Volumetric Electron Microscopy

{{short description|Electron microscopy method for ultrastructure/cellular imaging}}

{{distinguish|Electron tomography}}

Volumetric Electron Microscopy (Volume EM) is an electron microscopy method used to generate 3D reconstructions of thick (>500 nm) samples. The initial role of electron microscopes in imaging two-dimensional slices (TEM) or a specimen surface (SEM with secondary electrons) has also increasingly expanded into the depth of samples.{{cite journal | vauthors = Peddie CJ, Genoud C, Kreshuk A, Meechan K, Micheva KD, Narayan K, Pape C, Parton RG, Schieber NL, Schwab Y, Titze B, Verkade P, Aubrey A, Collinson LM | title = Volume electron microscopy | journal = Nature Reviews. Methods Primers | volume = 2 | issue = | pages = 51 | date = July 2022 | pmid = 37409324 | pmc = 7614724 | doi = 10.1038/s43586-022-00131-9 }} An early example of these volume EM workflows was simply to stack TEM images of serial sections cut through a sample. The next development was virtual reconstruction of a thick section (200-500 nm) volume by backprojection of a set of images taken at different tilt angles - TEM tomography.{{cite journal | vauthors = Crowther RA, Amos LA, Finch JT, De Rosier DJ, Klug A | title = Three dimensional reconstructions of spherical viruses by fourier synthesis from electron micrographs | journal = Nature | volume = 226 | issue = 5244 | pages = 421–425 | date = May 1970 | pmid = 4314822 | doi = 10.1038/226421a0 | bibcode = 1970Natur.226..421C }}

To acquire volume EM datasets of larger depths than TEM tomography (micrometers or millimeters in the z axis), a series of images taken through the sample depth can be used. For example, ribbons of serial sections can be imaged in a TEM as described above, and when thicker sections are used, serial TEM tomography can be used to increase the z-resolution. More recently, back scattered electron (BSE) images can be acquired of a larger series of sections collected on silicon wafers, known as SEM array tomography.{{cite book |doi=10.1016/bs.mcb.2022.12.023 |chapter=A practical guide to starting SEM array tomography—An accessible volume EM technique |title=Volume Electron Microscopy |series=Methods in Cell Biology |date=2023 |volume=177 |pages=171–196 |isbn=978-0-323-91607-3 | vauthors = White IJ, Burden JJ |pmid=37451766 }}{{cite journal | vauthors = Kolotuev I | title = Work smart, not hard: How array tomography can help increase the ultrastructure data output | journal = Journal of Microscopy | volume = 295 | issue = 1 | pages = 42–60 | date = July 2024 | pmid = 37626455 | doi = 10.1111/jmi.13217 | doi-access = free }} An alternative approach is to use BSE SEM to image the block surface instead of the section, after each section has been removed. By this method, an ultramicrotome installed in an SEM chamber can increase automation of the workflow; the specimen block is loaded in the chamber and the system programmed to continuously cut and image through the sample. This is known as serial block face SEM.{{cite journal | vauthors = Denk W, Horstmann H | title = Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure | journal = PLOS Biology | volume = 2 | issue = 11 | pages = e329 | date = November 2004 | pmid = 15514700 | pmc = 524270 | doi = 10.1371/journal.pbio.0020329 | doi-access = free }} A related method uses focused ion beam milling instead of an ultramicrotome to remove sections. In these serial imaging methods, the output is essentially a sequence of images through a specimen block that can be digitally aligned in sequence and thus reconstructed into a volume EM dataset. The increased volume available in these methods has expanded the capability of electron microscopy to address new questions, such as mapping neural connectivity in the brain,{{cite journal | vauthors = Abbott LF, Bock DD, Callaway EM, Denk W, Dulac C, Fairhall AL, Fiete I, Harris KM, Helmstaedter M, Jain V, Kasthuri N, LeCun Y, Lichtman JW, Littlewood PB, Luo L, Maunsell JH, Reid RC, Rosen BR, Rubin GM, Sejnowski TJ, Seung HS, Svoboda K, Tank DW, Tsao D, Van Essen DC | title = The Mind of a Mouse | journal = Cell | volume = 182 | issue = 6 | pages = 1372–1376 | date = September 2020 | pmid = 32946777 | doi = 10.1016/j.cell.2020.08.010 | doi-access = free }} and membrane contact sites between organelles.{{cite journal | vauthors = Prinz WA, Toulmay A, Balla T | title = The functional universe of membrane contact sites | journal = Nature Reviews. Molecular Cell Biology | volume = 21 | issue = 1 | pages = 7–24 | date = January 2020 | pmid = 31732717 | pmc = 10619483 | doi = 10.1038/s41580-019-0180-9 }}