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pipeline:window:cryolo:picking [2019/09/14 10:12]
twagner created
pipeline:window:cryolo:picking [2020/05/17 11:04]
twagner
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-You can now use the model weights saved in ''model.h5'' (//if you come to this section from another point of the tutorial, this filename might be different like ''gmodel_phosnet_X_Y.h5''//) to pick all your images in the directory ''full_data''. To do this, run:  +Select the action "predict" and fill all arguments in the //"Required arguments"// tab
-<code> +{{ :pipeline:window:cryolo:cryolo_prediction_202003.png?700 |}}
-cryolo_predict.py -c config.json -w model.h5 -i full_data/ -g 0 -o boxfiles/ +
-</code>+
  
-You will find the picked particles in the directory ''boxfiles''.+<note tip> 
 +**Adjusting confidence threshold**
  
-If you want to pick less conservatively or more conservatively you might want to change the selection threshold from the default of 0.3 to a less conservative value like 0.2 or more conservative value like 0.4 using the //-t// parameter:+In crYOLO, all particles have an assigned confidence value. By default, all particles with a confidence value below 0.3 are discarded. If you want to pick less or more conservatively you might want to change this confidence threshold to a less (e.g. 0.2or more (e.g. 0.4) conservative value in the //"Optional arguments"// tab. 
 +However, it is much easier to select the best threshold after picking using the ''CBOX'' files written by crYOLO as described in the next section. 
 + 
 +**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 //"Optional arguments"// tab. 
 + 
 +</note> 
 + 
 +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 confidenceand size-distribution. Moroever, it contains a machine readable text-file the summary statistics about these distributions and their raw data in separate text-files. 
 + 
 + 
 +<html> 
 +<div style="background-color: #cfc ; padding: 10px; border: 1px solid green;">  
 +<b>&#9658; Press the the [Start] button to run the prediction.  </b> 
 +</div> 
 +</html> 
 + 
 + 
 +<html> 
 +<div style="background-color: LightCyan ; padding: 10px; border: 1px solid Black;">  
 +<b>Alternative: Run prediction from the command line</b> 
 +</div> 
 +</html> 
 + 
 +<hidden initialState="visible"> 
 +To pick all your images in the directory ''full_data'' with the  model weight file ''cryolo_model.h5'' (//e.g. or ''gmodel_phosnet_X_Y.h5'' when using the general model//) and and a confidence threshold of 0.3 run:
 <code> <code>
-cryolo_predict.py -c config.json -w 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
 </code> </code>
-However, it is much easier to select the best threshold after picking using the ''CBOX'' files written by crYOLO as described in the next section+You will find the picked particles in the directory ''boxfiles''
 +</hidden> 
 + 
 +<html> 
 +<div style="background-color: LightCyan ; padding: 10px; border: 1px solid Black;">  
 +<b> </b> 
 +</div> 
 +</html>
pipeline/window/cryolo/picking.txt · Last modified: 2020/05/17 11:04 by twagner