Simultaneous mesoscopic and two-photon imaging of neuronal activity in cortical circuits

Abstract

Spontaneous and sensory-evoked activity propagates across varying spatial scales in the mammalian cortex, but technical challenges have limited conceptual links between the function of local neuronal circuits and brain-wide network dynamics. We present a method for simultaneous cellular-resolution two-photon calcium imaging of a local microcircuit and mesoscopic widefield calcium imaging of the entire cortical mantle in awake mice. Our multi-scale approach employs an orthogonal axis design where the mesoscopic objective is oriented above the brain and the twophoton objective is oriented horizontally, with imaging performed through a microprism. We also introduce a viral method for robust and widespread gene delivery in the mouse brain. These approaches allow us to identify the behavioral state-dependent functional connectivity of pyramidal neurons and vasoactive intestinal peptide (VIP)-expressing interneurons with long-Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI

“…The resulting signal constitutes a cell type-specific measurement of activity as Ca 2+ sensors can be genetically targeted ( 1 ). During mesoscopic imaging, neuropil is the dominant signal source ( 2 ). However, Ca 2+ imaging is limited to optically accessible tissue, and the expression of Ca 2+ indicators necessitates invasive manipulation of the nervous system, practically limiting its application to animal models.…”

The sensory representation of causally controlled objects

“…Having identified brain areas implicated in BMI control, we recorded spiking from individual units while animals performed the task, to investigate the task-dependent increase in calcium signals with cellular resolution. We chose to record from functionally identified area AM, due to its recruitment over learning, and used multi-channel silicon probes to record spikes from individual neurons while simultaneously imaging the rest of the dorsal cortex ( Figure 5 A; see Method Details ; Xiao et al., 2017 ; Clancy et al., 2019 ; Barson et al., 2020 ; Peters et al., 2019 ). We obtained 16–49 single units per recording, spanning all cortical layers.…”

“…To understand the relationship between the firing rate of individual neurons and dorsal cortex-wide activity, we correlated the spike trains of individual units with fluorescence activity across the brain to build affiliation maps for each unit ( Xiao et al., 2017 ; Clancy et al., 2019 ; Barson et al., 2020 ; Peters et al., 2019 ). We aligned these maps to the common coordinate framework of the Allen Brain Atlas using stereotaxic marks on the skull and sorted these maps by units’ preference for different cursor locations.…”

Flexible annotation atlas of the mouse brain: combining and dividing brain structures of the Allen Brain Atlas while maintaining anatomical hierarchy

“…Whole-brain imaging study with tissue-clearing techniques or a serial-sectioning imaging system would benefit from consistent and flexible ROIs provided by FAA, once registered to the Allen reference atlas 55 – 58 . Two-dimensional wide-field cortical imaging can also use FAA 59 – 62 through a flat-map projection of the Allen reference atlas 63 , 64 . FAA facilitates integration of these data with open source resources for which datasets are registered to the Allen Brain Atlas 65 , 66 , thereby promoting cellular level whole-brain investigation 67 .…”