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Imaging, Specimen Preparation

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Encyclopedia of Computational Neuroscience

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Before specimens can be imaged for analysis using computational neuroanatomy techniques, they must be properly prepared. Computational neuroanatomy encompasses a wide range of analysis, and correspondingly, a wide range of specimens can be analyzed. This discussion will focus on the preparation of specimens for high-throughput 3D microscopy technologies that are being rapidly developed. Methodologies that emphasize 3D molecular and morphological imaging, including ultrahigh-resolution electron microscopy imaging, provide complementary perspectives that can be applied to computational neuroanatomy. Through such analyses, it is possible to carry out detailed descriptions of local circuits that will help further elucidate neuronal function. These microscopy technologies together with high-performance computing power that continue to be improved enable data-driven, multi-scale modeling and simulation of large-scale neuronal circuits (such as the complete connectome of the mouse...

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References

  • Carson FL, Hladik C (2009) Histotechnology – a self-instructional text, 3rd edn. ASCP Press, Hong Cong

    Google Scholar 

  • Choe Y, Mayerich D, Kwon J, Miller DE, Sung C, Chung JR et al (2011) Specimen preparation, imaging, and analysis protocols for knife-edge scanning microscopy. J Vis Exp 58:e3248. doi:10.3791/3248

    Google Scholar 

  • Gage GJ, Kipke DR, Shain W (2012) Whole animal perfusion fixation for rodents. J Vis Exp 65:e3564. doi:10.3791/3564

    Google Scholar 

  • Jaeger D (2001) Chapter 6. Accurate reconstruction of neuronal morphology. In: De Schutter E (ed) Computational neuroscience: realistic modeling for experimentalists. CRC Press, Boca Raton, pp 159–178

    Google Scholar 

  • Kleinfeld D, Bharioke A, Blinder P, Bock DD, Briggman KL, Chklovskii DB, Denk W, Helmstaedter M, Kaufhold JP, Lee WC, Meyer HS, Micheva KD, Oberlaender M, Prohaska S, Reid RC, Smith SJ, Takemura S, Tsai PS, Sakmann B (2011) Large-scale automated histology in the pursuit of connectomes. J Neurosci 31(45):16125–16138. doi:10.1523/JNEUROSCI.4077-11

    PubMed Central  CAS  PubMed  Google Scholar 

  • Luby-Phelps K, Ning G, Fogerty J, Besharse JC (2003) Visualization of identified GFP-expressing cells by light and electron microscopy. J Histochem Cytochem 51(3):271–274

    CAS  PubMed  Google Scholar 

  • Mayerich D, Abbott LC, McCormick B (2008a) Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain. J Microsc 231(1):134–143

    CAS  PubMed  Google Scholar 

  • Mayerich D, Abbott LC, Keyser J (2008b) Visualization of cellular and microvascular relationships. IEEE Trans Vis Comput Graph 14(6):1611–1618, Art. No. 4658182

    PubMed  Google Scholar 

  • Mikula S, Binding J, Denk W (2012) Staining and embedding the whole mouse brain for electron microscopy. Nat Methods 12:1198–1201. doi:10.1038/nmeth.2213 (Epub 21 Oct 2012)

    Google Scholar 

  • Senda T, Iizuka-Kogo A, Shimomura A (2005) Visualization of the nuclear lamina in mouse anterior pituitary cells and immunocytochemical detection of lamin A/C by quick-freeze freeze-substitution electron microscopy. J Histochem Cytochem 53(4):497–507

    CAS  PubMed  Google Scholar 

  • Tapia JC, Kasthuri N, Hayworth KJ, Schalek R, Lichtman JW, Smith SJ, Buchanan J (2012) High-contrast en bloc staining of neuronal tissue for field emission scanning electron microscopy. Nat Protoc 7(2):193–206. doi:10.1038/nprot.2011.439

    PubMed Central  CAS  PubMed  Google Scholar 

Further Reading

  • De Schutter E (ed) (2001) Computational neuroscience: realistic modeling for experimentalists. CRC Press, Boca Raton

    Google Scholar 

  • Helmstaedter M, Briggman KL, Denk W (2011) High-accuracy neurite reconstruction for high-throughput neuroanatomy. Nat Neurosci 14(8):1081–1088. doi:10.1038/nn.2868

    CAS  PubMed  Google Scholar 

  • Lichtman JW, Denk W (2011) The big and the small: challenges of imaging the brain’s circuits [Review]. Science 334(6056):618–623. doi:10.1126/science.1209168

    CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA

    Louise C. Abbott

Authors
  1. Louise C. Abbott
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Corresponding author

Correspondence to Louise C. Abbott .

Editor information

Editors and Affiliations

  1. Department of Biology, Emory University, Atlanta, GA, USA

    Dieter Jaeger

  2. Department of Biomedical Engineering, Florida International University, Miami, FL, USA

    Ranu Jung

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Abbott, L.C. (2015). Imaging, Specimen Preparation. In: Jaeger, D., Jung, R. (eds) Encyclopedia of Computational Neuroscience. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6675-8_283

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