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 TE zebrafish strains were used for imaging. Imaging started at 2.25 hpf and ended at 26.5 hpf. Images of embryos were acquired at 580 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.