Serial block-face scanning electron microscopy

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Serial block-face scanning electron microscopy (SBEM, SBSEM or SBFSEM) is a method to generate high resolution three-dimensional images from small samples. The technique was developed for brain tissue, but it is widely applicable for any biological samples.[1] A serial block-face scanning electron microscope consists of an ultramicrotome mounted inside the vacuum chamber of a scanning electron microscope. Samples are prepared by methods similar to that in transmission electron microscopy (TEM), typically by fixing the sample with aldehyde, staining with heavy metals such as osmium and uranium then embedding in an epoxy resin.[2][3] The surface of the block of resin-embedded sample is imaged by detection of back-scattered electrons. Following imaging the ultramicrotome is used to cut a thin section (typically around 30 nm) from the face of the block. After the section is cut, the sample block is raised back to the focal plane and imaged again. This sequence of sample imaging, section cutting and block raising can acquire many thousands of images in perfect alignment in an automated fashion. Practical SBFSEM was invented in 2004 by Winfried Denk at the Max-Planck-Institute in Heidelberg and is commercially available from Gatan Inc.[4] and Thermo Fisher Scientific (VolumeScope).[5]


One of the first applications of SBFSEM was to analyze the connectivity of axons in the brain. The resolution is sufficient to trace even the thinnest axons and to identify synapses.By now, serial block face imaging contributed to many fields, like developmental biology, plant biology, cancer research, studying neuro-degenerative diseases etc. SBFSEM can generate extremely large data sets, and development of algorithms for automatic segmentation of the very large data sets generated is still a challenge. However much work is being done on this area currently. The EyeWire project harnesses human computation in a game to trace neurons through images of a volume of retina obtained using SBEM.[6]

Many different samples can be prepared for SBFSEM and the ultramicrotome is able to cut many materials, therefore this technique has wider applicability. It is starting to find applications in many other areas ranging from cell and developmental biology [7] to materials science.


  1. ^ Denk W, Horstmann H (2004) Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. PLoS Biol 2(11): e329. doi:10.1371/journal.pbio.0020329
  2. ^ Mukherjee, Konark; Clark, Helen R.; Chavan, Vrushali; Benson, Emily K.; Kidd, Grahame J.; Srivastava, Sarika (2016-07-09). "Analysis of Brain Mitochondria Using Serial Block-Face Scanning Electron Microscopy". Journal of Visualized Experiments (113). doi:10.3791/54214. ISSN 1940-087X.
  3. ^ Hua, Yunfeng; Laserstein, Philip; Helmstaedter, Moritz (2015-08-03). "Large-volume en-bloc staining for electron microscopy-based connectomics". Nature Communications. 6: 7923. doi:10.1038/ncomms8923. ISSN 2041-1723. PMC 4532871. PMID 26235643.
  4. ^
  5. ^ "Teneo VolumeScope SEM for Life Sciences". Mark Anderson. 2017-10-02. Retrieved 2017-10-09.
  6. ^ "Challenge << EyeWire". Archived from the original on April 14, 2012. Retrieved March 27, 2012.

[7] Holland ND (2018). Formation of the initial kidney and mouth opening in larval amphioxus studied with serial blockface scanning electron microscopy (SBSEM). EvoDevo |volume=9|number 16|doi=10.1186.

External links[edit]

  • [1] Original Publication in PloS Biology
  • [2] Gatan's 3View
  • [3] Cell Centered Data Base, SBEM datasets