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You can now use the model weights file (e.g. model.h5 in training from scratch or gmodel_phosnet_X_Y.h5 when using the general model) to pick all your images in the directory full_data. To do this, run:

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

You will find the picked particles in the directory boxfiles.

If you want to pick less conservatively or more conservatively you might want to change the selection threshold from the default of 0.3 to a less conservative value like 0.2 or more conservative value like 0.4 using the -t parameter:

cryolo_predict.py -c config.json -w model.h5 -i full_data/ -g 0 -o boxfiles/ -t 0.2

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