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Quantiphyse is a data viewer and analysis platform for volumetric medical imaging data

Project description


Viewer and data processing for 3D/4D medical imaging data


Quantiphyse provides tools for modelling and analysis of 3D/4D volumetric data, principally MRI data.

Core features:

  • Loading/Saving 3D/4D NIFTI files
  • Analysis tools including single/multiple voxel analysis and data comparison
  • Generic processing including smoothing, resampling, clustering

Features available via plugins

  • Registration, motion correction
  • Modelling tools for DCE, ASL, DSC and CEST MRI
  • Integration of selected FSL tools

See: for full documentation.


Quantiphyse is available free under an academic (non-commercial) license. See the LICENSE file for full details, and contact OUI if interested in commercial licensing.


See for current installation instructions

Running from source code (for developers)

Running from source is recommended only if your are interested in developing the software further.

  1. Install the dependencies:

The list of Python dependencies is in requirements.txt

For example:

pip install -r requirements.txt
  1. Build extensions

python build_ext --inplace

  1. Run from source directory



The scripts packaging/ is used to build a frozen distribution package in the form of a compressed archive (tar.gz or .zip) and a platform-dependent package (deb, msi or dpg). It should run autonomously, however you may need to input the sudo password on Linux in order to build a deb package.

The --snapshot option removes the version number from package filenames so you can provided them for download without having to change the link URLs.

The --maxi option builds a package which includes selected plugins, assuming these are downloaded

To Do list

Issue tracker

Current issues can be viewed on the GitHub issue tracker (


v0.6 (Released June 2018)

  • ASL tools first version (preprocess, model fit, calibration, multiphase)
  • Improved viewer (full resolution, aligned)

v0.8 (Target Mar 2019)

  • Integration of selected FSL tools (FLIRT, FAST, BET, FSL_ANAT?) [x]
  • Improved registration support (apply transform) [x]
  • Improved ASL tools based on oxasl (inc. ENABLE, VEASL, DEBLUR) [x]
  • Fabber T1 [x]
  • Fabber DCE [x]
  • DSC widget [x]
  • Improvements to ROI builder - working 'paint' tool [x]
  • Motion simulation [x]
  • Add noise [x]

v0.10 (Target 2020)

  • Stable interface for QpWidget, QpData, Process [ ]
  • Python 3 [x]
  • Support PySide and PySide2 - ideally the latter by default [x]
  • Improved manual data alignment tools [ ]
  • Multi-overlay view [x]
  • Perfusion simulator [x]

Migration to PySide2

  • Current version of Quantipihyse is targeted at Pyside2
  • Should still run under Pyside1 but not guaranteed
  • Currently using our own fork of pyqtgraph awaiting official release with Pyside2 support

Vague Plans for Future

  • MoCo/Registration

    • Bartek's MC method
  • 3D view

    • Probably not that useful but fun and may be easy(?) with vispy. Reliant on good refactoring of ImageView
    • Application to surfaces (Tom K?)
    • Use VisPy?
  • Add Jola's texture analysis which sounds cool, whatever it is

  • PK modelling validation

    • QIBA [x]
    • QIN
  • Simplify/rewrite generic Fabber interface

  • Improve memory usage by swapping out data which are not being displayed?

  • All widgets which process within ROI should work with the subimage within the bounding box of the ROI, not the whole image.

    • Supervoxels does this already with great performance improvement.
  • Support other file formats using NIBABEL.

    • DICOM conversion included where DCMSTACK is available
  • Add semiquantitative measures

    • Area under the curve
    • Enhancing fraction

Project details

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quantiphyse-0.9.10.tar.gz (1.3 MB view hashes)

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