Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Resource
  • Published:

A comprehensive thalamocortical projection map at the mesoscopic level

Nature Neuroscience volume 17, pages 1276–1285 (2014)Cite this article

Subjects

An Author Correction to this article was published on 24 March 2021

This article has been updated

Abstract

The thalamus relays sensori-motor information to the cortex and is an integral part of cortical executive functions. The precise distribution of thalamic projections to the cortex is poorly characterized, particularly in mouse. We employed a systematic, high-throughput viral approach to visualize thalamocortical axons with high sensitivity. We then developed algorithms to directly compare injection and projection information across animals. By tiling the mouse thalamus with 254 overlapping injections, we constructed a comprehensive map of thalamocortical projections. We determined the projection origins of specific cortical subregions and verified that the characterized projections formed functional synapses using optogenetic approaches. As an important application, we determined the optimal stereotaxic coordinates for targeting specific cortical subregions and expanded these analyses to localize cortical layer–preferential projections. This data set will serve as a foundation for functional investigations of thalamocortical circuits. Our approach and algorithms also provide an example for analyzing the projection patterns of other brain regions.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Systematic mapping of fluorescently labeled thalamocortical projections using high-throughput, high-resolution imaging.
Figure 2: Assessment of variability across brains, atlas alignment and injection coverage of the thalamus.
Figure 3: Localization of the thalamic origins of cortical projections.
Figure 4: Localizing thalamic subdivisions on the basis of cortical projection patterns.
Figure 5: Targeting anatomically defined thalamocortical projections to verify that they form functional synapses.
Figure 6: Nuclear localization of the thalamic origins of frontal projections.
Figure 7: Cortical layer preferences of thalamic projections to vM1.

Similar content being viewed by others

Change history

References

  1. Bohland, J.W. et al. A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale. PLoS Comput. Biol. 5, e1000334 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  2. Luo, L., Callaway, E.M. & Svoboda, K. Genetic dissection of neural circuits. Neuron 57, 634–660 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Lichtman, J.W. & Denk, W. The big and the small: challenges of imaging the brain's circuits. Science 334, 618–623 (2011).

    Article  CAS  PubMed  Google Scholar 

  4. Jones, E.G. The Thalamus, 2 Volume Set (Cambridge University Press, 2007).

  5. Sherman, S.M. & Guillery, R.W. Exploring the Thalamus and Its Role in Cortical Function (MIT Press, Massachusetts, 2009).

  6. Groenewegen, H.J., Berendse, H.W., Wolters, J.G. & Lohman, A.H. The anatomical relationship of the prefrontal cortex with the striatopallidal system, the thalamus and the amygdala: evidence for a parallel organization. Prog. Brain Res. 85, 95–118 (1990).

    Article  CAS  PubMed  Google Scholar 

  7. Evarts, E.V. & Thach, W.T. Motor mechanisms of the CNS: cerebrocerebellar interrelations. Annu. Rev. Physiol. 31, 451–498 (1969).

    Article  CAS  PubMed  Google Scholar 

  8. Steriade, M. & Llinás, R.R. The functional states of the thalamus and the associated neuronal interplay. Physiol. Rev. 68, 649–742 (1988).

    Article  CAS  PubMed  Google Scholar 

  9. Asanuma, H. & Fernandez, J.J. Organization of projection from the thalamic relay nuclei to the motor cortex in the cat. Brain Res. 71, 515–522 (1974).

    Article  CAS  PubMed  Google Scholar 

  10. Nauta, W.J. The problem of the frontal lobe: a reinterpretation. J. Psychiatr. Res. 8, 167–187 (1971).

    Article  CAS  PubMed  Google Scholar 

  11. Kolb, B. Studies on the caudate-putamen and the dorsomedial thalamic nucleus of the rat: implications for mammalian frontal-lobe functions. Physiol. Behav. 18, 237–244 (1977).

    Article  CAS  PubMed  Google Scholar 

  12. Weinberger, D.R. A connectionist approach to the prefrontal cortex. J. Neuropsychiatry Clin. Neurosci. 5, 241–253 (1993).

    Article  CAS  PubMed  Google Scholar 

  13. Berman, A.L. & Jones, E.G. The Thalamus and Basal Telencephalon of the Cat (University of Wisconsin Press, 1982).

  14. Walker, A.E. The Primate Thalamus (University of Chicago Press, 1938).

  15. Bota, M., Dong, H.W. & Swanson, L.W. Combining collation and annotation efforts toward completion of the rat and mouse connectomes in BAMS. Front. Neuroinform. 6, 2 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Mao, T. et al. Long-range neuronal circuits underlying the interaction between sensory and motor cortex. Neuron 72, 111–123 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Harris, J.A., Oh, S.W. & Zeng, H. Adeno-associated viral vectors for anterograde axonal tracing with fluorescent proteins in nontransgenic and Cre driver mice. Curr. Protoc. Neurosci. 1, 1.20.1–1.20.18 (2012).

