Enhanced FIB-SEM systems for large-volume 3D imaging
Abstract
Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 10 6 ?m 3 . These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1363984
- Alternate Identifier(s):
- OSTI ID: 1363985; OSTI ID: 1379848
- Grant/Contract Number:
- Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division - SISGRKN; AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- eLife
- Additional Journal Information:
- Journal Name: eLife Journal Volume: 6; Journal ID: ISSN 2050-084X
- Publisher:
- eLife Sciences Publications, Ltd.
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Xu, C. Shan, Hayworth, Kenneth J., Lu, Zhiyuan, Grob, Patricia, Hassan, Ahmed M., Garc?a-Cerd?n, Jos? G., Niyogi, Krishna K., Nogales, Eva, Weinberg, Richard J., and Hess, Harald F. Enhanced FIB-SEM systems for large-volume 3D imaging. United States: N. p., 2017.
Web. doi:10.7554/eLife.25916.
Xu, C. Shan, Hayworth, Kenneth J., Lu, Zhiyuan, Grob, Patricia, Hassan, Ahmed M., Garc?a-Cerd?n, Jos? G., Niyogi, Krishna K., Nogales, Eva, Weinberg, Richard J., & Hess, Harald F. Enhanced FIB-SEM systems for large-volume 3D imaging. United States. https://doi.org/10.7554/eLife.25916
Xu, C. Shan, Hayworth, Kenneth J., Lu, Zhiyuan, Grob, Patricia, Hassan, Ahmed M., Garc?a-Cerd?n, Jos? G., Niyogi, Krishna K., Nogales, Eva, Weinberg, Richard J., and Hess, Harald F. Sat .
"Enhanced FIB-SEM systems for large-volume 3D imaging". United States. https://doi.org/10.7554/eLife.25916.
@article{osti_1363984,
title = {Enhanced FIB-SEM systems for large-volume 3D imaging},
author = {Xu, C. Shan and Hayworth, Kenneth J. and Lu, Zhiyuan and Grob, Patricia and Hassan, Ahmed M. and Garc?a-Cerd?n, Jos? G. and Niyogi, Krishna K. and Nogales, Eva and Weinberg, Richard J. and Hess, Harald F.},
abstractNote = {Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 10 6 ?m 3 . These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.},
doi = {10.7554/eLife.25916},
journal = {eLife},
number = ,
volume = 6,
place = {United States},
year = {Sat May 13 00:00:00 EDT 2017},
month = {Sat May 13 00:00:00 EDT 2017}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.7554/eLife.25916
https://doi.org/10.7554/eLife.25916
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 195 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
C HLAMYDOMONAS AS A M ODEL O RGANISM
journal, June 2001
- Harris, Elizabeth H.
- Annual Review of Plant Physiology and Plant Molecular Biology, Vol. 52, Issue 1
Synaptic circuits and their variations within different columns in the visual system of Drosophila
journal, October 2015
- Takemura, Shin-ya; Xu, C. Shan; Lu, Zhiyuan
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 44
Determination of quantitative distributions of heavy-metal stain in biological specimens by annular dark-field STEM
journal, April 2008
- Sousa, A. A.; Hohmann-Marriott, M.; Aronova, M. A.
- Journal of Structural Biology, Vol. 162, Issue 1
Contacts between the endoplasmic reticulum and other membranes in neurons
journal, May 2017
- Wu, Yumei; Whiteus, Christina; Xu, C. Shan
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 24
Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics
journal, February 2015
- Hayworth, Kenneth J.; Xu, C. Shan; Lu, Zhiyuan
- Nature Methods, Vol. 12, Issue 4
Serial Section Scanning Electron Microscopy of Adult Brain Tissue Using Focused Ion Beam Milling
journal, March 2008
- Knott, G.; Marchman, H.; Wall, D.
- Journal of Neuroscience, Vol. 28, Issue 12
Post-acquisition image based compensation for thickness variation in microscopy section series
conference, April 2015
- Hanslovsky, Philipp; Bogovic, John A.; Saalfeld, Stephan
- 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI 2015), 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)
Cellular-resolution connectomics: challenges of dense neural circuit reconstruction
journal, May 2013
- Helmstaedter, Moritz
- Nature Methods, Vol. 10, Issue 6
Focused ion beams in biology
journal, October 2015
- Narayan, Kedar; Subramaniam, Sriram
- Nature Methods, Vol. 12, Issue 11
Serial Section Electron Tomography: A Method for Three-Dimensional Reconstruction of Large Structures
journal, June 1994
- Soto, Gabriel E.; Young, Stephen J.; Martone, Maryann E.
- NeuroImage, Vol. 1, Issue 3
Low-Dosage Maximum- A-Posteriori Focusing and Stigmation
journal, February 2013
- Binding, Jonas; Mikula, Shawn; Denk, Winfried
- Microscopy and Microanalysis, Vol. 19, Issue 1
Volume electron microscopy for neuronal circuit reconstruction
journal, February 2012
- Briggman, Kevin L.; Bock, Davi D.
- Current Opinion in Neurobiology, Vol. 22, Issue 1
Connectome studies on Drosophila : a short perspective on a tiny brain
journal, April 2016
- Meinertzhagen, Ian A.
