Abstract
Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structures with nanometre resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations in that they visualize only a single slice or a relatively small volume of the cell, respectively. Focused ion beam-scanning electron microscopy (FIB-SEM) has demonstrated the ability to image small volumes of cellular samples with 4-nm isotropic voxels1. Owing to advances in the precision and stability of FIB milling, together with enhanced signal detection and faster SEM scanning, we have increased the volume that can be imaged with 4-nm voxels by two orders of magnitude. Here we present a volume EM atlas at such resolution comprising ten three-dimensional datasets for whole cells and tissues, including cancer cells, immune cells, mouse pancreatic islets and Drosophila neural tissues. These open access data (via OpenOrganelle2) represent the foundation of a field of high-resolution whole-cell volume EM and subsequent analyses, and we invite researchers to explore this atlas and pose questions.
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Data availability
All FIB-SEM datasets in this work have been deposited to OpenOrganelle repository (https://openorganelle.janelia.org) and made publicly available with DOIs: wild-type interphase HeLa cell 2017-06-21 (https://doi.org/10.25378/janelia.13114211), wild-type interphase HeLa cell 2017-08-09 (https://doi.org/10.25378/janelia.13114244), wild-type mitotic HeLa cell 2019-05-30 (https://doi.org/10.25378/janelia.13114472), wild-type THP-1 macrophage 2018-11-11 (https://doi.org/10.25378/janelia.13114343), wild-type immortalized T-cells (Jurkat) 2018-08-10 (https://doi.org/10.25378/janelia.13114259), wild-type immortalized breast cancer cell 2017-11-21 (https://doi.org/10.25378/janelia.13114352), killer T-cell attacking cancer cell 2020-02-04 (https://doi.org/10.25378/janelia.13114454), isolated murine pancreatic islets 2019-03-01 (https://doi.org/10.25378/janelia.13114499), Drosophila fan-shaped body from a 5-day-old male 2019-09-14 (https://doi.org/10.25378/janelia.13114529), Drosophila accessory calyx from a 5-day old male 2019-12-06 (https://doi.org/10.25378/janelia.13114514). Source data are provided with this paper.
Code availability
FIB-SEM image acquisition LabVIEW code used in this work is available from. https://github.com/cshanxu/Enhanced_FIB-SEM. Python code for resolution characterizations using ribosomes is available from. https://github.com/gleb-shtengel/FIB-SEM_resolution_evaluation.
Change history
03 November 2021
A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-04132-8
References
Xu, C. S. et al. Enhanced FIB-SEM systems for large-volume 3D imaging. eLife 6, e25916 (2017).
Heinrich, L. et al. Whole cell organelle segmentation in volumetric electron microscopy. Nature https://doi.org/10.1038/s41586-021-03977-3 (2021).
Lodish, H. et al. Molecular Cell Biology 8th edn (W. H. Freeman, 2016).
Porter, K. R., Claude, A., & Fullam, E. F. A study of tissue culture cells by electron microscopy: methods and preliminary observations. J. Exp. Med. 81, 233–246 (1945).
Denk, W., & Horstmann, H. Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol. 2, e329 (2004).
Titze, B. Techniques to Prevent Sample Surface Charging and Reduce Beam Damage Effects for SBEM Imaging. Dissertation, Heidelberg University (2013).
Xu, C. S., Hayworth, K. J., & Hess, H. F. Enhanced FIB-SEM systems for large-volume 3D imaging. US Patent 10, 600, 615 (2020).
Xu, C. S., Pang, S., Hayworth, K. J., & Hess, H. F. in: Volume Microscopy Neuromethods vol. 155 (eds Wacker, I. et al.) (Humana, 2020).
Xu, C. S. et al. A connectome of the adult Drosophila central brain. Preprint at https://doi.org/10.1101/2020.01.21.911859 (2020).
Wu, Y. et al. Contacts between the endoplasmic reticulum and other membranes in neurons. Proc. Natl Acad. Sci. USA 114, E4859–E4867 (2017).
Stinchcombe, J. C., Bossi, G., Booth, S., & Griffiths, G. M. The immunological synapse of CTL contains a secretory domain and membrane bridges. Immunity 15, 751–761 (2001).
