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pipeline:window:cryolo:picking [2019/09/16 16:59] twagner |
pipeline:window:cryolo:picking [2020/03/16 15:24] twagner |
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- | {{ : | + | Select the action " |
+ | {{ : | ||
- | You can now use the model weights file (//e.g. '' | + | <note tip> |
- | <code> | + | **Adjusting confidence threshold** |
- | cryolo_predict.py -c config.json -w cryolo_model.h5 -i full_data/ -g 0 -o boxfiles/ | + | |
- | </ | + | |
- | You will find the picked | + | In crYOLO, all particles |
+ | However, it is much easier to select the best threshold after picking using the '' | ||
+ | </ | ||
- | If you want to pick less conservatively or more conservatively you might want to change | + | After picking is done, you can find four folders in your specified output folder: |
+ | * **CBOX:** Contains a coordinate file in .cbox format each input micrograph. It contains all detected particles, even those with a confidence lower the selected confidence | ||
+ | * **EMAN:** Contains a coordinate file in .box format each input micrograph. Only particles with the an confidence higher then the selected (default: 0.3) are contained in those files. | ||
+ | * **STAR:** Contains | ||
+ | * **DISTR:** Contains | ||
+ | |||
+ | |||
+ | < | ||
+ | <div style=" | ||
+ | < | ||
+ | </div> | ||
+ | </ | ||
+ | |||
+ | |||
+ | < | ||
+ | <div style=" | ||
+ | < | ||
+ | </div> | ||
+ | </ | ||
+ | |||
+ | <hidden initialState=" | ||
+ | To pick all your images in the directory '' | ||
< | < | ||
- | cryolo_predict.py -c config.json -w cryolo_model.h5 -i full_data/ -g 0 -o boxfiles/ -t 0.2 | + | cryolo_predict.py -c config.json -w cryolo_model.h5 -i full_data/ -g 0 -o boxfiles/ -t 0.3 |
</ | </ | ||
- | However, it is much easier to select | + | You will find the picked particles in the directory |
+ | </ | ||
+ | |||
+ | < | ||
+ | <div style=" | ||
+ | <b> </ | ||
+ | </ | ||
+ | </ |