A lightweight segmentation and lineage tracking tool for noisy, low frame rate 4D fluorescence microscopy data

4D fluorescence microscopy allows the study of spatiotemporal cell dynamics in embryonic development in unprecedented detail, yet the uneven scattering of light within developing embryos presents challenges in discerning fine details. We present a tool which pre-processes large in vivo 4D microscopy datasets and can then track the movements and lineage histories of rapidly dividing embryonic stem cells. This solution offers a robust, simple segmentation technique to segment high intensity fluorescent features in highly scattered datasets, such as from deep within a developing zebrafish embryo. This tool then offers lineage tracing functionality by tracking rapidly dividing nuclei and their progeny, while also accounting for the jumps rapidly moving features make between frames in low frame rate data. Based on the user having prior knowledge of their imaging subject, this tool has applications in datasets with limitations with signal to noise, and frame rate. It can provide information regarding the position and movement of rapidly dividing nuclei. We demonstrate this pipeline in developing early zebrafish embryos.