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Published January 8, 2024 | Submitted
Discussion Paper Open

Data-driven system matrix manipulation enabling fast functional imaging and intra-image nonrigid motion correction in tomography

  • 1. ROR icon California Institute of Technology


Tomographic imaging modalities are described by large system matrices. Sparse sampling and tissue motion degrade system matrix and image quality. Various existing techniques improve the image quality without correcting the system matrices. Here, we compress the system matrices to improve computational efficiency (e.g., 42 times) using singular value decomposition and fast Fourier transform. Enabled by the efficiency, we propose (1) fast sparsely sampling functional imaging by incorporating a densely sampled prior image into the system matrix, which maintains the critical linearity while mitigating artifacts and (2) intra-image nonrigid motion correction by incorporating the motion as subdomain translations into the system matrix and reconstructing the translations together with the image iteratively. We demonstrate the methods in 3D photoacoustic computed tomography with significantly improved image qualities and clarify their applicability to X-ray CT and MRI or other types of imperfections due to the similarities in system matrices.

Copyright and License

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.


This work was supported in part by National Institutes of Health grants R01 NS102213, U01 EB029823 (BRAIN Initiative), and R35 CA220436 (Outstanding Investigator Award).

Data Availability

All data used in this study are available from the corresponding author upon reasonable request.

Code Availability

The image reconstruction and data processing algorithms are described in detail in the Methods and Supplementary Information. We have opted not to make the codes available because they are proprietary and used for other projects.

Conflict of Interest

L.V.W. has a financial interest in Microphotoacoustics, Inc., CalPACT, LLC, and Union Photoacoustic Technologies, Ltd., which, however, did not support this work.


The animal experiments followed the protocol approved by the Institutional Animal Care and Use Committee of the California Institute of Technology. The human imaging experiment followed the protocol approved by the Institutional Review Board of the California Institute of Technology.


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Additional details

June 13, 2024
June 13, 2024