Introductory vEM papers
Please find below a selection of introductory vEM papers broken down into the following categories:
General vEM reviews
Developing 3D SEM in a broad biological context.
Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens A, Holt M, Janssens S, Krols M, Larsimont JC, Mc Guire C, Nowack MK, Saelens X, Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, VAN Brempt R, Visser Y, Guérin CJ. J Microsc. 2015 Aug;259(2):80-96. doi: 10.1111/jmi.12211. Epub 2015 Jan 26. PMID: 25623622; PMCID: PMC4670703.
https://pubmed.ncbi.nlm.nih.gov/25623622/
Three-dimensional SEM - the future of cell imaging.
Hawes C, Hummel E. . J Microsc. 2015 Aug;259(2):79. doi: 10.1111/jmi.12286. PMID: 26191645.
https://pubmed.ncbi.nlm.nih.gov/26191645/
Exploring the third dimension: volume electron microscopy comes of age.
Peddie CJ, Collinson LM. Micron. 2014 Jun;61:9-19. doi: 10.1016/j.micron.2014.01.009. Epub 2014 Feb 12. PMID: 24792442.
https://pubmed.ncbi.nlm.nih.gov/24792442/
Volume scanning electron microscopy for imaging biological ultrastructure.
Titze B, Genoud C. Biol Cell. 2016 Nov;108(11):307-323. doi: 10.1111/boc.201600024. Epub 2016 Aug 12. PMID: 27432264.
https://pubmed.ncbi.nlm.nih.gov/27432264/
Sample prep
High-contrast en bloc staining of neuronal tissue for field emission scanning electron microscopy.
Tapia JC, Kasthuri N, Hayworth KJ, Schalek R, Lichtman JW, Smith SJ, Buchanan J. Nat Protoc. 2012 Jan 12;7(2):193-206. doi: 10.1038/nprot.2011.439. PMID: 22240582; PMCID: PMC3701260.
https://pubmed.ncbi.nlm.nih.gov/22240582/
High-resolution whole-brain staining for electron microscopic circuit reconstruction.
Mikula S, Denk W. Nat Methods. 2015 Jun;12(6):541-6. doi: 10.1038/nmeth.3361. Epub 2015 Apr 13. PMID: 25867849.
https://pubmed.ncbi.nlm.nih.gov/25867849/
Investigation of resins suitable for the preparation of biological sample for 3-D electron microscopy.
Kizilyaprak C, Longo G, Daraspe J, Humbel BM. J Struct Biol. 2015 Feb;189(2):135-46. doi: 10.1016/j.jsb.2014.10.009. Epub 2014 Nov 26. PMID: 25433274.
https://pubmed.ncbi.nlm.nih.gov/25433274/
Array tomography
Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits.
Micheva KD, Smith SJ. Neuron. 2007 Jul 5;55(1):25-36. doi: 10.1016/j.neuron.2007.06.014. Erratum in: Neuron. 2007 Sep 6;55(5):824. PMID: 17610815; PMCID: PMC2080672
https://pubmed.ncbi.nlm.nih.gov/17610815/
Array tomography.
Wacker I, Schroeder RR. J Microsc. 2013 Nov;252(2):93-9. doi: 10.1111/jmi.12087. Epub 2013 Sep 20. PMID: 24111814.
https://pubmed.ncbi.nlm.nih.gov/24111814/
Multi-Beam Scanning Electron Microscopy for High-Throughput Imaging in Connectomics Research.
Eberle AL, Zeidler D. Front Neuroanat. 2018 Dec 11;12:112. doi: 10.3389/fnana.2018.00112. PMID: 30618653; PMCID: PMC6297274.
https://pubmed.ncbi.nlm.nih.gov/30618653/
FIB SEM
Volume microscopy in biology: FIB-SEM tomography.
Kizilyaprak C, Stierhof YD, Humbel BM. Tissue Cell. 2019 Apr;57:123-128. doi: 10.1016/j.tice.2018.09.006. Epub 2018 Sep 26. PMID: 30385054.
https://pubmed.ncbi.nlm.nih.gov/30385054/
Correlative 3D imaging: CLSM and FIB-SEM tomography using high-pressure frozen, freeze-substituted biological samples.
Lucas MS, Guenthert M, Gasser P, Lucas F, Wepf R. Methods Mol Biol. 2014;1117:593-616. doi: 10.1007/978-1-62703-776-1_26. PMID: 24357381.
https://pubmed.ncbi.nlm.nih.gov/24357381/
Focused ion beams in biology.
