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Counting synapses using FIB/SEM microscopy: a true revolution for ultrastructural volume reconstruction
Open accessAbstract
The advent of transmission electron microscopy (TEM) in the 1950s represented a fundamental step in the study of neuronal circuits. The application of this technique soon led to the realization that the number of synapses changes during the course of normal life, as well as under certain pathological or experimental circumstances. Since then, one of the main goals in neurosciences has been to define simple and accurate methods to estimate the magnitude of these changes. Contrary to analysing single sections, TEM reconstructions are extremely time-consuming and difficult. Therefore, most quantitative studies use stereological methods to define the three-dimensional characteristics of synaptic junctions that are studied in two dimensions. Here, to count the exact number of synapses per unit of volume we have applied a new three-dimensional reconstruction method that involves the combination of focused ion beam milling and scanning electron microscopy (FIB/SEM). We show that the images obtained with FIB/SEM are similar to those obtained with TEM, but with the advantage that FIB/SEM permits serial reconstructions of large volumes of tissue to be generated rapidly and automatically. Furthermore, we compared the estimates of the number of synapses obtained with stereological methods with the values obtained by FIB/SEM reconstructions. We concluded that FIB/SEM not only provides the actual number of synapses per volume but it is also much easier and faster to use than other currently available TEM methods. More importantly, it also avoids most of the errors introduced by stereological methods and overcomes the difficulties associated with these techniques.
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“Fortunately, the recent introduction of automated volume electron microscopy methods has proven to be a valuable and efficient approach for identifying synapses in three dimensions, becoming the gold standard technique for this purpose for this task (Merchán-Pérez et al., 2009).”
From Unambiguous identification of asymmetric and symmetric synapses using volume electron microscopy (2024) · cites this paper as Merchán-Pérez et al., 2009
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“This technology was chosen because it enables automated serial sectioning of large volumes of tissue, without any mechanical interaction with the sample (e.g., see Knott et al., 2008; Merchán-Pérez et al., 2009; Titze and Genoud, 2016; Kubota et al., 2018; Rollenhagen et al., 2020).”
From Unambiguous identification of asymmetric and symmetric synapses using volume electron microscopy (2024) · cites this paper as Merchán-Pérez et al., 2009
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Cites
Two new Later Stone Age sites from the Final Pleistocene in the Falémé Valley, eastern Senegal
Ndiaye, M., Lespez, L., Tribolo, C., Rassé, M., Hadjas, I., Davidoux, S., Huysecom, É., & Douze, K. (2024) · Monash University Research Portal (Monash University) · doi:10.3929/ethz-b-000667478 · Cited by 24,214
The structure of the nervous system of the nematode Caenorhabditis elegans
White, J. G., Southgate, E., Thomson, J. N., & Brenner, S. (1986) · Philosophical Transactions of the Royal Society of London. B, Biological Sciences · doi:10.1098/rstb.1986.0056 · Cited by 5,589
GUNDERSEN, H. J. G., BENDTSEN, T. F., KORBO, L., MARCUSSEN, N., MØLLER, A., NIELSEN, K., NYENGAARD, J. R., PAKKENBERG, B., SØRENSEN, F. B., VESTERBY, A., et al. (1988) · APMIS · doi:10.1111/j.1699-0463.1988.tb05320.x · Cited by 2,929
The unbiased estimation of number and sizes of arbitrary particles using the disector
Sterio, D. C. (1984) · Journal of Microscopy · doi:10.1111/j.1365-2818.1984.tb02501.x · Cited by 2,533
Gundersen, H. J. G., Bagger, P. V., Bendtsen, T. F., Evans, S. M., Korbo, L., Marcussen, N., Møller, A., Nielsen, K. N., Nyengaard, J. R., Pakkenberg, B., et al. (1988) · Apmis · doi:10.1111/j.1699-0463.1988.tb00954.x · Cited by 2,480
The Fine Structure of the Nervous System.
Tennyson, V. M. (1970) · Archives of Neurology · doi:10.1001/archneur.1970.00480240094019 · Cited by 1,946
Axo-somatic and axo-dendritic synapses of the cerebral cortex: an electron microscope study.