Kupfer, A. & Dennert, G. Reorientation of the microtubule-organizing center and the Golgi apparatus in cloned cytotoxic lymphocytes triggered by binding to lysable target cells. J. Immunol. 133, 2762-2766 (1984).
Stinchcombe, J. C., Majorovits, E., Bossi, G., Fuller, S. & Griffiths, G. M. Centrosome polarization delivers secretory granules to the immunological synapse. Nature. 443, 462–465 (2006); correction 444, 236 (2006).
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).
Müller, A. et al. 3D FIB-SEM reconstruction of microtubule–organelle interaction in whole primary mouse β cells. J. Cell Biol. 220, e202010039 (2021).
Takemura, S. Y. et al. A connectome of a learning and memory center in the adult Drosophila brain. eLife 6, e26975 (2017).
Aso, Y. et al. Nitric oxide acts as a cotransmitter in a subset of dopaminergic neurons to diversify memory dynamics. eLife 8, e49257 (2019).
Bullen, A. et al. Inner ear tissue preservation by rapid freezing: Improving fixation by high-pressure freezing and hybrid methods. Hear. Res. 315, 49–60 (2014).
Sartori, N., Richter, K., & Dubochet, J. Vitrification depth can be increased more than 10‐fold by high‐pressure freezing. J. Microsc. 172, 55–61 (1993).
National Research Council. Guide for the Care and Use of Laboratory Animals Eighth Edition (National Academies Press, 2011).
Gotoh, M., Maki, T., Kiyoizumi, T., Satomi, S., & Monaco, A. P. An improved method for isolation of mouse pancreatic islets. Transplantation 40, 437–438 (1985).
Müller, A. et al. A global approach for quantitative super resolution and electron microscopy on cryo and epoxy sections using self-labeling protein tags. Sci Rep. 7, 23 (2017).
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).
Lu, Z. et al. En bloc preparation of Drosophila brains enables high-throughput FIB-SEM connectomics. Preprint at https://doi.org/10.1101/855130 (2019).
Saalfeld, S., Cardona, A., Hartenstein, V. & Tomančák, P. As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets. Bioinformatics 26, i57–i63 (2010).
van der Walt, S. et al. scikit-image: image processing in Python. PeerJ. 2, e453 (2014).
Acknowledgements
We thank K.J. Hayworth and W. Qiu at Howard Hughes Medical Institute (HHMI) Janelia Research Campus (JRC) for invaluable discussions and data collection support; P.K. Rivlin, S.M. Plaza and I.A. Meinertzhagen for the JRC EM shared resource; the FlyEM project team support for staining protocols development; the electron microscopy facility of MPI-CBG and of the CMCB Technology Platform at TU Dresden for their services; Y. Wu from the laboratory of P. De Camilli at Yale for advice. C.S.X., S.P., G.S., S.T., Z.L., H.A.P., N.I., D.B., A.V.W., M.F., T.C.W., J.L.-S. and H.F.H. are funded by Howard Hughes Medical Institute (HHMI). A.M. received support from the Carl Gustav Carus Faculty of Medicine at TU Dresden via a MeDDrive GRANT. A.M. and M.S. were supported with funds from the German Center for Diabetes Research (DZD e.V.) by the German Ministry for Education and Research (BMBF), from the German-Israeli Foundation for Scientific Research and Development (GIF) (grant I-1429-201.2/2017) and from the German Research Foundation (DFG) jointly with the Agence nationale de la recherche (ANR) (grant SO 818/6-1) to M.S. A.T.R. and I.M. are funded by Genentech/Roche. H.K.H and S.B.v.E. are funded by NIAID grant R01AI138625. R.V.F. is supported by NIH R01GM124348. T.C.W. is supported by NIH R01GM097194. J.C. is a fellow of the Damon Runyon Cancer Research Foundation.
