Open-source software

Much of my personal software are available to view and download from GitHub:

Other software I have collaborated on are available from a number of public resources including:

Software portfolio

Here I highlight selected software, including personal and collaborative projects, and work carried out while working as a Research Associate at UCL and Oxford.


GIFT-Cloud was developed by Tom Doel and Dzhoshkun Shakir while research associates at UCL on the GIFT-Surg project.

GIFT-Cloud is a data sharing and collaboration platform for medical imaging research. Extending the XNAT platform, it provides researchers with a web interface to anonymised research data and data processing pipelines. Clinical collaborators can anonymise and upload data directly from the hospital PACS systems which are integrated with GIFT-Cloud using custom gateway software.

GIFT-Cloud is built using cross platform frameworks including Java Web Start, Tomcat, PostgreSQL and Apache Velocity.

Presentation by Tom Doel at UCL Research Programming Technical Social – Data Sharing with GIFT-Cloud

Publication by Tom Doel et al – GIFT-Cloud: A data sharing and collaboration platform for medical imaging research

Case study on XNAT website – XNAT for Clinical Translation: GIFT-SURG


Pulmonary Toolkit (PTK)

PTK screenshot

Originally developed by Tom Doel while studying for a PhD at the University of Oxford, the Pulmonary Toolkit (PTK) is now used by image analysis researchers in universities worldwide.

PTK is an image analysis framework that combines a library of state-of-the-art pulmonary image analysis segmentation and analysis tools, an easy-to-use graphical user interface, a full API and a stand-alone fully automated command-line application.

PTK is open source and built using object orientated Matlab and optimised C++ code. Pre-built executables do not require a Matlab licence.

PTK homepage on GitHub




Image Split – a pip-installable utility developed using Python/NumPy for dividing large image volumes into smaller volumes to aim image processing, and for robust recombination. Developed by Tom Doel while working on the GIFT-Surg project at CMIC at UCL. Soure Code

Python Template– a CookieCutter template for creating a fully working Python “hello world” application with tox unit testing, Python 2 and 3 compatibility, sphinx documentation,   GitLab CI or GitHub Travis integration. Developed by Tom Doel while working at the WEISS centre at UCL.

Mpg2Dcm– A Java MPEG-2 video to DICOM converter.

DicoMat– A Dicom library for Matlab that groups 2D images into 3D volumes

Other open source utilities developed by Tom Doel can be found on my GitHub page.



These are some of the software projects developed by other researchers which I have contributed to.

NiftyNet – a TensorFlow-based open-source convolutional neural networks (CNNs) platform for research in medical image analysis and image-guided therapy.  Source on GitHub     Journal publication

DyBaORF– Dynamically Balanced Online Random Forest by Guotai Wang et al

NiftyMIC– A research-focussed toolkit for motion-correction and volumetric image reconstruction of 2D ultra-fast MRI by Michael Ebner et al.

SlicSeg– An API and GUI application for semi-automated interactive segmentation of medical images by Guotai Wang et al.

VesselTools – Scripts and utility programs by Maria A Zuluaga et al. for extracting and processing vasculature


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