Eg, G. (1959) · PubMed · Cited by 1,768
Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure
Denk, W., & Horstmann, H. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020329 · Cited by 1,644
(1991) · Medical Entomology and Zoology · Cited by 1,512
Notes on the estimation of the numerical density of arbitrary profiles: the edge effect
Gundersen, H. J. G. (1977) · Journal of Microscopy · doi:10.1111/j.1365-2818.1977.tb00062.x · Cited by 1,265
Markram, H. (2006) · Nature reviews. Neuroscience · doi:10.1038/nrn1848 · Cited by 1,227
DeFelipe, J., & Fariñas, I. (1992) · Progress in Neurobiology · doi:10.1016/0301-0082(92)90015-7 · Cited by 975
Megı́as, M., Emri, Z., Freund, T. F., & Gulyás, A. I. (2001) · Neuroscience · doi:10.1016/s0306-4522(00)00496-6 · Cited by 950
Colonnier, M. (1968) · Brain Research · doi:10.1016/0006-8993(68)90234-5 · Cited by 946
Reconstruct : a free editor for serial section microscopy
Fiala, J. C. (2005) · Journal of Microscopy · doi:10.1111/j.1365-2818.2005.01466.x · Cited by 889
fine structure of the nervous system
Peters, A., Palay, S. L., & Webster, H. D. (1976) · Cited by 796
Micheva, K. D., & Smith, S. J. (2007) · Neuron · doi:10.1016/j.neuron.2007.06.014 · Cited by 787
Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling
Knott, G., Marchman, H., Wall, D., & Lich, B. (2008) · The Journal of Neuroscience · doi:10.1523/jneurosci.3189-07.2008 · Cited by 692
Microstructure of the neocortex: comparative aspects
DeFelipe, J., Alonso-Nanclares, L., & Arellano, J. I. (2002) · Journal of Neurocytology · doi:10.1023/a:1024130211265 · Cited by 686
Gatenby, J. B., & Tahmisian, T. N. (1957) · Journal of the Royal Microscopical Society · doi:10.1111/j.1365-2818.1957.tb02020.x · Cited by 544
Structure, development, and plasticity of dendritic spines
Harris, K. M. (1999) · Current Opinion in Neurobiology · doi:10.1016/s0959-4388(99)80050-6 · Cited by 523
The small pyramidal neuron of the rat cerebral cortex: The synapses upon dendritic spines
Peters, A., & Kaiserman-Abramof, I. R. (1969) · Zeitschrift f�r Zellforschung und Mikroskopische Anatomie · doi:10.1007/bf00344370 · Cited by 441
Mayhew, T. M., & Gundersen, H. J. G. (1996) · PubMed · Cited by 291
Untangling Dendrites with Quantitative Models
Segev, I., & London, M. (2000) · Science · doi:10.1126/science.290.5492.744 · Cited by 285
Towards neural circuit reconstruction with volume electron microscopy techniques
Briggman, K. L., & Denk, W. T. (2006) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2006.08.010 · Cited by 272
GABA Neurons in the Cerebral Cortex
Houser, C. R., Vaughn, J. E., Hendry, S. H. C., Jones, E. G., & Peters, A. (1984) · Cerebral cortex · doi:10.1007/978-1-4615-6610-6_3 · Cited by 261
Uniform Serial Sectioning for Transmission Electron Microscopy
Harris, K. M., Perry, E., Bourne, J. N., Feinberg, M. D., Ostroff, L. E., & Hurlburt, J. L. (2006) · Journal of Neuroscience · doi:10.1523/jneurosci.3994-06.2006 · Cited by 211
Peters, A., & Palay, S. L. (1996) · Journal of Neurocytology · doi:10.1007/bf02284835 · Cited by 209
