  Fiber photometry permits monitoring fluorescent indicators of neural activity
in behaving animals. Optical fibers are typically used to excite and collect
fluorescence from genetically-encoded calcium indicators expressed by a subset
of neurons in a circuit of interest. However, a quantitative understanding of
the brain volumes from which signal is collected and how this depends on the
properties of the optical fibers are lacking. Here we analytically model and
experimentally measure the light emission and collection fields for optical
fibers in solution and scattering tissue, providing a comprehensive
characterization of fibers commonly employed for fiber photometry. Since
photometry signals depend on both excitation and collection efficiency, a
combined confocal/2-photon microscope was developed to evaluate these
parameters independently. We find that the 80% of the effective signal arises
from a 10^5-10^6 um3 volume extending ~200 um from the fiber face, and thus
permitting a spatial interpretation of measurements made with fiber photometry.
