Deep Learning-Based Cell Tracking in Deforming Organs and Moving Animals.

Cell tracking is an essential step in extracting cellular signals from moving cells, which is vital for understanding the mechanisms underlying various biological functions and processes, particularly in organs such as the brain and heart. However, cells in living organisms often exhibit extensive and complex movements caused by organ deformation and whole-body motion. These movements pose a challenge in obtaining high-quality time-lapse cell images and tracking the intricate cell movements in the captured images. Recent advances in deep learning techniques provide powerful tools for detecting cells in low-quality images with densely packed cell populations, as well as estimating cell positions for cells undergoing large nonrigid movements. This chapter introduces the challenges of cell tracking in deforming organs and moving animals, outlines the solutions to these challenges, and presents a detailed protocol for data preparation, as well as for performing cell segmentation and tracking using the latest version of 3DeeCellTracker. This protocol is expected to enable researchers to gain deeper insights into organ dynamics and biological processes.