| Summary: | The advent of multi-photon microscopes and highly sensitive protein sensors enables the recording of astrocyte activities on a large population of cells over a long-time period in vivo. Existing tools cannot fully characterize these activities, both within single cells and at the population-level, because of the insufficiency of current region-of-interest-based approaches to describe the activity that is often spatially unfixed, size-varying, and propagative. Here, we present Astrocyte Quantitative Analysis (AQuA), an analytical framework that releases astrocyte biologists from the ROI-based paradigm. The framework takes an event-based perspective to model and accurately quantify the complex activity in astrocyte imaging datasets, with an event defined jointly by its spatial occupancy and temporal dynamics. To model the signal propagation in astrocyte, we developed graphical time warping (GTW) to align curves with graph-structured constraints and integrated it into AQuA. To make AQuA easy to use, we designed a comprehensive software package. The software implements the detection pipeline in an intuitive step by step GUI with visual feedback. The software also supports proof-reading and the incorporation of morphology information. With synthetic data, we showed AQuA performed much better in accuracy compared with existing methods developed for astrocytic data and neuronal data. We applied AQuA to a range of ex vivo and in vivo imaging datasets. Since AQuA is data-driven and based on machine learning principles, it can be applied across model organisms, fluorescent indicators, experimental modes, and imaging resolutions and speeds, enabling researchers to elucidate fundamental astrocyte physiology. === Doctor of Philosophy === Astrocyte is an important type of glial cell in the brain. Unlike neurons, astrocyte cannot be electrically excited. However, the concentrations of many different molecules inside and near astrocytes change over space and time and show complex patterns. Recording, analyzing, and deciphering these activity patterns enables the understanding of various roles astrocyte may play in the nervous system. Many of these important roles, such as sensory-motor integration and brain state modulation, were traditionally considered the territory of neurons, but recently found to be related to astrocytes. These activities can be monitored in the intracellular and extracellular spaces in either brain slices and living animals, thanks to the advancement of microscopes and genetically encoded fluorescent sensors. However, sophisticated analytical tools lag far behind the impressive capability of generating the data. The major reason is that existing tools are all based on the region-of-interest-based (ROI) approach. This approach assumes the field of view can be segmented to many regions, and all pixels in the region should be active together. In neuronal activity analysis, all pixels in an ROI (region of interest) correspond to a neuron and are assumed to share a common activity pattern (curve). This is not true for astrocyte activity data because astrocyte activities are spatially unfixed, size-varying, and propagative. In this dissertation, we developed a framework called AQuA to detect the activities directly. We designed an accurate and flexible detection pipeline that works with different types of astrocyte activity data sets. We designed a machine learning model to characterize the signal propagation for the pipeline. We also implemented a compressive and user-friendly software package. The advantage of AQuA is confirmed in both simulation studies and three different types of real data sets.
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