Baddeley, A. J., & Jensen, E. B. V. (2005) · Technometrics · doi:10.1198/tech.2005.s344 · Cited by 204
Extending Unbiased Stereology of Brain Ultrastructure to Three-dimensional Volumes
Fiala, J. C., & Harris, K. M. (2001) · Journal of the American Medical Informatics Association · doi:10.1136/jamia.2001.0080001 · Cited by 203
Estimation of the number of synapses in the cerebral cortex: methodological considerations
DeFelipe, J. (1999) · Cerebral Cortex · doi:10.1093/cercor/9.7.722 · Cited by 193
Baddeley, A. J., & Jensen, E. B. V. (2004) · Chapman & Hall/CRC eBooks · doi:10.1201/9780203496817 · Cited by 183
Automating the Collection of Ultrathin Serial Sections for Large Volume TEM Reconstructions
Hayworth, K. J., Kasthuri, N., Schalek, R. L., & Lichtman, J. W. (2006) · Microscopy and Microanalysis · doi:10.1017/s1431927606066268 · Cited by 179
3D structural imaging of the brain with photons and electrons
Helmstaedter, M. N., Briggman, K. L., & Denk, W. T. (2008) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2009.03.005 · Cited by 175
Unbiased stereological estimation of the total number of synapses in a brain region
Geinisman, Y., Gundersen, H. J. G., van der Zee, E., & West, M. J. (1996) · Journal of Neurocytology · doi:10.1007/bf02284843 · Cited by 161
Cortical circuits: Synaptic organization of the cerebral cortex. Structure, function and theory
Divac, I. (1990) · Trends in Neurosciences · doi:10.1016/0166-2236(90)90047-e · Cited by 155
Stereology: A method for analyzing images
Royet, J. (1991) · Progress in Neurobiology · doi:10.1016/0301-0082(91)90009-p · Cited by 151
Soto, G. E., Young, S. J., Martone, M. E., Deerinck, T. J., Lamont, S., Carragher, B. O., Hama, K., & Ellisman, M. H. (1994) · NeuroImage · doi:10.1006/nimg.1994.1008 · Cited by 147
Cylindrical diameters method for calibrating section thickness in serial electron microscopy
Fiala, J. C., & Harris, K. M. (2001) · Journal of Microscopy · doi:10.1046/j.1365-2818.2001.00926.x · Cited by 144
A systematic approach to reconstructing microcircuitry by electron microscopy of serial sections
Stevens, J. K., Davis, T. L., Friedman, N., & Sterling, P. (1980) · Brain Research Reviews · doi:10.1016/0165-0173(80)90010-7 · Cited by 133
Fariñas, I., & DeFelipe, J. (1991) · The Journal of Comparative Neurology · doi:10.1002/cne.903040106 · Cited by 129
White, E. L., & Rock, M. P. (1980) · Journal of Neurocytology · doi:10.1007/bf01205029 · Cited by 127
Mayhew, T. M. (1979) · Journal of Neurocytology · doi:10.1007/bf01175556 · Cited by 122
Focused ion beams techniques for nanomaterials characterization
Langford, R. M. (2006) · Microscopy Research and Technique · doi:10.1002/jemt.20324 · Cited by 120
Colonnier, M., & Beaulieu, C. (1985) · The Journal of Comparative Neurology · doi:10.1002/cne.902310205 · Cited by 114
Fariñas, I., & DeFelipe, J. (1991) · The Journal of Comparative Neurology · doi:10.1002/cne.903040105 · Cited by 113
A simple and reliable method for correlative light and electron microscopic studies.
