The data comprises bright-field time-lapse images of zebrafish embryos acquired in multiple batches within multi-well plates using an Acquifer Imaging Machine. Embryos from a cross of Tg(sebox:EGFP) and TE zebrafish strains were used for imaging. Images of embryos were acquired at 30 acquisition time points with a time interval of 5:00 minutes between each acquisition time point from approximately 2.5 to 5 hours post fertilization. Individual embryo segments were identified and extracted using a trained neural network for object detection. Within this experiment folder, data are organized by microscope position and embryo number.