CAVE: An Open-Source Tool for Combined Analysis of Head-Mounted Calcium Imaging and Behavior in MATLAB

Calcium imaging in freely behaving rodents using head-mounted miniature microscopes is currently becoming an increasingly popular technique in neuroscience. Due to the large amounts of complex data that the technique produces, user friendly software is needed for quick and efficient processing. Here, we present a new tool for analyzing calcium imaging data from head-mounted microscopes together with simultaneously acquired behavioral data: CAVE (Calcium ActiVity Explorer). CAVE bundles a unique set of algorithms specifically tailored to the analysis of single-photon imaging data from awake behaving animals including efficient motion correction and automatic ROI selection with manual audit and refinement. For behavioral analysis, CAVE can automatically track animal position and orientation. Individual behavioral epochs and external events can then be analyzed in correlation to calcium imaging and tracking data. Our program is written in MATLAB, the source code is open source and particularly focuses on providing a streamlined workflow for novice users while also retaining detailed configuration options for advanced users. We evaluate the performance of CAVE by investigating neural activity in hippocampus and somatosensory cortex. The fast analysis provided by CAVE allowed us to track activity in a large set of animals over the course of several months during exploration behavior, detailing the properties of onset and offset of observable activity and the visible cells per imaging location

SMART IMAGE-GUIDED NEEDLE INSERTION FOR TISSUE BIOPSY

M.S

Non-inertial Undulatory Locomotion Across Scales

Locomotion is crucial to behaviors such as predator avoidance, foraging, and mating. In particular, undulatory locomotion is one of the most common forms of locomotion. From microscopic flagellates to swimming fish and slithering snakes, this form of locomotion is a remarkably robust self-propulsion strategy that allows a diversity of organisms to navigate myriad environments. While often thought of as exclusive to limbless organisms, a variety of locomotors possessing few to many appendages rely on waves of undulation for locomotion. In inertial regimes, organisms can leverage the forces generated by their body and the surrounding medium's inertia to enhance their locomotion (e.g., coast or glide). On the other hand, in non-inertial regimes self-propulsion is dominated by damping (viscous or frictional), and thus the ability for organisms to generate motion is dependent on the sequence of internal shape changes. In this thesis, we study a variety of undulating systems that locomote in highly damped regimes. We perform studies on systems ranging from zero to many appendages. Specifically, we focus on four distinct undulatory systems: 1) C. elegans, 2) quadriflagellate algae (bearing four flagella), 3) centipedes on terrestrial environments, and 4) centipedes on fluid environments. For each of these systems, we study how the coordination of their many degrees of freedom leads to specific locomotive behaviors. Further, we propose hypotheses for the observed behaviors in the context of each of these system's ecology.Ph.D