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Select the action “predict” and fill all arguments in the “Required arguments” tab:
In crYOLO, all particles have an assigned confidence value. By default, all particles with a confidence value below 0.3 are discarded. If you want to pick less or more conservatively you might want to change this confidence threshold to a less (e.g. 0.2) or more (e.g. 0.4) conservative value 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.
You will find the picked particles in your specified output directory.
Alternative: Run prediction from the command line
Alternative: Run prediction from the command line
To pick all your images in the directory full_data
with the model weight file cryolo_model.h5
(e.g. or gmodel_phosnet_X_Y.h5
when using the general model) and and a confidence threshold of 0.3 run::
cryolo_predict.py -c config.json -w cryolo_model.h5 -i full_data/ -g 0 -o boxfiles/ -t 0.3
You will find the picked particles in the directory boxfiles
.