Calcium imaging has emerged as a powerful tool for studying cellular dynamics, with applications spanning neuroscience, cell biology, and beyond. In this chapter, we present a comprehensive guide to the computational analysis of calcium flux data using the R programming language. Using an example of in vivo live imaging of GCaMP signal in zebrafish hepatocytes, we demonstrate techniques for segmentation, normalization, and quantification of calcium transients. We provide a step-by-step code example showcasing extraction of meaningful information from calcium imaging datasets. The code allows insights into the number of oscillating cells, number of oscillations per cell within a time frame, and generation of publication-ready plots for showcasing calcium dynamics. This chapter serves as a valuable resource for researchers seeking to leverage freely available computational tools for analyzing calcium flux data at cellular resolution and uncovering novel insights into cellular physiology.