Narayan K, Subramaniam S. Nat Methods. 2015 Nov;12(11):1021-31. doi: 10.1038/nmeth.3623. PMID: 26513553; PMCID: PMC6993138.
https://pubmed.ncbi.nlm.nih.gov/26513553/
A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster.
Zheng Z, Lauritzen JS, Perlman E, Robinson CG, Nichols M, Milkie D, Torrens O, Price J, Fisher CB, Sharifi N, Calle-Schuler SA, Kmecova L, Ali IJ, Karsh B, Trautman ET, Bogovic JA, Hanslovsky P, Jefferis GSXE, Kazhdan M, Khairy K, Saalfeld S, Fetter RD, Bock DD. Cell. 2018 Jul 26;174(3):730-743.e22. doi: 10.1016/j.cell.2018.06.019. Epub 2018 Jul 19. PMID: 30033368; PMCID: PMC6063995.
https://pubmed.ncbi.nlm.nih.gov/30033368/
FIB-SEM as a Volume Electron Microscopy Approach to Study Cellular Architectures in SARS-CoV-2 and Other Viral Infections: A Practical Primer for a Virologist.
Baena V, Conrad R, Friday P, Fitzgerald E, Kim T, Bernbaum J, Berensmann H, Harned A, Nagashima K, Narayan K. Viruses. 2021 Apr 2;13(4):611. doi: 10.3390/v13040611. PMID: 33918371; PMCID: PMC8066521.
https://pubmed.ncbi.nlm.nih.gov/33918371/
SBF SEM
Deconstructing complexity: serial block-face electron microscopic analysis of the hippocampal mossy fiber synapse.
Wilke SA, Antonios JK, Bushong EA, Badkoobehi A, Malek E, Hwang M, Terada M, Ellisman MH, Ghosh A. J Neurosci. 2013 Jan 9;33(2):507-22. doi: 10.1523/JNEUROSCI.1600-12.2013. PMID: 23303931; PMCID: PMC3756657.
https://pubmed.ncbi.nlm.nih.gov/23303931/
Serial block face-scanning electron microscopy for volume electron microscopy.
Lippens S, Kremer A, Borghgraef P, Guérin CJ. Methods Cell Biol. 2019;152:69-85. doi: 10.1016/bs.mcb.2019.04.002. Epub 2019 Jun 17. PMID: 31326027.
https://pubmed.ncbi.nlm.nih.gov/31326027/
Combining serial block face and focused ion beam scanning electron microscopy for 3D studies of rare events.
Guérin CJ, Kremer A, Borghgraef P, Shih AY, Lippens S. Methods Cell Biol. 2019;152:87-101. doi: 10.1016/bs.mcb.2019.03.014. Epub 2019 May 7. PMID: 31326028.
https://pubmed.ncbi.nlm.nih.gov/31326028/
Using transmission electron microscopy and 3View to determine collagen fibril size and three-dimensional organization.
Starborg T, Kalson NS, Lu Y, Mironov A, Cootes TF, Holmes DF, Kadler KE. Nat Protoc. 2013;8(7):1433-48. doi: 10.1038/nprot.2013.086. Epub 2013 Jun 27. PMID: 23807286; PMCID: PMC5642902.
https://pubmed.ncbi.nlm.nih.gov/23807286/
Serial block face scanning electron microscopy in cell biology: Applications and technology.
Smith D, Starborg T. Tissue Cell. 2019 Apr;57:111-122. doi: 10.1016/j.tice.2018.08.011. Epub 2018 Sep 3. PMID: 30220487.
https://pubmed.ncbi.nlm.nih.gov/30220487/
Development of protocols for the first serial block-face scanning electron microscopy (SBF SEM) studies of bone tissue.
Goggin P, Ho EML, Gnaegi H, Searle S, Oreffo ROC, Schneider P. Bone. 2020 Feb;131:115107. doi: 10.1016/j.bone.2019.115107. Epub 2019 Oct 24. PMID: 31669251; PMCID: PMC6961117.
https://pubmed.ncbi.nlm.nih.gov/31669251/
SBEMimage: Versatile Acquisition Control Software for Serial Block-Face Electron Microscopy.
Titze B, Genoud C, Friedrich RW. Front Neural Circuits. 2018 Jul 31;12:54. doi: 10.3389/fncir.2018.00054. PMID: 30108489; PMCID: PMC6079252. https://pubmed.ncbi.nlm.nih.gov/30108489/
Challenges of microtome-based serial block-face scanning electron microscopy in neuroscience.
