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 with embryos between 1.5-2.5 hpf and ended with embryos between 11.5-12.5 hpf. Images of embryos were acquired at 241 acquisition time points with a time interval of 150 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.