In crYOLO, all particles have a assigned confidence value. By default, all particle with confidence value below 0.3 are discarded. If you want to pick less conservatively or more conservatively you might want to change this confidence threshold to a less conservative value like 0.2 or more conservative value like 0.4 in the “Optional arguments” tab. However, it is much easier to select the best threshold after picking using the CBOX files written by crYOLO as described in the next section.

cryolo_predict.py -c config.json -w cryolo_model.h5 -i full_data/ -g 0 -o boxfiles/