Volume 263, Issue 1 pp. 3-9

Invited Review

Reporting methods for processing and analysis of data from serial block face scanning electron microscopy

S. BORRETT,

S. BORRETT

Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford, OX1 3RE U.K.

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L. HUGHES,

Corresponding Author

L. HUGHES

Department of Biological & Medical Sciences, Gipsy Lane, Oxford Brookes University, Oxford, OX3 0BP U.K.

Correspondence to: Louise Hughes, Department of Biological & Medical Sciences, Gipsy Lane, Oxford Brookes University, Oxford OX3 0BP, U.K. Tel: +44-1865-484351; fax 44 (0)1865 483955; e-mail: [email protected]Search for more papers by this author

S. BORRETT,

S. BORRETT

Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford, OX1 3RE U.K.

Search for more papers by this author

L. HUGHES,

Corresponding Author

L. HUGHES

Department of Biological & Medical Sciences, Gipsy Lane, Oxford Brookes University, Oxford, OX3 0BP U.K.

First published: 21 January 2016

https://doi.org/10.1111/jmi.12377

Citations: 34

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Summary

Serial block face scanning electron microscopy is rapidly becoming a popular tool for collecting large three-dimensional data sets of cells and tissues, filling the resolution and volume gap between fluorescence microscopy and high-resolution electron microscopy. The automated collection of data within the instrument occupies the smallest proportion of the time required to prepare and analyse biological samples. It is the processing of data once it has been collected that proves the greatest challenge. In this review we discuss different methods that are used to process data. We suggest potential workflows that can be used to facilitate the transfer of raw image stacks into quantifiable data as well as propose a set of criteria for reporting methods for data analysis to enable replication of work.

Lay description

A three-dimensional (3D) microscopy technique, serial block face scanning electron microscopy (SBFSEM), is becoming increasingly popular in biological research. The technique results in large volumes of data being produced, which can cause issues such as for data analysis. This review explores the different methods being used in published work and makes suggestions about how these methods can be reported to enable replication of the research conducted.

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Volume263, Issue1

July 2016

Pages 3-9

Reporting methods for processing and analysis of data from serial block face scanning electron microscopy

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Reporting methods for processing and analysis of data from serial block face scanning electron microscopy

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