Wanner AA, Kirschmann MA, Genoud C. J Microsc. 2015 Aug;259(2):137-142. doi: 10.1111/jmi.12244. Epub 2015 Apr 23. PMID: 25907464; PMCID: PMC4745002. https://pubmed.ncbi.nlm.nih.gov/25907464/
Data processing
DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation.
Belevich I, Jokitalo E. PLoS Comput Biol. 2021 Mar 2;17(3):e1008374. doi: 10.1371/journal.pcbi.1008374. PMID: 33651804; PMCID: PMC7954287.
https://pubmed.ncbi.nlm.nih.gov/33651804/
eC-CLEM: flexible multidimensional registration software for correlative microscopies.
Paul-Gilloteaux P, Heiligenstein X, Belle M, Domart MC, Larijani B, Collinson L, Raposo G, Salamero J. Nat Methods. 2017 Jan 31;14(2):102-103. doi: 10.1038/nmeth.4170. PMID: 28139674.
https://pubmed.ncbi.nlm.nih.gov/28139674/
A guide to analysis and reconstruction of serial block face scanning electron microscopy data.
Cocks E, Taggart M, Rind FC, White K. J Microsc. 2018 May;270(2):217-234. doi: 10.1111/jmi.12676. Epub 2018 Jan 15. PMID: 29333754; PMCID: PMC5947172.
https://pubmed.ncbi.nlm.nih.gov/29333754/
ilastik: interactive machine learning for (bio)image analysis.
Berg S, Kutra D, Kroeger T, Straehle CN, Kausler BX, Haubold C, Schiegg M, Ales J, Beier T, Rudy M, Eren K, Cervantes JI, Xu B, Beuttenmueller F, Wolny A, Zhang C, Koethe U, Hamprecht FA, Kreshuk A. Nat Methods. 2019 Dec;16(12):1226-1232. doi: 10.1038/s41592-019-0582-9. Epub 2019 Sep 30. PMID: 31570887.
https://pubmed.ncbi.nlm.nih.gov/31570887/
From voxels to knowledge: a practical guide to the segmentation of complex electron microscopy 3D-data.
Tsai WT, Hassan A, Sarkar P, Correa J, Metlagel Z, Jorgens DM, Auer M. J Vis Exp. 2014 Aug 13;(90):e51673. doi: 10.3791/51673. PMID: 25145678; PMCID: PMC4448944.
https://pubmed.ncbi.nlm.nih.gov/25145678/
- General vEM Reviews
- Sample preparation
- Array tomography
- FIB-SEM
- SBF-SEM
- Data Processing
General vEM reviews
Developing 3D SEM in a broad biological context.
Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens A, Holt M, Janssens S, Krols M, Larsimont JC, Mc Guire C, Nowack MK, Saelens X, Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, VAN Brempt R, Visser Y, Guérin CJ. J Microsc. 2015 Aug;259(2):80-96. doi: 10.1111/jmi.12211. Epub 2015 Jan 26. PMID: 25623622; PMCID: PMC4670703.
https://pubmed.ncbi.nlm.nih.gov/25623622/
Three-dimensional SEM - the future of cell imaging.
Hawes C, Hummel E. . J Microsc. 2015 Aug;259(2):79. doi: 10.1111/jmi.12286. PMID: 26191645.
https://pubmed.ncbi.nlm.nih.gov/26191645/
Exploring the third dimension: volume electron microscopy comes of age.
Peddie CJ, Collinson LM. Micron. 2014 Jun;61:9-19. doi: 10.1016/j.micron.2014.01.009. Epub 2014 Feb 12. PMID: 24792442.
https://pubmed.ncbi.nlm.nih.gov/24792442/
Volume scanning electron microscopy for imaging biological ultrastructure.
Titze B, Genoud C. Biol Cell. 2016 Nov;108(11):307-323. doi: 10.1111/boc.201600024. Epub 2016 Aug 12. PMID: 27432264.
https://pubmed.ncbi.nlm.nih.gov/27432264/
Sample prep
High-contrast en bloc staining of neuronal tissue for field emission scanning electron microscopy.
Tapia JC, Kasthuri N, Hayworth KJ, Schalek R, Lichtman JW, Smith SJ, Buchanan J. Nat Protoc. 2012 Jan 12;7(2):193-206. doi: 10.1038/nprot.2011.439. PMID: 22240582; PMCID: PMC3701260.
https://pubmed.ncbi.nlm.nih.gov/22240582/
High-resolution whole-brain staining for electron microscopic circuit reconstruction.
Mikula S, Denk W. Nat Methods. 2015 Jun;12(6):541-6. doi: 10.1038/nmeth.3361. Epub 2015 Apr 13. PMID: 25867849.
https://pubmed.ncbi.nlm.nih.gov/25867849/
Investigation of resins suitable for the preparation of biological sample for 3-D electron microscopy.