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Authors and Affiliations
Contributions
C.S.X. and H.F.H. supervised the project; C.S.X., S.P., G.S. and H.F.H. wrote the manuscript with input from all co-authors; C.S.X. developed the enhanced FIB-SEM platform for large-volume high-resolution imaging and optimized imaging conditions; C.S.X., S.P. and G.S. conducted FIB-SEM experiments; C.S.X. and S.P. performed image post-processing; S.P., G.S., A.M., A.T.R., H.K.H., S.B.v.E., Z.L., H.A.P., N.I., J.C., A.V.W. and M.F. prepared samples; G.S., A.M., A.T.R. and S.T. analysed data; D.B. prepared and uploaded data to the OpenOrganelle website; S.B.v.E., T.C.W., R.V.F., J.L.-S., I.M. and M.S. proposed biological questions and provided samples.
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Competing interests
Portions of the technology described here are covered by U.S. Patent 10,600,615 titled ‘Enhanced FIB-SEM systems for large-volume 3D imaging’, which was issued to C.S.X., K.J.H. and H.F.H. and assigned to Howard Hughes Medical Institute on 24 March 2020. The other authors declare no competing interests.
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Peer review information Nature thanks Robert Murphy, Jason Swedlow and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.
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Extended data figures and tables
Extended Data Fig. 1 Isotropic voxel (representing the minimal voxel size dictated by the worst-case axial resolution) vs. volume for comparing different volume EM methods.
The light green space represents the Resolution-Volume regime accessible with enhanced FIB-SEM technology through long term imaging. The present work of whole cell volumes colored in yellow matches the resolutions at 4-nm isotropic voxels shown in Fig. 1b, compared to the prior work of smaller volumes colored in red. Adopted from ref. 1 with modifications.
Extended Data Fig. 2 Murine CTL engaging an ovarian cancer cell.
Zooms on regions showing different immunological synapse topology features. a, Interdigitation. b, Flat apposition. c, Filopodia caught between cells. Scale bars, 0.5 μm.
Extended Data Fig. 3 Edge transition distributions determined from ribosomes in cultured cells datasets.
a, Distributions of 37%–63% transition distances in X-, Y- (left), Ztop-(center), and Zbot- (right) directions. b, Distributions of 20%–80% transition distances in X-, Y- (left), Ztop-(center), and Zbot- (right) directions.
Extended Data Fig. 4 Cross-sections of the example of ribosomes from the dataset Interphase HeLa Cell 2017-06-21 and the profiles with the transition analysis.
The top three rows are the brightest ribosomes and the bottom three rows are the dimmest ribosomes.
Extended Data Fig. 5 Cross-sections of the example of ribosomes from the dataset Interphase HeLa Cell 2017-08-09 and the profiles with the transition analysis.
The top three rows are the brightest ribosomes and the bottom three rows are the dimmest ribosomes.
Extended Data Fig. 6 Cross-sections of the example of ribosomes from the dataset Wild-type THP-1 Macrophage 2018-11-11 and the profiles with the transition analysis.
The top three rows are the brightest ribosomes and the bottom three rows are the dimmest ribosomes.
Extended Data Fig. 7 Cross-sections of the example of ribosomes from the dataset Immortalized T-cells (Jurkat) 2018-08-10 and the profiles with the transition analysis.
The top three rows are the brightest ribosomes and the bottom three rows are the dimmest ribosomes.
Extended Data Fig. 8 Cross-sections of the example of ribosomes from the dataset Immortalized breast cancer cell (SUM159) 2017-11-21 and the profiles with the transition analysis.
The top three rows are the brightest ribosomes and the bottom three rows are the dimmest ribosomes.
Extended Data Fig. 9 Cross-sections of the example of ribosomes from the dataset Killer T-cell attacking cancer cell 2020-02-04 on Cancer Cell and the profiles with the transition analysis.
The top three rows are the brightest ribosomes and the bottom three rows are the dimmest ribosomes.
Supplementary information
Supplementary Information
This file contains Supplementary Methods, legends for Supplementary Videos 1 and 2, and Supplementary References.
Supplementary Video 1
A new paradigm of high-resolution whole-cell imaging enabled by enhanced FIB-SEM.
Supplementary Video 2
T cell attacking cancer cell revealed by FIB-SEM with 4-nm voxels.
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Xu, C.S., Pang, S., Shtengel, G. et al. An open-access volume electron microscopy atlas of whole cells and tissues. Nature 599, 147–151 (2021). https://doi.org/10.1038/s41586-021-03992-4
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DOI: https://doi.org/10.1038/s41586-021-03992-4
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