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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?) DONE
  • Improved registration support (apply transform) DONE
  • Improved ASL tools based on oxasl (inc. ENABLE, VEASL, DEBLUR) DONE
  • Fabber T1 DONE
  • Fabber DCE DONE
  • DSC widget DONE
  • Improvements to ROI builder - working 'paint' tool DONE
  • Motion simulation DONE
  • Add noise DONE

v1.0 (Target June 2019)

  • Stable interface for QpWidget, QpData, Process
  • Python 3 DONE needs testing
  • Support PySide and PySide2 - ideally the latter by default pyside2 branch needs testing
  • Improved manual data alignment tools PART DONE
  • Otherwise no firm plans yet - selection from 'Vague plans' below

Migration to PySide2

  • The current implementation uses PySide which is based on Qt4
  • Update to PySide2 when released which uses Qt5
  • Will provide support for HiDPI screens and proper scaling in OSx
  • PyQtgraph is currently the stumbling block as release version does not support Pyside2
  • Current git version has PySide2 modifications but not yet tested
  • Consider move to VisPy if this does not come to fruition

Vague Plans for Future

  • Refactoring of view classes

    • This is a mess at the moment. Need all view options to be stored as metadata and cleaner separation between the ImageView widget and the individual OrthoView widgets.
  • 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?)
  • Add Jola's texture analysis which sounds cool, whatever it is

  • PK modelling validation

    • QIBA in progress
    • 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
  • Simulation tools

    • Fabber test data
    • 'Simulated brain'

Project details

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