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| Main Authors: | , , , , , |
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| Format: | Preprint |
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2024
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2401.11101 |
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| _version_ | 1866913202304974848 |
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| author | Nikitin, Viktor Wildenberg, Gregg Mittone, Alberto Shevchenko, Pavel Deriy, Alex De Carlo, Francesco |
| author_facet | Nikitin, Viktor Wildenberg, Gregg Mittone, Alberto Shevchenko, Pavel Deriy, Alex De Carlo, Francesco |
| contents | Despite the increased brilliance of the new generation synchrotron sources, there is still a challenge with high-resolution scanning of very thick and absorbing samples, such as the whole mouse brain stained with heavy elements, and, extending further, brains of primates. Samples are typically cut into smaller parts, to ensure a sufficient X-ray transmission, and scanned separately. Compared to the standard tomography setup where the sample would be cut into many pillars, the laminographic geometry operates with slab-shaped sections significantly reducing the number of sample parts to be prepared, the cutting damage and data stitching problems. In this work, we present a laminography pipeline for imaging large samples (> 1 cm) at micrometer resolution. The implementation includes a low-cost instrument setup installed at the 2-BM micro-CT beamline of the Advanced Photon Source (APS). Additionally, we present sample mounting, scanning techniques, data stitching procedures, a fast reconstruction algorithm with low computational complexity, and accelerated reconstruction on multi-GPU systems for processing large-scale datasets. The applicability of the whole laminography pipeline was demonstrated with imaging 4 sequential slabs throughout the entire mouse brain sample stained with osmium, in total generating approximately 12TB of raw data for reconstruction. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2401_11101 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Laminography as a tool for imaging large-size samples with high resolution Nikitin, Viktor Wildenberg, Gregg Mittone, Alberto Shevchenko, Pavel Deriy, Alex De Carlo, Francesco Computational Physics Medical Physics Despite the increased brilliance of the new generation synchrotron sources, there is still a challenge with high-resolution scanning of very thick and absorbing samples, such as the whole mouse brain stained with heavy elements, and, extending further, brains of primates. Samples are typically cut into smaller parts, to ensure a sufficient X-ray transmission, and scanned separately. Compared to the standard tomography setup where the sample would be cut into many pillars, the laminographic geometry operates with slab-shaped sections significantly reducing the number of sample parts to be prepared, the cutting damage and data stitching problems. In this work, we present a laminography pipeline for imaging large samples (> 1 cm) at micrometer resolution. The implementation includes a low-cost instrument setup installed at the 2-BM micro-CT beamline of the Advanced Photon Source (APS). Additionally, we present sample mounting, scanning techniques, data stitching procedures, a fast reconstruction algorithm with low computational complexity, and accelerated reconstruction on multi-GPU systems for processing large-scale datasets. The applicability of the whole laminography pipeline was demonstrated with imaging 4 sequential slabs throughout the entire mouse brain sample stained with osmium, in total generating approximately 12TB of raw data for reconstruction. |
| title | Laminography as a tool for imaging large-size samples with high resolution |
| topic | Computational Physics Medical Physics |
| url | https://arxiv.org/abs/2401.11101 |