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pipeline:window:cryolo:picking [2019/09/17 13:36] twagner |
pipeline:window:cryolo:picking [2020/05/17 11:04] (current) 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 '' | ||
+ | |||
+ | **Monitor mode** | ||
+ | |||
+ | When this option is activated, crYOLO will monitor your input folder. This especially useful for automation purposes. You can stop the monitor mode by writing an empty file with the name “stop.cryolo” in the input directory. Just add --monitor in the command line or check the monitor box in in the //" | ||
+ | |||
</ | </ | ||
+ | |||
+ | 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 the confidence and the estimated diameter for each particle. Importing those files into the boxmanager allows you advanced filtering e.g. according size or 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 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. | ||
+ | |||
< | < | ||
<div style=" | <div style=" | ||
- | < | + | <b>&# |
</ | </ | ||
</ | </ | ||
- | You will find the picked particles in your specified output directory. | + | < |
+ | <div style=" | ||
+ | < | ||
+ | </ | ||
+ | </ | ||
- | < | + | < |
- | To pick all your images in the directory '' | + | 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> | ||
+ | </ | ||
+ | </ |