Peddie, C. J. & Collinson, L. M. Exploring the third dimension: volume electron microscopy comes of age. Micron 61, 9–19 (2014).
Peddie, C. J. et al. Volume electron microscopy. Nat. Rev. Methods Prim. 2, 51 (2022).
Hua, Y., Laserstein, P. & Helmstaedter, M. Large-volume en-bloc staining for electron microscopy-based connectomics. Nat. Commun. 6, 7923 (2015).
Article ADS CAS PubMed Google Scholar
Kievits, A. J., Lane, R., Carroll, E. C. & Hoogenboom, J. P. How innovations in methodology offer new prospects for volume electron microscopy. J. Microsc. 287, 114–137 (2022).
Article PubMed PubMed Central Google Scholar
Graham, B. J. et al. High-throughput transmission electron microscopy with automated serial sectioning. Preprint at bioRxiv https://doi.org/10.1101/657346 (2019).
Yin, W. et al. A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy. Nat. Commun. 11, 4949 (2020).
Article ADS CAS PubMed PubMed Central Google Scholar
Phelps, J. S. et al. Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy. Cell 184, 759–774.e18 (2021).
Article CAS PubMed PubMed Central Google Scholar
Xu, C. S. et al. Enhanced FIB-SEM systems for large-volume 3D imaging. eLife 6, e25916 (2017).
Article PubMed PubMed Central Google Scholar
Motta, A. et al. Dense connectomic reconstruction in layer 4 of the somatosensory cortex. Science 366, eaay3134 (2019).
Article CAS PubMed Google Scholar
Scheffer, L. K. et al. A connectome and analysis of the adult Drosophila central brain. eLife 9, e57443 (2020).
Article CAS PubMed PubMed Central Google Scholar
Müller, A. et al. 3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse β. cells J. Cell Biol. 220, e202010039 (2021).
Parlakgül, G. et al. Regulation of liver subcellular architecture controls metabolic homeostasis. Nature 603, 736–742 (2022).
Article ADS PubMed PubMed Central Google Scholar
Sheu, S.-H. et al. A serotonergic axon-cilium synapse drives nuclear signaling to alter chromatin accessibility. Cell 185, 3390–3407.e18 (2022).
Article CAS PubMed PubMed Central Google Scholar
Weigel, A. V. et al. ER-to-Golgi protein delivery through an interwoven, tubular network extending from ER. Cell 184, 2412–2429.e16 (2021).
Article CAS PubMed Google Scholar
Uwizeye, C. et al. Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging. Nat. Commun. 12, 1049 (2021).
Article ADS CAS PubMed PubMed Central Google Scholar
Musser, J. M. et al. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution. Science 374, 717–723 (2021).
Article ADS CAS PubMed PubMed Central Google Scholar
Bharathan, N. K. et al. Architecture and dynamics of a desmosome–endoplasmic reticulum complex. Nat. Cell Biol. 25, 823–835 (2023).
Article CAS PubMed Google Scholar
Malong, L. et al. Characterization of the structure and control of the blood-nerve barrier identifies avenues for therapeutic delivery. Dev. Cell 58, 174–191.e8 (2023).
Article CAS PubMed Google Scholar
Cortese, M. et al. Integrative imaging reveals SARS-CoV-2-induced reshaping of subcellular morphologies. Cell Host Microbe 28, 853–866.e5 (2020).
Article CAS PubMed PubMed Central Google Scholar
Vergara, H. M. et al. Whole-body integration of gene expression and single-cell morphology. Cell 184, 4819–4837.e22 (2021).
Article CAS PubMed PubMed Central Google Scholar
Iudin, A., Korir, P. K., Salavert-Torres, J., Kleywegt, G. J. & Patwardhan, A. EMPIAR: a public archive for raw electron microscopy image data. Nat. Methods 13, 387–388 (2016).
Article CAS PubMed Google Scholar
Conrad, R. & Narayan, K. CEM500K, a large-scale heterogeneous unlabeled cellular electron microscopy image dataset for deep learning. eLife 10, e65894 (2021).
Article CAS PubMed PubMed Central Google Scholar
Xu, C. S. et al. An open-access volume electron microscopy atlas of whole cells and tissues. Nature 599, 147–151 (2021).
Article ADS CAS PubMed PubMed Central Google Scholar
Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996).
Article CAS PubMed Google Scholar
Noske, A. B., Costin, A. J., Morgan, G. P. & Marsh, B. J. Expedited approaches to whole cell electron tomography and organelle mark-up in situ in high-pressure frozen pancreatic islets. J. Struct. Biol. 161, 298–313 (2008).
Wu, Y. et al. Contacts between the endoplasmic reticulum and other membranes in neurons. Proc. Natl Acad. Sci. USA 114, E4859–E4867 (2017).
Article CAS PubMed PubMed Central Google Scholar
Kaynig, V. et al. Large-scale automatic reconstruction of neuronal processes from electron microscopy images. Med. Image Anal. 22, 77–88 (2015).
Article PubMed PubMed Central Google Scholar
Dorkenwald, S. et al. Automated synaptic connectivity inference for volume electron microscopy. Nat. Methods 14, 435–442 (2017).
Article CAS PubMed Google Scholar
Buhmann, J. et al. Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set. Nat. Methods 18, 771–774 (2021).
Article CAS PubMed PubMed Central Google Scholar
Heinrich, L. et al. Whole-cell organelle segmentation in volume electron microscopy. Nature 599, 141–146 (2021).
Article ADS CAS PubMed Google Scholar
Spiers, H. et al. Deep learning for automatic segmentation of the nuclear envelope in electron microscopy data, trained with volunteer segmentations. Traffic 22, 240–253 (2021).
Article CAS PubMed Google Scholar
Gallusser, B. et al. Deep neural network automated segmentation of cellular structures in volume electron microscopy. J. Cell Biol. 222, e202208005 (2022).
Article PubMed PubMed Central Google Scholar
Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001).
Falk, T. et al. U-Net: deep learning for cell counting, detection, and morphometry. Nat. Methods 16, 67–70 (2019).
Article CAS PubMed Google Scholar
Belevich, I., Joensuu, M., Kumar, D., Vihinen, H. & Jokitalo, E. Microscopy image browser: a platform for segmentation and analysis of multidimensional datasets. PLoS Biol. 14, e1002340 (2016).
Article PubMed PubMed Central Google Scholar
Tu, Z. & Bai, X. Auto-context and its application to high-level vision tasks and 3D brain image segmentation. IEEE Trans. Pattern Anal. Mach. Intell. 32, 1744–1757 (2010).
Berg, S. et al. ilastik: interactive machine learning for (bio)image analysis. Nat. Methods 16, 1226–1232 (2019).
Article CAS PubMed Google Scholar
Kreshuk, A. & Zhang, C. in Computer Optimized Microscopy: Methods and Protocols (eds Rebollo, E. & Bosch, M.) 449–463 (Springer, 2019).
Weigert, M. et al. Content-aware image restoration: pushing the limits of fluorescence microscopy. Nat. Methods 15, 1090–1097 (2018).
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