Two-Stage Alignment of FIB-SEM Images of Rock Samples
Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) tomography provides a stack of images that represent serial slices of the sample. These images are displaced relatively to each other, and an alignment procedure is required. Traditional methods for alignment of a 3D image are based on a compar...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-10-01
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| Series: | Journal of Imaging |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2313-433X/6/10/107 |
| _version_ | 1797551428946886656 |
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| author | Iryna Reimers Ilia Safonov Anton Kornilov Ivan Yakimchuk |
| author_facet | Iryna Reimers Ilia Safonov Anton Kornilov Ivan Yakimchuk |
| author_sort | Iryna Reimers |
| collection | DOAJ |
| description | Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) tomography provides a stack of images that represent serial slices of the sample. These images are displaced relatively to each other, and an alignment procedure is required. Traditional methods for alignment of a 3D image are based on a comparison of two adjacent slices. However, such algorithms are easily confused by anisotropy in the sample structure or even experiment geometry in the case of porous media. This may lead to significant distortions in the pore space geometry, if there are no stable fiducial marks in the frame. In this paper, we propose a new method, which meaningfully extends existing alignment procedures. Our technique allows the correction of random misalignments between slices and, at the same time, preserves the overall geometrical structure of the specimen. We consider displacements produced by existing alignment algorithms as a signal and decompose it into low and high-frequency components. Final transformations exclude slow variations and contain only high frequency variations that represent random shifts that need to be corrected. The proposed algorithm can operate with not only translations but also with arbitrary affine transformations. We demonstrate the performance of our approach on a synthetic dataset and two real FIB-SEM images of natural rock. |
| first_indexed | 2024-03-10T15:44:35Z |
| format | Article |
| id | doaj.art-a672d2fb52f542d9b7031b5dcfba7265 |
| institution | Directory Open Access Journal |
| issn | 2313-433X |
| language | English |
| last_indexed | 2024-03-10T15:44:35Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Imaging |
| spelling | doaj.art-a672d2fb52f542d9b7031b5dcfba72652023-11-20T16:34:13ZengMDPI AGJournal of Imaging2313-433X2020-10-0161010710.3390/jimaging6100107Two-Stage Alignment of FIB-SEM Images of Rock SamplesIryna Reimers0Ilia Safonov1Anton Kornilov2Ivan Yakimchuk3Schlumberger Moscow Research Center, 125171 Moscow, RussiaSchlumberger Moscow Research Center, 125171 Moscow, RussiaSchlumberger Moscow Research Center, 125171 Moscow, RussiaSchlumberger Moscow Research Center, 125171 Moscow, RussiaFocused Ion Beam Scanning Electron Microscopy (FIB-SEM) tomography provides a stack of images that represent serial slices of the sample. These images are displaced relatively to each other, and an alignment procedure is required. Traditional methods for alignment of a 3D image are based on a comparison of two adjacent slices. However, such algorithms are easily confused by anisotropy in the sample structure or even experiment geometry in the case of porous media. This may lead to significant distortions in the pore space geometry, if there are no stable fiducial marks in the frame. In this paper, we propose a new method, which meaningfully extends existing alignment procedures. Our technique allows the correction of random misalignments between slices and, at the same time, preserves the overall geometrical structure of the specimen. We consider displacements produced by existing alignment algorithms as a signal and decompose it into low and high-frequency components. Final transformations exclude slow variations and contain only high frequency variations that represent random shifts that need to be corrected. The proposed algorithm can operate with not only translations but also with arbitrary affine transformations. We demonstrate the performance of our approach on a synthetic dataset and two real FIB-SEM images of natural rock.https://www.mdpi.com/2313-433X/6/10/107FIB-SEMalignmentdigital rockstack of imagesporous media |
| spellingShingle | Iryna Reimers Ilia Safonov Anton Kornilov Ivan Yakimchuk Two-Stage Alignment of FIB-SEM Images of Rock Samples Journal of Imaging FIB-SEM alignment digital rock stack of images porous media |
| title | Two-Stage Alignment of FIB-SEM Images of Rock Samples |
| title_full | Two-Stage Alignment of FIB-SEM Images of Rock Samples |
| title_fullStr | Two-Stage Alignment of FIB-SEM Images of Rock Samples |
| title_full_unstemmed | Two-Stage Alignment of FIB-SEM Images of Rock Samples |
| title_short | Two-Stage Alignment of FIB-SEM Images of Rock Samples |
| title_sort | two stage alignment of fib sem images of rock samples |
| topic | FIB-SEM alignment digital rock stack of images porous media |
| url | https://www.mdpi.com/2313-433X/6/10/107 |
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