2. EVARplugin for OsiriX provides dedicated and easy-to-use functionality for AAA analysis and EVAR measurements, with automatic centerline computation, interactive planning sheets, and much more. The plugin is compatible with all OsiriX versions (except OsiriX HD) and for non-clinical use only.

    Evaluate the plugin for free and easily upgrade to a perpetual license any time later! All information and instructions for download/purchase can be found at [Link is dead].

  3. pankaj says:

    i want to see the demo tutorial vedio for umm perfusion

  4. Joel Spaltenstein says:

    I wrote a plugin a while back to get rid of the various Not for Medical Usage banners and alerts. I put the sources up at https://github.com/spalte/unImportantNotice and a compiled version can be downloaded from http://download.naturalimage.ch/UnImportantNotice2-0.zip.

    • Reinier says:

      Thank you very much for this plugin!

    • alan white says:

      I have read the information on github. What is next step ? Should i remove osirix ver 5.9 and reinstall it adding your plugin?

      (korrigierte deutsche Übersetzung durch den Moderator): Ich habe die Informationen auf GitHub gelesen. Wie soll ich weiter verfahren? Soll ich OsiriX v5.9 komplett neu installieren und dann das Plugin hinzufügen?

      thank you
      alan

      • René Laqua says:

        The plugin should be working on any OsiriX version before 6.0. So if you already have OsiriX 5.9 (free version) you don’t need to reinstall, just add the plugin and restart OsiriX.

  5. I wrote a plugin that extends the OsiriX 3D Curved MPR Viewer features to allow the user to perform dental implant treatment planning. More informations at http://www.amdentalsoft.net/software/dental-3d-plugin/
    PS : thank you for your blog, it has helped me a lot to start OsiriX plugin development !

  6. Matteo Minestrini says:

    Which of the plugins listed above allows to register MRI or CT imaging with SPET?

    Thx in advance.

  7. VenkatRaman says:

    Is there plug-in available for Diffusion kurtosis imaging processing?, similar to DTI plug-in.
    Thanks a lot,

  8. Alan says:

    Looking for a plug-in to archive off old (added 12 months ago) images to share storage and update links reference on Osirix to drive.

  9. petitpierre says:

    Hello,
    is there a plugin to separate different phases of diffusion images when there are packed together ?
    thx

    • René Laqua says:

      What kind of MRI diffusion imaging are we talking about? Do you want to separate different b-values? What purpose would it have?

  10. Alex says:

    Hi, I am a radiologist and I am seeking for an open plugin and viewer to analyze the Ivim model on breast exams. Have you any suggestions?

  11. Alex says:

    I will try it! Thank you so much

  12. David says:

    Hello! I am a researcher at a university in Philadelphia. Our research group is trying to quantify the surface area (spread) of a specific high contrast agent in tissue. Do you know of any plugin that would allow us to calculate Surface Area from the surface rendering images performed by the program? We do not own OsiriX and are currently trying to figure out which imaging software can provide us with quantitative data for both volume and surface area. Any help would be greatly appreciated. Thank you.

    • René Laqua says:

      Hey David,

      I don’t know a OsiriX plugin or any other software which could help you.

    • Reinier says:

      If you have a single 2d image you can hand trace a ROI and it will report area and pixel info inside that ROI.
      Also if you hand trace a stack of images then you get volume.
      You can do this in osirix lite or horos no problem. Both free. I think j-image also, which is multiplatform.

      • David says:

        Thank you very much for your response. We used segmentation in Horos with the ROI tool to create a 3D volume and were able to obtain a value. However, in addition to volume we were hoping to quantify 3D surface area. The segmentation technique gives you the area for each 2D slide but we were hoping there was a plugin that could provide us with a 3D surface area measurement. I believe we could do surface integration from the 2D measurements to get a 3D value but it is computationally intensive so we are trying to figure out a different way.

  13. zulzaki says:

    how do i analyse cerebral vasoCT (angiogram) using osirix?

    • René Laqua says:

      Hi Zulzaki,

      I am not sure what you mean with analyze CT Brain Angiograms. You can use the MIP-Modus for visual inspection.

  14. enigma says:

    Hello, sorry to bother but since the last osirix update the export ROI plugin is not working anymore with nifti files.
    I need to export ROI’s values for dozens of ROIs and it would be too time consuming to do it manually. When I start to export the bar loads up to roughly half to its length and then it suddenly closes without creating the files. It is the same with CSV and xml.
    could someone advice please?

  15. amir says:

    Updating to Osirix 7 or 8 I can not read nifti files which is a vital feature neuro-imaging research. I tried proposed plugins too like Exporter and nifti2dicom but they are not launching with the mentioned Osirix versions.
    I appreciate if the Osirix development team points me to a solution.

  16. Kirilov says:

    Hello, I am new Osiris user and I’m looking for some plugins:
    – Recist, Dynamic flow evaluation in perfusion series MRI prostate breast,CT…. and also any plugins for volume calculating in Lung micro-nodules
    Thanks !

  17. Joël Spaltenstein says:

    Andreas Holzamer from the University of Regensburg and I wrote a free OsiriX/Horos plugin a while back for TAVI/TAVR measurements. You can download the plugin from http://www.prosizeav.com, and view instructions at https://www.youtube.com/user/Levosim.

  18. Dan Duma says:

    Hi is there a plugin for Osirix or Horos to measure the volume of abdominal fat (VAT) on CT?
    Thank you.

  19. Abrar ALQATTAN says:

    Hello
    is there is anyway to calculate the ADC value for each B value separately?

    • René Laqua says:

      Not that I know. You could circumvent the restriction of the plugin and remove the not needed b-values from your local database (please make sure you have a backup).

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