Supplementary Figure 1: Design and operation of the MPC-based tracking microscope.
From: Pan-neuronal calcium imaging with cellular resolution in freely swimming zebrafish
(a) 3-D rendering of the tracking microscope. (b) Design of behavior chamber wall with terraced layers of PDMS. The terraced design allows fluorescent light from the brain to reach the imaging objective (NA = 1.0) without obstruction. (c) A custom Model Predictive Control (MPC) implementation is used to keep the brain within the field of view of the DIFF microscope while the animal moves freely in the behavior arena. (d) Schematic of axial motion cancellation. During each piezo Z sweep (black line), each structured fluorescence image is analyzed in real-time to compute an estimate for its axial location (red line) within the targeted brain volume (red shaded region). Near the end of each sweep, the estimated axial brain position is used to adjust the range of the next piezo Z sweep to recenter the brain. (e) Example of closed-loop live Z tracking. As the targeted brain volume shifts axially (red line and shaded region), the piezo Z sweeps are adjusted to center the brain within the next axial sweep.
