Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 1,023

The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.

Long-term, high-resolution imaging in the mouse neocortex through a chronic cranial window

Open access
Holtmaat, Anthony, Bonhoeffer, Tobias, Chow, David K, Chuckowree, Jyoti, De Paola, Vincenzo, Hofer, Sonja B, Hübener, Mark, Keck, Tara, Knott, Graham, Lee, Wei-Chung A, Mostany, Ricardo, Mrsic-Flogel, Tom D, Nedivi, Elly, Portera-Cailliau, Carlos, Svoboda, Karel, Trachtenberg, Joshua T, Wilbrecht, Linda·2009·Nature Protocols
DOI 10.1038/nprot.2009.89
Open this paper in CoChat — free account

Abstract

To understand the cellular and circuit mechanisms of experience-dependent plasticity, neurons and their synapses need to be studied in the intact brain over extended periods of time. Two-photon excitation laser scanning microscopy (2PLSM), together with expression of fluorescent proteins, enables high-resolution imaging of neuronal structure in vivo. In this protocol we describe a chronic cranial window to obtain optical access to the mouse cerebral cortex for long-term imaging. A small bone flap is replaced with a coverglass, which is permanently sealed in place with dental acrylic, providing a clear imaging window with a large field of view (∼0.8–12 mm2). The surgical procedure can be completed within ∼1 h. The preparation allows imaging over time periods of months with arbitrary imaging intervals. The large size of the imaging window facilitates imaging of ongoing structural plasticity of small neuronal structures in mice, with low densities of labeled neurons. The entire dendritic and axonal arbor of individual neurons can be reconstructed.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/nprot.2009.89

