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Serial Block-Face Scanning Electron Microscopy (SBF-SEM) of Biological Tissue Samples

Published: March 26th, 2021



1College of Optometry, University of Houston, 2Department of Biology, DePauw University, 3Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center, 4Children’s Nutrition Center, Baylor College of Medicine

This protocol outlines a routine method for using serial block-face scanning electron microscopy (SBF-SEM), a powerful 3D imaging technique. Successful application of SBF-SEM hinges on proper fixation and tissue staining techniques, as well as careful consideration of imaging settings. This protocol contains practical considerations for the entirety of this process.

Serial block-face scanning electron microscopy (SBF-SEM) allows for the collection of hundreds to thousands of serially-registered ultrastructural images, offering an unprecedented three-dimensional view of tissue microanatomy. While SBF-SEM has seen an exponential increase in use in recent years, technical aspects such as proper tissue preparation and imaging parameters are paramount for the success of this imaging modality. This imaging system benefits from the automated nature of the device, allowing one to leave the microscope unattended during the imaging process, with the automated collection of hundreds of images possible in a single day. However, without appropriate tissue preparation cellular ultrastructure can be altered in such a way that incorrect or misleading conclusions might be drawn. Additionally, images are generated by scanning the block-face of a resin-embedded biological sample and this often presents challenges and considerations that must be addressed. The accumulation of electrons within the block during imaging, known as "tissue charging," can lead to a loss of contrast and an inability to appreciate cellular structure. Moreover, while increasing electron beam intensity/voltage or decreasing beam-scanning speed can increase image resolution, this can also have the unfortunate side effect of damaging the resin block and distorting subsequent images in the imaging series. Here we present a routine protocol for the preparation of biological tissue samples that preserves cellular ultrastructure and diminishes tissue charging. We also provide imaging considerations for the rapid acquisition of high-quality serial-images with minimal damage to the tissue block.

Serial block face scanning electron microscopy (SBF-SEM) was first described by Leighton in 1981 where he fashioned a scanning electron microscope augmented with an in-built microtome which could cut and image thin sections of tissue embedded in resin. Unfortunately, technical limitations restricted its use to conductive samples, as non-conductive samples such as biological tissue accumulated unacceptable levels of charging (electron buildup within the tissue sample)1. While coating the block-face between cuts with evaporated carbon reduced tissue charging, this greatly increased imaging acquisition time and image storage remained a problem as ....

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All animals were handled according to the guidelines described in the Association for Research in Vision and Ophthalmology Statement for the Use of Animals in Vision and Ophthalmic Research and the University of Houston College of Optometry animal handling guidelines. All animal procedures were approved by the institutions in which they were handled: Mouse, rat, rabbit, guinea pig, and non-human primate procedures were approved by the University of Houston Animal Care and Use Committee, zebrafish procedures were approved.......

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Mouse Cornea
This protocol has been applied extensively to the mouse cornea. Using SBF-SEM imaging a network of elastin-free microfibril bundles (EFMBs) were shown to be present within the adult mouse cornea. It was previously believed that this network was only present during embryonic and early postnatal development. SBF-SEM revealed an extensive EFMB network throughout the cornea, with individual fibers found to be 100-200 nm in diameter when measured in cross-section. It was also found that thi.......

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The purpose of this methods paper is to highlight the tissue preparation and imaging methodology that has allowed our lab to reliably capture high-resolution serial electron microscopy images, and to point out critical steps that lead to this outcome as well as potential pitfalls that can occur when conducting SBF-SEM imaging. Success using this protocol requires proper fixation of tissue, impregnation of heavy metals into the sample, modifications of the embedding resin to reduce charging, as well as an understanding of.......

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We would like to thank Dr. Sam Hanlon, Evelyn Brown, and Margaret Gondo for their excellent technical assistance. This research was supported in part by National Institutes of Health (NIH) R01 EY-018239 and P30 EY007551 (National Eye Institute), in part by the Lion's Foundation for Sight, and in part by NIH 1R15 HD084262-01 (National Institute of Child Health & Human Development).


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Name Company Catalog Number Comments
1/16 x 3/8 Aluminum Rivets Industrial Rivet & Fastener Co. 6N37RFLAP/1100 Used as specimen pins.
2.5mm Flathead Screwdriver Wiha Quality Tools 27225
Acetone Electron Microscopy Sciences RT 10000 Used to dilute silver paint.
Aspartic Acid Sigma-Aldrich A8949
Calcium Chloride FisherScientific C79-500
Conductive Silver Paint Ted Pella 16062
Denton Desk-II Vacuum Sputtering Device equipped with standard gold foil target Denton Vacuum N/A This is the gold-sputtering device used by the authors, alternates are acceptable.
Double-edged Razors Fisher Scientific 50-949-411
Embed 812 Electron Microscopy Sciences 14120
Gatan 3View2 mounted in a Tescan Mira3 Field emission SEM Gatan & Tescan N/A This is the SBF-SEM device used by the authors, alternates are acceptable.
Glass Shell Vials, 0.5 DRAM (1.8 ml) Electron Microscopy Sciences 72630-05
Gluteraldehyde Electron Microscopy Sciences 16320
Gorilla Super Glue - Impact Tough NA NA Refered to as cyanoacrylate glue in text.
Ketjen Black HM Royal EC-600JD Refered to as carbon black in text.
KOH FisherScientific 18-605-593
Lead Nitrate Fisher Scientific L62-100
Microwave Pelco BioWave Pro This is the microwave used by the authors, alternates are acceptable.
Osmium Tetroxide Sigma-Aldrich 201030
Potassium Ferrocyanide Sigma-Aldrich P9387
Silicone Embedding Mold Ted Pella 10504
Sodium Cacodylate Trihydrate Electron Microscopy Sciences 12300
Samco Transfer Pipette ThermoFisher Scientific 202 Used to make specimen pin storage tubes.
Swiss Pattern Needle Files Electron Microscopy Sciences 62115
Thiocarbohydrazide Sigma-Aldrich 223220
Uranyl Acetate Polysciences, Inc. 21447-25
Reconstruction Software
Amira Software Thermo Scientific N/A Used to create the reconstructions found in figures 5-7 and 9.
Fiji (Fiji is Just ImageJ) N/A TrakEM2 can be added to Fiji to asist in manual segmentation.
Microscopy Image Browser (MIB) University of Helsinki, Institute of Biotechnology N/A
Reconstuct Software Neural Systems Lab N/A
SuRVoS Workbench Diamond Light Source & The University of Nottingham N/A
SyGlass IstoVisio, Inc. N/A Allows for reconstruction in virtual reality and histogram-based reconstruction methods.

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