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
Next revision Both sides next revision
pipeline:window:cryolo:picking [2019/09/17 15:25]
twagner 		pipeline:window:cryolo:picking [2019/09/19 15:47]
twagner
Line 3: Line 3:
  
 <note tip> <note tip>
 +**Adjusting confidence threshold**
 +
 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. 0.2) or more (e.g. 0.4) conservative value in the //"Optional arguments"// tab. 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. 0.2) or 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. 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.
 </note> </note>
 +
 +You will find the picked particles in your specified output directory.
  
 <html> <html>
Line 14: Line 18:
  
  
-You will find the picked particles in your specified output directory. +<html> 
- +<div style="background-color: LightCyan ; padding: 10px; border: 1px solid Black;">  
-<hidden **Alternative:** Run prediction from the command line>+<b>Alternative: Run prediction from the command line</b> 
 +</div> 
 +</html> 
 +<hidden>
 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>
Line 24: Line 31:
 You will find the picked particles in the directory ''boxfiles''. You will find the picked particles in the directory ''boxfiles''.
 </hidden> </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

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