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pipeline:window:cryolo:picking [2019/09/17 09:53] twagner |
pipeline:window:cryolo:picking [2020/03/13 09:02] twagner |
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- | Select the action | + | Select the action |
{{ : | {{ : | ||
<note tip> | <note tip> | ||
- | In crYOLO, all particles have a assigned confidence value. By default, all particle | + | **Adjusting confidence threshold** |
+ | |||
+ | In crYOLO, all particles have an assigned confidence value. By default, all particles | ||
However, it is much easier to select the best threshold after picking using the '' | However, it is much easier to select the best threshold after picking using the '' | ||
</ | </ | ||
- | Press the the Start button to run the prediction. You will find the picked | + | 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 threshold. Additionally it contains | ||
+ | * **EMAN:** Contains a coordinate file in .box format each input micrograph. Only particles | ||
+ | * **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. | ||
- | <hidden **Run prediction from the command line**> | + | |
- | To pick all your images in the directory '' | + | <html> |
+ | <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 | 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 '' | You will find the picked particles in the directory '' | ||
</ | </ | ||
+ | |||
+ | < | ||
+ | <div style=" | ||
+ | <b> </b> | ||
+ | </ | ||
+ | </ |