Imaging ONEWORLD - 'Enhanced FIB-SEM: Large Volume Whole Cells and Tissues Imaging at Fine Resolutions' - Dr C. Shan Xu

28 June 2021


RMS Hosted Event

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This week will feature Dr C. Shan Xu, HHMI Janelia Research Campus

Scientific Organisers: Stefanie Reichelt, Alex Sossick, Nick Barry, Alessandro Esposito and Kirti Prakash

The meeting will begin at 1pm BST.

As part of the 'Imaging ONEWORLD' series, the focus of these lectures is on microscopy and image analysis methods and how to apply these to your research. Almost all aspects of imaging such as sample preparation, labelling strategies, experimental workflows, ‘how-to’ image and analyse, as well as facilitating collaborations and inspiring new scientific ideas will be covered. Speakers will be available for questions and answers. The organisers, CRUK CI core facility staff, Gurdon Institute, MRC-LMB, MRC Cancer Unit and NPL will be able to continue the discussion and provide advice on your imaging projects.


  • Dr C. Shan Xu

    C. Shan Xu’s primary research interest is transformative instrumentation development enabling discoveries from basic science to engineering. His interdisciplinary inventions (20 plus patents) and numerous publications cover areas of physical chemistry, semiconductor engineering, and biology. Shan received his B.S. degree from University of Science and Technology of China, and his Ph.D. degree from University of California at Berkeley, both in Physical Chemistry. After graduation, he joined Lam Research Corporation in 1997, growing from an entry level engineer to a technical director in the R&D department, developing and disseminating advanced technology/equipment to serve worldwide customers. Curiosity of how the brain works led Shan to join the Howard Hughes Medical Institute in 2009, where he has pioneered and developed the enhanced FIB-SEM technology for large-volume 3D imaging at Janelia Research Campus. Over the past decade, Shan has transformed FIB-SEM from a conventional lab tool lacking long term reliability to a robust imaging platform with 100% effective reliability, expanding the imageable volume by more than four orders of magnitude, enabling the largest and most detailed connectome to date, and revealing transformational discoveries in cell biology. As the head of FIB-SEM Technology division, Shan’s current focus is to develop new generation platforms offering even faster image acquisition with larger volumes, and to disseminate this transformative technology beyond life science to benefit much wider research communities world-wide.

Speaker's Abstract

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) offers unique benefits for volume imaging, such as isotropic high-resolution (< 10 nm) and robust image alignment. However, deficiencies of conventional systems in imaging speed and duration cap the maximum possible image volume. We transformed FIB-SEM from a lab tool lacking long term reliability to a robust imaging platform with 100% effective reliability: capable of years of continuous imaging without defects in the final image stack. As a result, we have expanded the imageable volume by more than four orders of magnitude from 103 µm3 to 3 x 107 µm3 while maintaining isotropic 8-nm voxels. Moreover, by trading off against imaging speed, the system can achieve even higher resolutions at 4-nm voxels.

The expanded volumes open up a new regime in scientific learning, where nano-scale resolution coupled with meso and even macro scale volumes enable fruitful discoveries. The largest connectome to date ( has been generated at 8-nm voxels. A reference library of whole cells and tissues imaged at 4-nm voxels has also been established: the higher resolution further improves the interpretation of otherwise ambiguous details, and the open access ( inspires wider research communities to explore comprehensive cellular architecture.

In this presentation, I will discuss the technological advances of enhanced FIB-SEM, followed by a variety of biological examples including Drosophila brain, mouse pancreas, mouse liver, and mammalian cells to illustrate the power of fine isotropic resolution coupled with large imaging volume.

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