Okapi-EM: A napari plugin for processing and analyzing cryogenic serial focused ion beam/scanning electron microscopy images.

Autor:	Perdigão LMA; Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK., Ho EML; Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK., Cheng ZC; Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK.; School of Chemistry, University of Edinburgh, Edinburgh, UK., Yee NB; Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK., Glen T; Structural Biology, The Rosalind Franklin Institute, Didcot, UK., Wu L; Structural Biology, The Rosalind Franklin Institute, Didcot, UK.; Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK., Grange M; Structural Biology, The Rosalind Franklin Institute, Didcot, UK.; Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK., Dumoux M; Structural Biology, The Rosalind Franklin Institute, Didcot, UK., Basham M; Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK.; Diamond Light Source, Didcot, UK., Darrow MC; Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK.
Jazyk:	angličtina
Zdroj:	Biological imaging [Biol Imaging] 2023 Mar 27; Vol. 3, pp. e9. Date of Electronic Publication: 2023 Mar 27 (Print Publication: 2023).
DOI:	10.1017/S2633903X23000119
Abstrakt:	An emergent volume electron microscopy technique called cryogenic serial plasma focused ion beam milling scanning electron microscopy (pFIB/SEM) can decipher complex biological structures by building a three-dimensional picture of biological samples at mesoscale resolution. This is achieved by collecting consecutive SEM images after successive rounds of FIB milling that expose a new surface after each milling step. Due to instrumental limitations, some image processing is necessary before 3D visualization and analysis of the data is possible. SEM images are affected by noise, drift, and charging effects, that can make precise 3D reconstruction of biological features difficult. This article presents Okapi-EM, an open-source napari plugin developed to process and analyze cryogenic serial pFIB/SEM images. Okapi-EM enables automated image registration of slices, evaluation of image quality metrics specific to pFIB-SEM imaging, and mitigation of charging artifacts. Implementation of Okapi-EM within the napari framework ensures that the tools are both user- and developer-friendly, through provision of a graphical user interface and access to Python programming. Competing Interests: M.C.D. is an employee of SPT Labtech. The remaining authors declare that they have no competing interests. (© The Author(s) 2023.)
Databáze:	MEDLINE
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