Protocol for imaging and quantitative analysis of yolk vesicle distribution and movement in syncytial Drosophila embryos

Drosophila embryos use maternally deposited yolk vesicles as their nutritional source during syncytial development. We present a protocol for imaging and quantifying yolk vesicle distribution and movement in mRFP-expressing embryos. We describe steps for imaging the embryo across nuclear division cycles, segmenting nuclei and yolk vesicles, and measuring density and size distribution. We detail procedures for analyzing cortical yolk vesicle movement with nuclei using particle image velocimetry and for quantifying net downward speed using particle tracking and a particle-conservation model. For complete details on the use and execution of this protocol, please refer to Thukral et al. 1