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pipeline:window:cryolo:picking [2019/09/17 08:17] twagner |
pipeline:window:cryolo:picking [2020/03/13 08:50] 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 in those files. | ||
+ | * **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 your specified output directory. | ||
+ | |||
+ | < | ||
+ | <div style=" | ||
+ | < | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | |||
+ | < | ||
+ | <div style=" | ||
+ | < | ||
+ | </ | ||
+ | </ | ||
+ | < | ||
+ | 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/ | + | cryolo_predict.py -c config.json -w cryolo_model.h5 -i full_data/ -g 0 -o boxfiles/ |
</ | </ | ||
You will find the picked particles in the directory '' | You will find the picked particles in the directory '' | ||
- | + | </hidden initialState=" | |
- | + | < | |
- | </hidden> | + | <div style=" |
+ | < | ||
+ | </ | ||
+ | </html> |