TomoPhantom

Software to generate 2D/3D/4D analytical phantoms and their Radon transforms (parallel beam) for image processing

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TomoPhantom [1] is a toolbox to generate customisable 2D-4D phantoms (with a temporal capability) and their analytical tomographic projection data for parallel-beam geometry. It can be used for testing various tomographic reconstruction methods, as well as image processing methods, such as, denoising, deblurring, segmentation, and machine/deep learning tasks.

NEW! VERSION 3.0

TomoPhantom has been refactored, please see changes. Everyone is welcome to Documentation page.

About TomoPhantom

TomoPhantom is recommended for various image processing tasks that require extensive numerical testing: image reconstruction, denoising, deblurring, etc. In particular, TomoPhantom is best-suited for testing various tomographic image reconstruction (TIR) methods. For TIR algorithms testing, the popular Shepp-Logan phantom is not always a good choice due to its piecewise-constant nature. This toolbox provides a simple modular approach to efficiently build customisable 2D-4D phantoms consisting of piecewise-constant, piecewise-smooth, and smooth analytical objects as well as their analytical Radon transforms .

What TomoPhantom can do:

Generate 2D and 3D synthetic phantoms made of Gaussians, parabolas, ellipses, cones and rectangulars.
Generate simple temporal extensions of 2D and 3D phantoms.
Calculate analytical Radon transforms of 2D-4D models and also their numerical projections.
Model a variety of tomographic data artefacts (noise models, zingers, rings, shifts, partial volume effect and others).

Installation:

Tomophantom is distributed as a Python conda package for Linux/Windows/Mac OS’s:

conda install -c httomo tomophantom

Please see more detailed information on Installation and development environments.

Related software projects on GitHub:

xdesign XDesign is an open-source Python package for generating configurable simulation phantoms for benchmarking tomographic image reconstruction.
syris Syris (synchrotron radiation imaging simulation) is a framework for simulations of X-ray absorption and phase contrast dynamic imaging experiments, like time-resolved radiography, tomography or laminography.

References:

[1] D. Kazantsev et al. 2018, TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks, Software X, Volume 7, January–June 2018, Pages 150–155

[2] D. Kazantsev, V. Pickalov “New iterative reconstruction methods for fan-beam tomography”, IPSE, 2017

Applications:

Software related questions/comments please e-mail to Daniil Kazantsev at [email protected]