    Google Scholar 

  18. McFarland, N.R., Lee, J.-S., Hyman, B.T. & McLean, P.J. Comparison of transduction efficiency of recombinant AAV serotypes 1, 2, 5, and 8 in the rat nigrostriatal system. J. Neurochem. 109, 838–845 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Aschauer, D.F., Kreuz, S. & Rumpel, S. Analysis of transduction efficiency, tropism and axonal transport of AAV serotypes 1, 2, 5, 6, 8 and 9 in the mouse brain. PLoS ONE 8, e76310 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Hoover, W.B. & Vertes, R.P. Anatomical analysis of afferent projections to the medial prefrontal cortex in the rat. Brain Struct. Funct. 212, 149–179 (2007).

    Article  PubMed  Google Scholar 

  21. Wang, Q. & Burkhalter, A. Area map of mouse visual cortex. J. Comp. Neurol. 502, 339–357 (2007).

    Article  PubMed  Google Scholar 

  22. Thompson, R.H. & Swanson, L.W. Hypothesis-driven structural connectivity analysis supports network over hierarchical model of brain architecture. Proc. Natl. Acad. Sci. USA 107, 15235–15239 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Otsu, N. A threshold selection method from gray-level histograms. IEEE Trans. Syst. Man. Cybern. 9, 62–66 (1975).

    Article  Google Scholar 

  24. Ragan, T. et al. Serial two-photon tomography for automated ex vivo mouse brain imaging. Nat. Methods 9, 255–258 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Paxinos, G. The Mouse Brain In Stereotaxic Coordinates (Academic Press, 2004).

  26. Knapska, E., Marcias, M. & Mikosz, M. Functional anatomy of neural circuits regulating fear and extinction. Proc. Natl. Acad. Sci. USA 109, 17093–17098 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Dantzker, J.L. & Callaway, E.M. Laminar sources of synaptic input to cortical inhibitory interneurons and pyramidal neurons. Nat. Neurosci. 3, 701–707 (2000).

    Article  CAS  PubMed  Google Scholar 

  28. Shepherd, G.M.G., Stepanyants, A., Bureau, I., Chklovskii, D. & Svoboda, K. Geometric and functional organization of cortical circuits. Nat. Neurosci. 8, 782–790 (2005).

    Article  CAS  PubMed  Google Scholar 

  29. Groenewegen, H.J. Organization of the afferent connections of the mediodorsal thalamic nucleus in the rat, related to the mediodorsal-prefrontal topography. Neuroscience 24, 379–431 (1988).

    Article  CAS  PubMed  Google Scholar 

  30. Ray, J.P. & Price, J.L. The organization of the thalamocortical connections of the mediodorsal thalamic nucleus in the rat, related to the ventral forebrain-prefrontal cortex topography. J. Comp. Neurol. 323, 167–197 (1992).

    Article  CAS  PubMed  Google Scholar 

  31. Lein, E.S. et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168–176 (2007).

    Article  CAS  PubMed  Google Scholar 

  32. Haque, T. et al. Thalamic afferent and efferent connectivity to cerebral cortical areas with direct projections to identified subgroups of trigeminal premotoneurons in the rat. Brain Res. 1346, 69–82 (2010).

    Article  CAS  PubMed  Google Scholar 

  33. Desbois, C. & Villanueva, L. The organization of lateral ventromedial thalamic connections in the rat: a link for the distribution of nociceptive signals to widespread cortical regions. Neuroscience 102, 885–898 (2001).

    Article  CAS  PubMed  Google Scholar 

  34. Berendse, H.W. & Groenewegen, H.J. Restricted cortical termination fields of the midline and intralaminar thalamic nuclei in the rat. Neuroscience 42, 73–102 (1991).

    Article  CAS  PubMed  Google Scholar 

  35. Vertes, R.P., Hoover, W.B. & Rodriguez, J.J. Projections of the central medial nucleus of the thalamus in the rat: node in cortical, striatal and limbic forebrain circuitry. Neuroscience 219, 120–136 (2012).

    Article  CAS  PubMed  Google Scholar 

  36. Van der Werf, Y.D., Witter, M.P. & Groenewegen, H.J. The intralaminar and midline nuclei of the thalamus. Anatomical and functional evidence for participation in processes of arousal and awareness. Brain Res. Brain Res. Rev. 39, 107–140 (2002).

    Article  PubMed  Google Scholar 

  37. Hooks, B.M. et al. Organization of cortical and thalamic input to pyramidal neurons in mouse motor cortex. J. Neurosci. 33, 748–760 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Hintiryan, H. et al. Comprehensive connectivity of the mouse main olfactory bulb: analysis and online digital atlas. Front. Neuroanat. 6, 30 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  39. Oh, S.W. et al. A mesoscale connectome of the mouse brain. Nature 508, 207–214 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Zingg, B. et al. Neural networks of the mouse neocortex. Cell 156, 1096–1111 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Spear, L.P. The adolescent brain and age-related behavioral manifestations. Neurosci. Biobehav. Rev. 24, 417–463 (2000).

