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 incrosses of Tg(sebox:EGFP) zebrafish strains were used for imaging. Imaging started at 4.5 hpf and ended at 28.5 hpf. Images of embryos were acquired at 720 acquisition time points with a time interval of 120 s between each acquisition time point. 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.