Long-Term Optical Access to an Estimated One Million Neurons in the Live Mouse Cortex

Abstract

SUMMARY A major technological goal in neuroscience is to enable the interrogation of individual cells across the live brain. By creating a curved glass replacement to the dorsal cranium and surgical methods for its installation, we developed a chronic mouse preparation providing optical access to an estimated 800,000–1,100,000 individual neurons across the dorsal surface of neocortex. Post-surgical histological studies revealed comparable glial activation as in control mice. In behaving mice expressing a Ca2+ indicator in cortical pyramidal neurons, we performed Ca2+ imaging across neocortex using an epi-fluorescence macroscope and estimated that 25,000–50,000 individual neurons were accessible per mouse across multiple focal planes. Two-photon microscopy revealed dendritic morphologies throughout neocortex, allowed time-lapse imaging of individual cells, and yielded estimates of >1 million accessible neurons per mouse by serial tiling. This approach supports a variety of optical techniques and enables studies of cells across >30 neocortical areas in behaving mice.

Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data

“…Data type (2). For this dataset we imaged adult Thy1-jRGECO1a mice (line GP8.20, purchased from Jackson Labs) (41).…”

Differential encoding in prefrontal cortex projection neuron classes across cognitive tasks

“…In recent years, technological advances in generating high-dimensional transcriptomic data from dissociated cells is complemented by advances in spatially-resolved transcriptomics (Lein et al, 2017;Chen et al, 2015;Wang et al, 2018), single-neuron morphological reconstructions, wide-field 2-photon Ca 2+ imaging (Kim et al, 2016;Sofroniew et al, 2016), and highly multiplexed neurophysiology recordings (Jun et al, 2017). A future systems-level understanding of the brain requires integrating these multimodal data into a common framework.…”

Ultrawidefield microscope for high-speed fluorescence imaging and targeted optogenetic stimulation

“…For instance, the FOV readily encompasses the entire body of a zebrafish embryo, enabling intra-vital Ca 2+ imaging [41]. The high light collection efficiency could be used to enhance sensitivity in wide-field Ca 2+ [42] and voltage [43] brain imaging applications. Patterned illumination at 405 nm wavelength can activate a variety of photochemical reactions, including activation of azobenzene-based crosslinkers and photoconversion of switchable fluorescent proteins.…”