    Article  CAS  PubMed  Google Scholar 

  42. Van Eden, C.G. & Uylings, H.B. Postnatal volumetric development of the prefrontal cortex in the rat. J. Comp. Neurol. 241, 268–274 (1985).

    Article  CAS  PubMed  Google Scholar 

  43. Casey, B.J., Getz, S. & Galvan, A. The adolescent brain. Dev. Rev. 28, 62–77 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Kolmac, C.I. & Mitrofanis, J. Organization of the reticular thalamic projection to the intralaminar and midline nuclei in rats. J. Comp. Neurol. 377, 165–178 (1997).

    Article  CAS  PubMed  Google Scholar 

  45. Dice, L.R. Measures of the amount of ecologic association between species. Ecology 26, 297–302 (1945).

    Article  Google Scholar 

  46. Petreanu, L., Mao, T., Sternson, S.M. & Svoboda, K. The subcellular organization of neocortical excitatory connections. Nature 457, 1142–1145 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Watson, C., Paxinos, G. & Puelles, L. The Mouse Nervous System (Academic Press, 2012).

Download references

Acknowledgements

All Nanozoomer images were collected in Janelia Farm Research Campus. We thank C. Mello, M. Qin, J. Qiu, J. Li, S.K. Petrie, A. Gilmore, Y. Zuo and D. Lioy for technical support. We thank K. Svoboda, J. Lichtman, K. Huang and B. Li for their discussions, and K. Svoboda, J. Williams and J. Adelman for comments on the manuscript. We thank R. Champieux and K. Banerjee for establishing the web data depository. We thank K. Svoboda and HHMI, Janelia Farm Research Campus for their generous support in the initiation and data collection phase of this project. This work was supported by an American Recovery and Reinvestment Act grant (P30 NS069305, R. Goodman), a National Science Foundation Graduate Research Fellowship Program fellowship (B.J.H.), Achievement Rewards for College Scientists Foundation Portland Chapter (B.J.H.), a US National Institutes of Health Director's Innovator Award (DP2 OD008425, H.Z.), a US National Institutes of Health R01 grant (R01 NS081071, T.M.) and the Medical Research Foundation (T.M.).

Author information

Author notes

  1. Brian R Long

    Present address: Present address: Allen Institute for Brain Science, Seattle, Washington, USA.,

  2. Barbara J Hunnicutt and Brian R Long: These authors contributed equally to the work.

Authors and Affiliations

  1. Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA

    Barbara J Hunnicutt, Brian R Long, Deniz Kusefoglu, Katrina J Gertz, Haining Zhong & Tianyi Mao

Authors
  1. Barbara J Hunnicutt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Brian R Long
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Deniz Kusefoglu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Katrina J Gertz
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Haining Zhong
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Tianyi Mao
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

All of the authors participated in designing the experiments. B.J.H., D.K., K.J.G. and T.M. performed the experiments. B.J.H., B.R.L., K.J.G., D.K., H.Z. and T.M. analyzed the data. B.J.H., B.R.L., K.J.G., H.Z. and T.M. wrote the manuscript.

Corresponding authors

Correspondence to Haining Zhong or Tianyi Mao.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–14 and Supplementary Table 1 (PDF 4872 kb)

Supplementary Methods Checklist (PDF 357 kb)

Full confidence maps as 3D stacks for AI.

Distance from bregma for each section is indicated. All scale bars are 1 mm. (AVI 1649 kb)

Full confidence maps as 3D stacks for LO.

Distance from bregma for each section is indicated. All scale bars are 1 mm. (AVI 1602 kb)

Full confidence maps as 3D stacks for VO.

Distance from bregma for each section is indicated. All scale bars are 1 mm. (AVI 1592 kb)

Full confidence maps as 3D stacks for MO.

Distance from bregma for each section is indicated. All scale bars are 1 mm. (AVI 1596 kb)

Full confidence maps as 3D stacks for IL.

Distance from bregma for each section is indicated. All scale bars are 1 mm. (AVI 1589 kb)

Full confidence maps as 3D stacks for PrL.

Distance from bregma for each section is indicated. All scale bars are 1 mm. (AVI 1616 kb)

Full confidence maps as 3D stacks for vACC.

Distance from bregma for each section is indicated. All scale bars are 1 mm. (AVI 1620 kb)

Full confidence maps as 3D stacks for dACC.

Distance from bregma for each section is indicated. All scale bars are 1 mm. (AVI 1632 kb)

Full confidence maps as 3D stacks for FrA.

Distance from bregma for each section is indicated. All scale bars are 1 mm. (AVI 1683 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hunnicutt, B., Long, B., Kusefoglu, D. et al. A comprehensive thalamocortical projection map at the mesoscopic level. Nat Neurosci 17, 1276–1285 (2014). https://doi.org/10.1038/nn.3780

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nn.3780

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing