Three-dimensional mapping of microcircuit correlation structure

R. James Cotton, Emmanouil Froudarakis, Patrick Storer, Peter Saggau, Andreas S. Tolias

Research output: Contribution to journalArticlepeer-review

48 Scopus citations


Great progress has been made toward understanding the properties of single neurons, yet the principles underlying interactions between neurons remain poorly understood. Given that connectivity in the neocortex is locally dense through both horizontal and vertical connections, it is of particular importance to characterize the activity structure of local populations of neurons arranged in three dimensions. However, techniques for simultaneously measuring microcircuit activity are lacking. We developed an in vivo 3D high-speed, random-access two-photon microscope that is capable of simultaneous 3D motion tracking. This allows imaging from hundreds of neurons at several hundred Hz, while monitoring tissue movement. Given that motion will induce common artifacts across the population, accurate motion tracking is absolutely necessary for studying population activity with random-access based imaging methods. We demonstrate the potential of this imaging technique by measuring the correlation structure of large populations of nearby neurons in the mouse visual cortex, and find that the microcircuit correlation structure is stimulus-dependent. Three-dimensional random access multiphoton imaging with concurrent motion tracking provides a novel, powerful method to characterize the microcircuit activity in vivo.

Original languageEnglish (US)
Article number151
JournalFrontiers in Neural Circuits
Issue numberOCT
StatePublished - Oct 10 2013
Externally publishedYes


  • Acousto-optical defiectors
  • Correlation structure
  • Microcircuit activity
  • Motion-tracking
  • Population coding
  • Two-photon imaging

ASJC Scopus subject areas

  • Neuroscience (miscellaneous)
  • Sensory Systems
  • Cognitive Neuroscience
  • Cellular and Molecular Neuroscience


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