Collecting 3D ED data manually is a time-consuming process, while sample sizes are often too small to represent the bulk sample, and minor phases may go undetected. High-throughput collection allows data to be collected on several hundreds of crystals per day, allowing phase analysis and structure determination of new crystal phases directly. In traditional 3D ED data collection, the user tends to pick crystals of well-defined morphology for data collection, because these are mostly likely to diffract well. High throughput data collection protocol provided the opportunity to minimize bias in crystal picking. Furthermore, by collecting data in batch mode, the operating time of the user is much shorter. The actual 3D ED data collection is automated and can run for several hours without supervision.