User Tools

Site Tools

pipeline:window:cryolo:picking

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
Last revision Both sides next revision
pipeline:window:cryolo:picking [2019/10/11 17:11]
twagner 		pipeline:window:cryolo:picking [2020/03/16 15:24]
twagner
Line 1: Line 1:
 Select the action "predict" and fill all arguments in the //"Required arguments"// tab: Select the action "predict" and fill all arguments in the //"Required arguments"// tab:
-{{ :pipeline:window:cryolo:cryolo_prediction.png?600 |}}+{{ :pipeline:window:cryolo:cryolo_prediction_202003.png?700 |}}
  
 <note tip> <note tip>
Line 9: Line 9:
 </note> </note>
  
-You will find the picked particles in your specified output directory.+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. 
  
 <html> <html>
Line 23: Line 28:
 </div> </div>
 </html> </html>
-<hidden>+ 
 +<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::  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 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
 </code> </code>
- 
 You will find the picked particles in the directory ''boxfiles''. You will find the picked particles in the directory ''boxfiles''.
-</hidden initialState="visible">+</hidden> 
 <html> <html>
 <div style="background-color: LightCyan ; padding: 10px; border: 1px solid Black;">  <div style="background-color: LightCyan ; padding: 10px; border: 1px solid Black;"> 
pipeline/window/cryolo/picking.txt · Last modified: 2020/05/17 11:04 by twagner

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: GNU Free Documentation License 1.3
GNU Free Documentation License 1.3 Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki