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 crosses of Tg(sebox:EGFP) and Tg(gsc:TurboRFP) zebrafish strains were used for imaging. Imaging started with embryos between 3.75-4 hpf and ended with embryos between 28.75-29 hpf. Images of embryos were acquired at 300 acquisition time points with a time interval of 300 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.