Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets

Peddie, C. J. & Collinson, L. M. Exploring the third dimension: volume electron microscopy comes of age. Micron 61, 9–19 (2014).

Article  PubMed  Google Scholar 

Peddie, C. J. et al. Volume electron microscopy. Nat. Rev. Methods Prim. 2, 51 (2022).

Article  CAS  Google Scholar 

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).

Article  PubMed  Google Scholar 

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).

Article  PubMed  Google Scholar 

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).

Article  Google Scholar 

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).

Article  PubMed  Google Scholar 

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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