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Here we provide quick run through example for training and picking with crYOLO. The main purpose is to check if your setup is running as expected. I will not provide detailed explanations in this text. Please note that there is a detailed tutorial.
We run this example on a machine with the following specification:
You can download the reference data (TcdA1) here:
Then unzip the data:
unzip toxin_reference.zip -d toxin_reference/ cd toxin_reference
toxin_reference directory contains multiple folders / files:
Before you start training / picking please activate your environment:
source activate cryolo
The training is done with this command:
cryolo_train.py -c config_phosnet.json -w 5 -e 5 -g 0
It needes 5 minutes 50 seconds to converge (5 warmup + 10 “normal” epochs). The best validation loss was 0.03042. These numbers might be a little bit different on your case.
cryolo_predict.py -c config_phosnet.json -w model.h5 -i unseen_examples/ -o my_results
It picked 1617 particles on 12 micrographs in 3 seconds. Including filtering the image and loading the model the command needed 38 seconds.
cryolo_boxmanager.py -i unseen_examples/ -b my_results/CBOX/