Pytomography: A Python Library for Medical Image Reconstruction

Pytomography: A Python Library for Medical Image Reconstruction Publisher

Polson LA^{1, 2} ; Fedrigo R^{1, 2} ; Li C^{1, 2} ; Sabouri M^{1, 2} ; Dzikunu O^{2, 3} ; Ahamed S^{1, 2} ; Karakatsanis N⁴ ; Kurkowska S^{6, 7} ; Sheikhzadeh P⁸ ; Esquinas P⁶ ; Rahmim A^{1, 2, 3, 5} ; Uribe C^{2, 5, 6}

Show Affiliations

1. Department of Physics & Astronomy, University of British Columbia, Vancouver, Canada
2. Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, Canada
3. School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
4. Department of Radiology, Weill Cornell Medical College, NY, United States
5. Department of Radiology, University of British Columbia, Vancouver, Canada
6. Molecular Imaging and Therapy Department, BC Cancer, Vancouver, Canada
7. Department of Nuclear Medicine, Pomeranian Medical University, Szczecin, Poland
8. Nuclear Medicine Department, IKHC, Faculty of Medicine, Tehran University of Medical Science, Tehran, Iran

Source: SoftwareX Published:2025

Abstract

There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent literature, such as those that employ artificial intelligence. The purpose of this research was to create and evaluate a GPU-accelerated, open-source, and user-friendly image reconstruction library, designed to serve as a central platform for the development, validation, and deployment of various tomographic reconstruction algorithms. PyTomography was developed using Python and inherits the GPU-accelerated functionality of PyTorch and parallelproj for fast computations. Its flexible and modular design decouples system matrices, likelihoods, and reconstruction algorithms, simplifying the process of integrating new imaging modalities using various python tools. Example use cases demonstrate the software capabilities in parallel hole SPECT and listmode PET imaging. Overall, we have developed and publicly share PyTomography, a highly optimized and user-friendly software for medical image reconstruction, with a class hierarchy that fosters the development of novel imaging applications. © 2024 The Authors

Experts (# of related papers)

Mehrshad Abbasi (1)

Peyman Sheikhzadeh (1)

Style	Citing Format
MLA	Polson LA, et al.. "Pytomography: A Python Library for Medical Image Reconstruction." SoftwareX, vol. 29, no. , 2025, pp. -.
APA	Polson LA, Fedrigo R, Li C, Sabouri M, Dzikunu O, Ahamed S, Karakatsanis N, Kurkowska S, Sheikhzadeh P, Esquinas P, Rahmim A, Uribe C (2025). Pytomography: A Python Library for Medical Image Reconstruction. SoftwareX, 29(), -.
Chicago	Polson LA, Fedrigo R, Li C, Sabouri M, Dzikunu O, Ahamed S, Karakatsanis N, et al.. "Pytomography: A Python Library for Medical Image Reconstruction." SoftwareX 29, no. (2025): -.
Harvard	Polson LA et al. (2025) 'Pytomography: A Python Library for Medical Image Reconstruction', SoftwareX, 29(), pp. -.
Vancouver	Polson LA, Fedrigo R, Li C, Sabouri M, Dzikunu O, Ahamed S, et al.. Pytomography: A Python Library for Medical Image Reconstruction. SoftwareX. 2025;29():-.
BibTex	@article{ author = {Polson LA and Fedrigo R and Li C and Sabouri M and Dzikunu O and Ahamed S and Karakatsanis N and Kurkowska S and Sheikhzadeh P and Esquinas P and Rahmim A and Uribe C}, title = {Pytomography: A Python Library for Medical Image Reconstruction}, journal = {SoftwareX}, volume = {29}, number = {}, pages = {-}, year = {2025} }
RIS	TY - JOUR AU - Polson LA AU - Fedrigo R AU - Li C AU - Sabouri M AU - Dzikunu O AU - Ahamed S AU - Karakatsanis N AU - Kurkowska S AU - Sheikhzadeh P AU - Esquinas P AU - Rahmim A AU - Uribe C TI - Pytomography: A Python Library for Medical Image Reconstruction JO - SoftwareX VL - 29 IS - SP - EP - PY - 2025 ER -

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