Overview

Quantiphyse is a visualization and analysis tool for medical imaging data, particularly supporting quantitive and physiological imaging methods. The aim is to bring advanced analysis methods to users in biomedical research via an easy-to-use interface, that also permits the creation of analysis pipelines to be used in research studies.

The software is designed a GUI that provides a range of visualisation and data interrogation tools, alongside various plug-ins that support a range of analysis methods. Quantiphyse also supports advanced usage via non-GUI batch processing and direct interaction with the underlying Python code.

Quantiphyse is particularly suited for quantitative, physiological or functional imaging data, typically these are comprised of multiple volumes in a 4D (time-) series and/or multimodal imaging data. Quantiphyse is built around the concept of making spatially resolved measurements of physical or physiological processes from imaging data using either model-based or model-free methods, in a large part exploiting Bayesian inference techniques. Quantiphyse can analyse data both voxelwise or within regions of interest that may be manually or automatically created, e.g. supervoxel or clustering methods.

Origins

Quantiphyse arose from a visualisation and analysis tool developed by Ben Irving for perfusion MRI data for use in the CRUK-EPSRC Cancer Imaging Centre in Oxford (CICO). It soon became clear that this tool could enable clinical collaborators in the centre to visualise and analyse their data, gaining access to new methods being developed in the Image Analysis Theme of CICO. 

Working with Michael Chappell (then Image Analysis Theme lead in CICO) and Martin Craig the original perfusion MRI tool was developed into the quantitative and physiological image analysis environment that is now Quantiphyse. Since the original implementation, a range of other physiological image analysis methods have been added drawing from the research being done in Michael's QuBIc group at the Institute of Biomedical Engineering. Quantiphyse now provides a major way for QuBIc to enable access to advanced image analysis methods by users of quantitative and physiological imaging techniques, that otherwise would require substantial technical knowledge and time to implement.