Miniature Microscopes

Cellular resolution optical imaging in behaving animals is a foundational method in modern neuroscience. Two primary approaches are taken – either two-photon imaging in head-fixed animals[1], or single photon imaging in freely moving animals through the use of a head mounted miniature fluorescence microscope [2-5] (“miniscope”). For some important studies, the latter is the only option compatible with natural behavior. One example is undirected singing in songbirds – a learning-intensive form of song practice in the zebra finch species that has not been possible to record in head-fixed birds.

Existing commercially-available miniscopes have been adopted by many labs, and have enabled exciting new science [6-11], but these devices still lack a number of desirable features such as user-configurability, wireless interfacing, color sensors, and low cost. To address the limitations of commercially available solutions, we developed an open source miniscope (Fig. 1) featuring a number of innovations including 3D printed housing for easy reconfiguration, wireless telemetry, and color CMOS sensors. In parallel we have developed software and hardware for controlling the device, as well as motorized commutators and flex cables for ultralight tethering in mice and small songbirds. This microscope has been extensively tested in songbirds in our laboratory, and has yielded high quality calcium signals with single neuron resolution in singing birds.

Figure 1. A custom head-mounted fluorescence and stereotyped single neuron calcium traces in singing birds. A, Calcium traces from 22 ROIs over 50 song-aligned trials in a single bird. B, Schematic of a 3D printed miniature head-mounted fluorescent microscope. C, Photograph of the 3D printed microscope.