- Journal of Neurogenetics, Vol. 30, Issue 2
The Big and the Small: Challenges of Imaging the Brain's Circuits
journal, November 2011
- Lichtman, J. W.; Denk, W.
- Science, Vol. 334, Issue 6056
Fiji: an open-source platform for biological-image analysis
journal, June 2012
- Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin
- Nature Methods, Vol. 9, Issue 7
A Closer Look at the Brain in 3D Using FIB-SEM
journal, July 2011
- Xu, C.; Hess, H.
- Microscopy and Microanalysis, Vol. 17, Issue S2
Point-spread functions for backscattered imaging in the scanning electron microscope
journal, December 2007
- Hennig, Philipp; Denk, Winfried
- Journal of Applied Physics, Vol. 102, Issue 12
Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure
journal, October 2004
- Denk, Winfried; Horstmann, Heinz; Harris, Kristen M.
- PLoS Biology, Vol. 2, Issue 11, Article No. e329
Osmium tetroxide fixation of lipids for electron microscopy a possible reaction mechanism
journal, July 1968
- Riemersma, J. C.
- Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism, Vol. 152, Issue 4
Challenges of microtome-based serial block-face scanning electron microscopy in neuroscience: CHALLENGES OF SBEM IN NEUROSCIENCE
journal, April 2015
- Wanner, A. A.; Kirschmann, M. A.; Genoud, C.
- Journal of Microscopy, Vol. 259, Issue 2
Assembly and Motility of Eukaryotic Cilia and Flagella. Lessons from Chlamydomonas reinhardtii
journal, December 2001
- Silflow, Carolyn D.; Lefebvre, Paul A.
- Plant Physiology, Vol. 127, Issue 4
Controlling FIB-SBEM slice thickness by monitoring the transmitted ion beam: FIB-SBEM SLICE THICKNESS CONTROL
journal, September 2013
- Boergens, K. M.; Denk, W.
- Journal of Microscopy, Vol. 252, Issue 3
SEM 3D Reconstruction of Stained Bulk Samples using Landing Energy Variation and Deconvolution
journal, July 2012
- Boughorbel, F.; Zhuge, X.; Potocek, P.
- Microscopy and Microanalysis, Vol. 18, Issue S2
High-resolution whole-brain staining for electron microscopic circuit reconstruction
journal, April 2015
- Mikula, Shawn; Denk, Winfried
- Nature Methods, Vol. 12, Issue 6
Volume scanning electron microscopy for imaging biological ultrastructure: Volume scanning electron microscopy
journal, August 2016
- Titze, Benjamin; Genoud, Christel
- Biology of the Cell, Vol. 108, Issue 11
Rootletin organizes the ciliary rootlet to achieve neuron sensory function in Drosophila
journal, October 2015
- Chen, Jieyan V.; Kao, Ling-Rong; Jana, Swadhin C.
- The Journal of Cell Biology, Vol. 211, Issue 2
Structural neurobiology: missing link to a mechanistic understanding of neural computation
journal, February 2012
- Denk, Winfried; Briggman, Kevin L.; Helmstaedter, Moritz
- Nature Reviews Neuroscience, Vol. 13, Issue 5
A visual motion detection circuit suggested by Drosophila connectomics
journal, August 2013
- Takemura, Shin-ya; Bharioke, Arjun; Lu, Zhiyuan
- Nature, Vol. 500, Issue 7461
High-resolution three-dimensional reconstruction of a whole yeast cell using focused-ion beam scanning electron microscopy
journal, July 2012
- Wei, Dongguang; Jacobs, Scott; Modla, Shannon
- BioTechniques, Vol. 53, Issue 1
Deceleration of probe beam by stage bias potential improves resolution of serial block-face scanning electron microscopic images
journal, September 2016
- Bouwer, James C.; Deerinck, Thomas J.; Bushong, Eric
- Advanced Structural and Chemical Imaging, Vol. 2, Issue 1
Automating the Collection of Ultrathin Serial Sections for Large Volume TEM Reconstructions
journal, July 2006
- Hayworth, Kj; Kasthuri, N.; Schalek, R.
- Microscopy and Microanalysis, Vol. 12, Issue S02
Computer Visualization of Three-Dimensional Image Data Using IMOD
journal, January 1996
- Kremer, James R.; Mastronarde, David N.; McIntosh, J. Richard
- Journal of Structural Biology, Vol. 116, Issue 1
Circular polysomes predominate on the rough endoplasmic reticulum of somatotropes and mammotropes in the rat anterior pituitary
journal, January 1987
- Christensen, A. Kent; Kahn, Larry E.; Bourne, Carol M.
- American Journal of Anatomy, Vol. 178, Issue 1
Basal bodies and centrioles: Their function and structure
book, January 1999
- Preble, Andrea M.; Giddings, Thomas M.; Dutcher, Susan K.
- Current Topics in Developmental Biology
Sharing of secondary electrons by in-lens and out-lens detector in low-voltage scanning electron microscope equipped with immersion lens
journal, March 2009
- Kumagai, Kazuhiro; Sekiguchi, Takashi
- Ultramicroscopy, Vol. 109, Issue 4
Weighted averaging of a set of noisy images for maximum signal-to-noise ratio
journal, May 1990
- Unser, M.; Eden, M.
- IEEE Transactions on Acoustics, Speech, and Signal Processing, Vol. 38, Issue 5