A scalable open-source MATLAB toolbox for reconstruction and analysis of multispectral optoacoustic tomography data
Abstract Multispectral photoacoustic tomography enables the resolution of spectral components of a tissue or sample at high spatiotemporal resolution. With the availability of commercial instruments, the acquisition of data using this modality has become consistent and standardized. However, the ana...
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Nature Portfolio
2021
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oai:doaj.org-article:947aff8483c8407089fb51ce97ce6eb42021-12-02T19:16:11ZA scalable open-source MATLAB toolbox for reconstruction and analysis of multispectral optoacoustic tomography data10.1038/s41598-021-97726-12045-2322https://doaj.org/article/947aff8483c8407089fb51ce97ce6eb42021-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97726-1https://doaj.org/toc/2045-2322Abstract Multispectral photoacoustic tomography enables the resolution of spectral components of a tissue or sample at high spatiotemporal resolution. With the availability of commercial instruments, the acquisition of data using this modality has become consistent and standardized. However, the analysis of such data is often hampered by opaque processing algorithms, which are challenging to verify and validate from a user perspective. Furthermore, such tools are inflexible, often locking users into a restricted set of processing motifs, which may not be able to accommodate the demands of diverse experiments. To address these needs, we have developed a Reconstruction, Analysis, and Filtering Toolbox to support the analysis of photoacoustic imaging data. The toolbox includes several algorithms to improve the overall quantification of photoacoustic imaging, including non-negative constraints and multispectral filters. We demonstrate various use cases, including dynamic imaging challenges and quantification of drug effect, and describe the ability of the toolbox to be parallelized on a high performance computing cluster.Devin O’KellyJames CampbellJeni L. GerberichPaniz KarbasiVenkat MalladiAndrew JamiesonLiqiang WangRalph P. MasonNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-18 (2021) |
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Medicine R Science Q |
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Medicine R Science Q Devin O’Kelly James Campbell Jeni L. Gerberich Paniz Karbasi Venkat Malladi Andrew Jamieson Liqiang Wang Ralph P. Mason A scalable open-source MATLAB toolbox for reconstruction and analysis of multispectral optoacoustic tomography data |
| description |
Abstract Multispectral photoacoustic tomography enables the resolution of spectral components of a tissue or sample at high spatiotemporal resolution. With the availability of commercial instruments, the acquisition of data using this modality has become consistent and standardized. However, the analysis of such data is often hampered by opaque processing algorithms, which are challenging to verify and validate from a user perspective. Furthermore, such tools are inflexible, often locking users into a restricted set of processing motifs, which may not be able to accommodate the demands of diverse experiments. To address these needs, we have developed a Reconstruction, Analysis, and Filtering Toolbox to support the analysis of photoacoustic imaging data. The toolbox includes several algorithms to improve the overall quantification of photoacoustic imaging, including non-negative constraints and multispectral filters. We demonstrate various use cases, including dynamic imaging challenges and quantification of drug effect, and describe the ability of the toolbox to be parallelized on a high performance computing cluster. |
| format |
article |
| author |
Devin O’Kelly James Campbell Jeni L. Gerberich Paniz Karbasi Venkat Malladi Andrew Jamieson Liqiang Wang Ralph P. Mason |
| author_facet |
Devin O’Kelly James Campbell Jeni L. Gerberich Paniz Karbasi Venkat Malladi Andrew Jamieson Liqiang Wang Ralph P. Mason |
| author_sort |
Devin O’Kelly |
| title |
A scalable open-source MATLAB toolbox for reconstruction and analysis of multispectral optoacoustic tomography data |
| title_short |
A scalable open-source MATLAB toolbox for reconstruction and analysis of multispectral optoacoustic tomography data |
| title_full |
A scalable open-source MATLAB toolbox for reconstruction and analysis of multispectral optoacoustic tomography data |
| title_fullStr |
A scalable open-source MATLAB toolbox for reconstruction and analysis of multispectral optoacoustic tomography data |
| title_full_unstemmed |
A scalable open-source MATLAB toolbox for reconstruction and analysis of multispectral optoacoustic tomography data |
| title_sort |
scalable open-source matlab toolbox for reconstruction and analysis of multispectral optoacoustic tomography data |
| publisher |
Nature Portfolio |
| publishDate |
2021 |
| url |
https://doaj.org/article/947aff8483c8407089fb51ce97ce6eb4 |
| work_keys_str_mv |
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| _version_ |
1718376986159611904 |