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pipeline:window:cryolo:picking [2019/09/17 08:17] twagner |
pipeline:window:cryolo:picking [2020/03/16 15:24] twagner |
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- | Select the actin prediction | + | Select the action " |
- | {{ : | + | {{ : |
<note tip> | <note tip> | ||
- | If you want to pick less conservatively | + | **Adjusting confidence threshold** |
- | However, it is much easier to select the best threshold after picking using the '' | + | |
+ | In crYOLO, all particles have an assigned confidence value. By default, all particles with a confidence value below 0.3 are discarded. | ||
+ | However, it is much easier to select the best threshold after picking using the '' | ||
</ | </ | ||
- | < | + | After picking is done, you can find four folders in your specified output folder: |
- | You can now use the model weights | + | |
- | < | + | * **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 |
- | cryolo_predict.py -c config.json -w cryolo_model.h5 -i full_data/ | + | * **STAR:** Contains a coordinate file in .star format each input micrograph. Only particles with the an confidence higher then the selected (default: 0.3) are contained in those files. |
- | </ | + | * **DISTR:** Contains the plots of confidence- and size-distribution. Moroever, it contains a machine readable text-file the summary statistics about these distributions and their raw data in separate text-files. |
- | You will find the picked particles in the directory '' | ||
+ | < | ||
+ | <div style=" | ||
+ | < | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | < | ||
+ | <div style=" | ||
+ | < | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | <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 0.3 | ||
+ | </ | ||
+ | You will find the picked particles in the directory '' | ||
</ | </ | ||
+ | |||
+ | < | ||
+ | <div style=" | ||
+ | <b> </b> | ||
+ | </ | ||
+ | </ |