Kizilyaprak C, Longo G, Daraspe J, Humbel BM. J Struct Biol. 2015 Feb;189(2):135-46. doi: 10.1016/j.jsb.2014.10.009. Epub 2014 Nov 26. PMID: 25433274.
https://pubmed.ncbi.nlm.nih.gov/25433274/
Array tomography
Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits.
Micheva KD, Smith SJ. Neuron. 2007 Jul 5;55(1):25-36. doi: 10.1016/j.neuron.2007.06.014. Erratum in: Neuron. 2007 Sep 6;55(5):824. PMID: 17610815; PMCID: PMC2080672
https://pubmed.ncbi.nlm.nih.gov/17610815/
Array tomography.
Wacker I, Schroeder RR. J Microsc. 2013 Nov;252(2):93-9. doi: 10.1111/jmi.12087. Epub 2013 Sep 20. PMID: 24111814.
https://pubmed.ncbi.nlm.nih.gov/24111814/
Multi-Beam Scanning Electron Microscopy for High-Throughput Imaging in Connectomics Research.
Eberle AL, Zeidler D. Front Neuroanat. 2018 Dec 11;12:112. doi: 10.3389/fnana.2018.00112. PMID: 30618653; PMCID: PMC6297274.
https://pubmed.ncbi.nlm.nih.gov/30618653/
FIB SEM
Volume microscopy in biology: FIB-SEM tomography.
Kizilyaprak C, Stierhof YD, Humbel BM. Tissue Cell. 2019 Apr;57:123-128. doi: 10.1016/j.tice.2018.09.006. Epub 2018 Sep 26. PMID: 30385054.
https://pubmed.ncbi.nlm.nih.gov/30385054/
Correlative 3D imaging: CLSM and FIB-SEM tomography using high-pressure frozen, freeze-substituted biological samples.
Lucas MS, Guenthert M, Gasser P, Lucas F, Wepf R. Methods Mol Biol. 2014;1117:593-616. doi: 10.1007/978-1-62703-776-1_26. PMID: 24357381.
https://pubmed.ncbi.nlm.nih.gov/24357381/
Focused ion beams in biology.
Narayan K, Subramaniam S. Nat Methods. 2015 Nov;12(11):1021-31. doi: 10.1038/nmeth.3623. PMID: 26513553; PMCID: PMC6993138.
https://pubmed.ncbi.nlm.nih.gov/26513553/
A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster.
Zheng Z, Lauritzen JS, Perlman E, Robinson CG, Nichols M, Milkie D, Torrens O, Price J, Fisher CB, Sharifi N, Calle-Schuler SA, Kmecova L, Ali IJ, Karsh B, Trautman ET, Bogovic JA, Hanslovsky P, Jefferis GSXE, Kazhdan M, Khairy K, Saalfeld S, Fetter RD, Bock DD. Cell. 2018 Jul 26;174(3):730-743.e22. doi: 10.1016/j.cell.2018.06.019. Epub 2018 Jul 19. PMID: 30033368; PMCID: PMC6063995.
https://pubmed.ncbi.nlm.nih.gov/30033368/
FIB-SEM as a Volume Electron Microscopy Approach to Study Cellular Architectures in SARS-CoV-2 and Other Viral Infections: A Practical Primer for a Virologist.
Baena V, Conrad R, Friday P, Fitzgerald E, Kim T, Bernbaum J, Berensmann H, Harned A, Nagashima K, Narayan K. Viruses. 2021 Apr 2;13(4):611. doi: 10.3390/v13040611. PMID: 33918371; PMCID: PMC8066521.
https://pubmed.ncbi.nlm.nih.gov/33918371/
SBF SEM
Deconstructing complexity: serial block-face electron microscopic analysis of the hippocampal mossy fiber synapse.
Wilke SA, Antonios JK, Bushong EA, Badkoobehi A, Malek E, Hwang M, Terada M, Ellisman MH, Ghosh A. J Neurosci. 2013 Jan 9;33(2):507-22. doi: 10.1523/JNEUROSCI.1600-12.2013. PMID: 23303931; PMCID: PMC3756657.
https://pubmed.ncbi.nlm.nih.gov/23303931/
Serial block face-scanning electron microscopy for volume electron microscopy.
Lippens S, Kremer A, Borghgraef P, Guérin CJ. Methods Cell Biol. 2019;152:69-85. doi: 10.1016/bs.mcb.2019.04.002. Epub 2019 Jun 17. PMID: 31326027.
https://pubmed.ncbi.nlm.nih.gov/31326027/
Combining serial block face and focused ion beam scanning electron microscopy for 3D studies of rare events.