DeFelipe, J., & Fairén, A. G. (1993) · Journal of Histochemistry & Cytochemistry · doi:10.1177/41.5.8468459 · Cited by 86
Fogel, R., Zhang, X., & Renehan, W. E. (1996) · The Journal of Comparative Neurology · doi:10.1002/(sici)1096-9861(19960101)364:1 · Cited by 65
Mayhew, T. M. (1996) · Journal of Neurocytology · doi:10.1007/bf02284842 · Cited by 64
Circuit reconstruction tools today
Smith, S. J. (2007) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2007.11.004 · Cited by 63
Micheva, K. D., & Smith, S. J. (2007) · Neuron · doi:10.1016/j.neuron.2007.08.007 · Cited by 53
Hoffpauir, B. K., Pope, B. A., & Spirou, G. A. (2007) · Nature Protocols · doi:10.1038/nprot.2007.9 · Cited by 39
Porter, L. L., & White, E. L. (1986) · The Journal of Comparative Neurology · doi:10.1002/cne.902480409 · Cited by 39
Anatomical circuitry of lateral inhibition in the eye of the horseshoe crab, Limulus polyphemus
Fahrenbach, W. H. (1985) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.1985.0060 · Cited by 38
Oorschot, D. E., Peterson, D. A., & Jones, D. G. (1991) · Progress in Neurobiology · doi:10.1016/0301-0082(91)90007-n · Cited by 37
Kubota, Y. (2009) · Frontiers in Neural Circuits · doi:10.3389/neuro.04.004.2009 · Cited by 36
Merchán-Pérez, Á., Rodríguez, J., Ribak, C. E., & DeFelipe, J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900330106 · Cited by 33
New Technique for Ultra-thin Serial Brain Section Imaging Using Scanning Electron Microscopy
Kasthuri, N., Hayworth, K. J., Lichtman, J. W., Erdman, N., & Ackerley, C. (2007) · Microscopy and Microanalysis · doi:10.1017/s1431927607078002 · Cited by 28
Witgen, B. M., Grady, M. S., Nyengaard, J. R., & Gundersen, H. J. G. (2006) · Journal of Microscopy · doi:10.1111/j.1365-2818.2006.01563.x · Cited by 17
The neuroanatomist's dream, the problems and solutions, and the ultimate aim
DeFelipe, J. (2008) · Frontiers in Neuroscience · doi:10.3389/neuro.01.018.2008 · Cited by 16
Efficiency evaluation of MEV spatial sampling strategies: a scenario analysis
Lafratta, G. (2004) · Computational Statistics & Data Analysis · doi:10.1016/j.csda.2004.10.010 · Cited by 9
Research works printed but not linked: 2
- Colonnier M. (1981). The electron-microscopic analysis of the neuronal organization of the cerebral cortex. In The Organization of the Cerebral Cortex, Schmitt F. O. Worden F. G. Adelman G. Dennis S. G., eds (Cambridge, MA, MIT Press), pp. 125– 152
- Peters A. (1987). Synaptic specificity in the cerebral cortex. In Synaptic Function, Edelman G. M. Gall W. E. Cowan W. M., eds (New York, John Wiley), pp. 373– 397
Cited by
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Gidon, A., & Segev, I. (2012) · Neuron · doi:10.1016/j.neuron.2012.05.015 · Cited by 233
Synapse pathology in Alzheimer’s disease
Griffiths, J., & Grant, S. G. N. (2022) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2022.05.028 · Cited by 212
The Diversity of Cortical Inhibitory Synapses
Kubota, Y., Karube, F., Nomura, M., & Kawaguchi, Y. (2016) · Frontiers in Neural Circuits · doi:10.3389/fncir.2016.00027 · Cited by 180
From the Connectome to the Synaptome: An Epic Love Story
DeFelipe, J. (2010) · Science · doi:10.1126/science.1193378 · Cited by 169
The power of correlative microscopy: multi-modal, multi-scale, multi-dimensional
Caplan, J. L., Niethammer, M., Taylor, R. M., & Czymmek, K. J. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.06.010 · Cited by 165
Metadata
- Authors
- Merchan-Pérez, A.
- Venue
- Frontiers in Neuroanatomy
- Publisher
- Frontiers Media SA
- Published
- 2009
- Volume
- 3
- Pages
- 18-18
- ISSN
- 1662-5129 (ISSN-L)
- PMC
- PMC2784681
- OpenAlex
- W2063752629
- Cited by
- 191
- References
- 60
- Citations by year
- 2026: 5 · 2025: 7 · 2024: 10 · 2023: 4 · 2022: 10 · 2021: 13 · 2020: 15 · 2019: 9 · 2018: 17 · 2017: 12 · 2016: 12 · 2015: 19 · 2014: 12 · 2013: 17 · 2012: 10
- FWCI
- 5.56
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Frontiers in Neuroanatomy (publishedVersion, cc-by)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- École Polytechnique Fédérale de Lausanne
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Physical Sciences › Materials Science › General Materials Science › Advanced Materials Characterization Techniques
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Keywords
- FIB-SEM, 3D reconstruction, stereology, synapses, synaptic density, serial sectioning, neural circuits, transmission electron microscopy
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