Cites

21 of 21 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 21 references

Research works printed but not linked: 31

  1. Denk, W., Strickler, J.H. & Webb, W.W. Two-photon laser scanning microscopy. Science 248, 73–76 (1990). · DOI · Paper page
  2. Gray, N.W., Weimer, R.M., Bureau, I. & Svoboda, K. Rapid redistribution of synaptic PSD-95 in the neocortex in vivo . PloS. Biol. 4, 2065–2075 (2006). · DOI · Paper page
  3. Feng, G. et al. Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP. Neuron 28, 41–51 (2000). · DOI · Paper page
  4. De Paola, V., Arber, S. & Caroni, P. AMPA receptors regulate dynamic equilibrium of presynaptic terminals in mature hippocampal networks. Nat. Neurosci. 6, 491–500 (2003). · DOI · Paper page
  5. Tsien, R.Y. The green fluorescent protein. Annu. Rev. Biochem. 67, 509–544 (1998). · DOI · Paper page
  6. Miyawaki, A. Innovations in the imaging of brain functions using fluorescent proteins. Neuron 48, 189–199 (2005). · DOI
  7. Mank, M. et al. A genetically encoded calcium indicator for chronic in vivo two-photon imaging. Nat. Methods (2008). · DOI · Paper page
  8. Holtmaat, A.J. et al. Transient and persistent dendritic spines in the neocortex in vivo . Neuron 45, 279–291 (2005). · DOI · Paper page
  9. Holtmaat, A., Wilbrecht, L., Knott, G.W., Welker, E. & Svoboda, K. Experience-dependent and cell-type-specific spine growth in the neocortex. Nature 441, 979–983 (2006). · DOI · Paper page
  10. Keck, T. et al. Massive restructuring of neuronal circuits during functional reorganization of adult visual cortex. Nat. Neurosci. 11, 1162–1167 (2008). · DOI · Paper page
  11. Xu, H.T., Pan, F., Yang, G. & Gan, W.B. Choice of cranial window type for in vivo imaging affects dendritic spine turnover in the cortex. Nat. Neurosci. 10, 549–551 (2007). · DOI · Paper page
  12. Zuo, Y., Lin, A., Chang, P. & Gan, W.B. Development of long-term dendritic spine stability in diverse regions of cerebral cortex. Neuron 46, 181–189 (2005). · DOI · Paper page
  13. Majewska, A.K., Newton, J.R. & Sur, M. Remodeling of synaptic structure in sensory cortical areas in vivo . J. Neurosci. 26, 3021–3029 (2006). · DOI · Paper page
  14. Nishiyama, H., Fukaya, M., Watanabe, M. & Linden, D.J. Axonal motility and its modulation by activity are branch-type specific in the intact adult cerebellum. Neuron 56, 472–487 (2007). · DOI
  15. Brown, C.E., Aminoltejari, K., Erb, H., Winship, I.R. & Murphy, T.H. In vivo voltage-sensitive dye imaging in adult mice reveals that somatosensory maps lost to stroke are replaced over weeks by new structural and functional circuits with prolonged modes of activation within both the peri-infarct zone and distant sites. J. Neurosci. 29, 1719–1734 (2009). · DOI · Paper page
  16. Lee, W.C. et al. A dynamic zone defines interneuron remodeling in the adult neocortex. Proc. Natl. Acad. Sci. USA 105, 19968–19973 (2008). · DOI · Paper page
  17. Helmchen, F., Fee, M.S., Tank, D.W. & Denk, W. A miniature head-mounted two-photon microscope. High-resolution brain imaging in freely moving animals. Neuron 31, 903–912 (2001). · DOI · Paper page
  18. Flusberg, B.A., Jung, J.C., Cocker, E.D., Anderson, E.P. & Schnitzer, M.J. In vivo brain imaging using a portabler3. r3.9 gram two-photon fluorescence microendoscope. Opt. Lett. 30, 2272–2274 (2005). · DOI · Paper page
  19. Fuhrmann, M., Mitteregger, G., Kretzschmar, H. & Herms, J. Dendritic pathology in prion disease starts at the synaptic spine. J. Neurosci. 27, 6224–6233 (2007). · DOI
  20. Livneh, Y., Feinstein, N., Klein, M. & Mizrahi, A. Sensory input enhances synaptogenesis of adult-born neurons. J. Neurosci. 29, 86–97 (2009). · DOI
  21. Bridge, K.E. et al. Late onset distal axonal swelling in YFP-H transgenic mice. Neurobiol. Aging 30, 309–321 (2009). · DOI
  22. Fukuchi-Shimogori, T. & Grove, E.A. Neocortex patterning by the secreted signaling molecule FGF8. Science 294, 1071–1074 (2001). · DOI · Paper page
  23. Tabata, H. & Nakajima, K. Efficient in utero gene transfer system to the developing mouse brain using electroporation: visualization of neuronal migration in the developing cortex. Neuroscience 103, 865–872 (2001). · DOI · Paper page
  24. Dittgen, T. et al. Lentivirus-based genetic manipulations of cortical neurons and their optical and electrophysiological monitoring in vivo . Proc. Natl. Acad. Sci. USA 101, 18206–18211 (2004). · DOI · Paper page
  25. Mainen, Z.F. et al. Two-photon imaging in living brain slices. Methods 18, 231–239 (1999). · DOI · Paper page
  26. Shepherd, G.M. & Harris, K.M. Three-dimensional structure and composition of CA3--CA1 axons in rat hippocampal slices: implications for presynaptic connectivity and compartmentalization. J. Neurosci. 18, 8300–8310 (1998). · DOI · Paper page
  27. Pologruto, T.A., Sabatini, B.L. & Svoboda, K. ScanImage: flexible software for operating laser-scanning microscopes. Biomed. Eng. OnLine 2, 13 (2003). · DOI · Paper page
  28. Abbondanzieri, E.A., Shaevitz, J.W. & Block, S.M. Picocalorimetry of transcription by RNA polymerase. Biophys. J. 89, L61–63 (2005). · doi:10.1529/biophysj.105.074195
  29. Konur, S., Rabinowitz, D., Fenstermaker, V.L. & Yuste, R. Systematic regulation of spine sizes and densities in pyramidal neurons. J. Neurobiol. 56, 95–112 (2003). · DOI
  30. Hubener, M., Schwarz, C. & Bolz, J. Morphological types of projection neurons in layer 5 of cat visual cortex. J. Comp. Neurol. 301, 655–674 (1990). · DOI
  31. Graeber, M.B. et al. The microglia/macrophage response in the neonatal rat facial nucleus following axotomy. Brain Res. 813, 241–253 (1998). · DOI · Paper page

Cited by

See all 1,023

Metadata

Authors
Holtmaat, A., Bonhoeffer, T., Chow, D. K., Chuckowree, J., De Paola, V., Hofer, S. B., Hübener, M., Keck, T., Knott, G., Lee, W.-C. A., Mostany, R., Mrsic-Flogel, T. D., Nedivi, E., Portera-Cailliau, C., Svoboda, K., Trachtenberg, J. T., & Wilbrecht, L.
Venue
Nature Protocols
Publisher
Springer Science and Business Media LLC
Published
2009-07-16
Volume
4
Issue
8
Pages
1128-1144
ISSN
  • 1750-2799 (ISSN-L)
  • 1754-2189
DOI
10.1038/nprot.2009.89
OpenAlex
W1976485053
Cited by
1,023
References
21
FWCI
21.00
Type
journal article
Language
en
Open access
green
Licence
www.springer.com/tdm (tdm)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Long-term, high-resolution imaging in the mouse neocortex through a chronic cranial window. https://app.cochat.ai/papers/10.1038/nprot.2009.89
The paper
Holtmaat, A., Bonhoeffer, T., Chow, D. K., Chuckowree, J., De Paola, V., Hofer, S. B., Hübener, M., Keck, T., Knott, G., Lee, W.-C. A., Mostany, R., Mrsic-Flogel, T. D., Nedivi, E., Portera-Cailliau, C., Svoboda, K., Trachtenberg, J. T., & Wilbrecht, L. (2009). Long-term, high-resolution imaging in the mouse neocortex through a chronic cranial window. Nature Protocols. https://doi.org/10.1038/nprot.2009.89

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.