Guérin CJ, Kremer A, Borghgraef P, Shih AY, Lippens S. Methods Cell Biol. 2019;152:87-101. doi: 10.1016/bs.mcb.2019.03.014. Epub 2019 May 7. PMID: 31326028.
https://pubmed.ncbi.nlm.nih.gov/31326028/
Using transmission electron microscopy and 3View to determine collagen fibril size and three-dimensional organization.
Starborg T, Kalson NS, Lu Y, Mironov A, Cootes TF, Holmes DF, Kadler KE. Nat Protoc. 2013;8(7):1433-48. doi: 10.1038/nprot.2013.086. Epub 2013 Jun 27. PMID: 23807286; PMCID: PMC5642902.
https://pubmed.ncbi.nlm.nih.gov/23807286/
Serial block face scanning electron microscopy in cell biology: Applications and technology.
Smith D, Starborg T. Tissue Cell. 2019 Apr;57:111-122. doi: 10.1016/j.tice.2018.08.011. Epub 2018 Sep 3. PMID: 30220487.
https://pubmed.ncbi.nlm.nih.gov/30220487/
Development of protocols for the first serial block-face scanning electron microscopy (SBF SEM) studies of bone tissue.
Goggin P, Ho EML, Gnaegi H, Searle S, Oreffo ROC, Schneider P. Bone. 2020 Feb;131:115107. doi: 10.1016/j.bone.2019.115107. Epub 2019 Oct 24. PMID: 31669251; PMCID: PMC6961117.
https://pubmed.ncbi.nlm.nih.gov/31669251/
SBEMimage: Versatile Acquisition Control Software for Serial Block-Face Electron Microscopy.
Titze B, Genoud C, Friedrich RW. Front Neural Circuits. 2018 Jul 31;12:54. doi: 10.3389/fncir.2018.00054. PMID: 30108489; PMCID: PMC6079252. https://pubmed.ncbi.nlm.nih.gov/30108489/
Challenges of microtome-based serial block-face scanning electron microscopy in neuroscience.
Wanner AA, Kirschmann MA, Genoud C. J Microsc. 2015 Aug;259(2):137-142. doi: 10.1111/jmi.12244. Epub 2015 Apr 23. PMID: 25907464; PMCID: PMC4745002. https://pubmed.ncbi.nlm.nih.gov/25907464/
Data processing
DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation.
Belevich I, Jokitalo E. PLoS Comput Biol. 2021 Mar 2;17(3):e1008374. doi: 10.1371/journal.pcbi.1008374. PMID: 33651804; PMCID: PMC7954287.
https://pubmed.ncbi.nlm.nih.gov/33651804/
eC-CLEM: flexible multidimensional registration software for correlative microscopies.
Paul-Gilloteaux P, Heiligenstein X, Belle M, Domart MC, Larijani B, Collinson L, Raposo G, Salamero J. Nat Methods. 2017 Jan 31;14(2):102-103. doi: 10.1038/nmeth.4170. PMID: 28139674.
https://pubmed.ncbi.nlm.nih.gov/28139674/
A guide to analysis and reconstruction of serial block face scanning electron microscopy data.
Cocks E, Taggart M, Rind FC, White K. J Microsc. 2018 May;270(2):217-234. doi: 10.1111/jmi.12676. Epub 2018 Jan 15. PMID: 29333754; PMCID: PMC5947172.
https://pubmed.ncbi.nlm.nih.gov/29333754/
ilastik: interactive machine learning for (bio)image analysis.
Berg S, Kutra D, Kroeger T, Straehle CN, Kausler BX, Haubold C, Schiegg M, Ales J, Beier T, Rudy M, Eren K, Cervantes JI, Xu B, Beuttenmueller F, Wolny A, Zhang C, Koethe U, Hamprecht FA, Kreshuk A. Nat Methods. 2019 Dec;16(12):1226-1232. doi: 10.1038/s41592-019-0582-9. Epub 2019 Sep 30. PMID: 31570887.
https://pubmed.ncbi.nlm.nih.gov/31570887/
From voxels to knowledge: a practical guide to the segmentation of complex electron microscopy 3D-data.
Tsai WT, Hassan A, Sarkar P, Correa J, Metlagel Z, Jorgens DM, Auer M. J Vis Exp. 2014 Aug 13;(90):e51673. doi: 10.3791/51673. PMID: 25145678; PMCID: PMC4448944.
https://pubmed.ncbi.nlm.nih.gov/25145678/