TomoPhantom

<table> <tr> <td> <div align="left"> <img src="docs/source/_static/tomophantom_logo.png" width="550"><br> </div> </td> <td> <font size="5"><b> TomoPhantom </b> <a href="https://doi.org/10.1016/j.softx.2018.05.003">[1]</a> 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. </font> </td> </tr> </table> <div align="center"> <img src="docs/source/_static/tomophantom_apps.png" height="350"><br> <img src="docs/source/_static/models2Dtime/2DtModel14.gif" height="175"><img src="docs/source/_static/models4D/model11_4D.gif "height="175" width="200"><br> </div>

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NEW!

Please see changes. <a href="https://dkazanc.github.io/TomoPhantom/index.html">Documentation</a> has been updated in January 2025 with a lot of additional information, API links, tutorials, etc.

<div class="post-content"> <h3 class="post-title">About TomoPhantom </h3> <p> 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 <a href="https://en.wikipedia.org/wiki/Shepp%E2%80%93Logan_phantom">Shepp-Logan phantom</a> 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 <a href="https://en.wikipedia.org/wiki/Radon_transform">Radon transforms</a> . </p> </div>

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 conda package in Python for Linux & Windows:

conda install -c httomo tomophantom

Please see more detailed information on <a href="https://dkazanc.github.io/TomoPhantom/howto/installation.html">Installation</a> 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:

• TOmographic MOdel-BAsed Reconstruction (ToMoBAR)
• Joint image reconstruction method with correlative multi-channel prior for X-ray spectral computed tomography
• Deep learning segmentation of synthetic tomographic data using Pytorch U-net

Software related questions/comments please e-mail to Daniil Kazantsev at dkazanc@hotmail.com