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pipeline:window:cryolo:picking_filaments [2019/09/19 08:15]
twagner [3. Configuration] 		pipeline:window:cryolo:picking_filaments [2019/09/19 15:44]
twagner [3. Configuration]
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 ==== 2. Start crYOLO ==== ==== 2. Start crYOLO ====
-{{page>pipeline:window:cryolo:start_cryolo}} 
- 
- 
-==== 3. Configuration ==== 
 If you followed the installation instructions, you now have to activate the crYOLO virtual environment with If you followed the installation instructions, you now have to activate the crYOLO virtual environment with
  
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 </code> </code>
  
 +{{page>pipeline:window:cryolo:start_cryolo}}
 +
 +
 +==== 3. Configuration ====
 {{page>pipeline:window:cryolo:configuration}} {{page>pipeline:window:cryolo:configuration}}
  
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 </html> </html>
  
 +<html>
 +<div style="background-color: LightCyan ; padding: 10px; border: 1px solid Black;"> 
 +<b>Alternative: Create the configuration file using the command line </b>
 +</div>
 +</html>
  
 {{page>pipeline:window:cryolo:configuration_cmdl_normal}} {{page>pipeline:window:cryolo:configuration_cmdl_normal}}
 +<html>
 +<div style="background-color: LightCyan ; padding: 10px; border: 1px solid Black;"> 
 +<b> </b>
 +</div>
 +</html>
 +
 ==== 4. Training ==== ==== 4. Training ====
  
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 {{ :pipeline:window:cryolo_filament.png?700 |}} {{ :pipeline:window:cryolo_filament.png?700 |}}
 +
 +The directory ''output_boxes'' will be created and all results are saved there. The format is the eman2 helix format with particle coordinates. 
 +
 +You can find a detailed description [[:cryolo_filament_import_relion|how to import crYOLO filament coordinates into Relion here]].
  
  
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 </html> </html>
  
-The directory ''output_boxes'' will be created and all results are saved there. The format is the eman2 helix format with particle coordinates. +<html> 
 +<div style="background-color: LightCyan ; padding: 10px; border: 1px solid Black;">  
 +<b> Alternative: Run prediction in commmand line</b> 
 +</div> 
 +</html>
  
-You can find a detailed description [[:cryolo_filament_import_relion|how to import crYOLO filament coordinates into Relion here]]. +<hidden>
- +
-<hidden **Alternative:** Run prediction in commmand line>+
 Let's assume you want to pick a filament with a width of 100 pixels (-fw 100). The box size is 200x200 and you want a 90% overlap (-bd 20). Moreover, you wish that each filament has at least 6 boxes (-mn 6). The micrographs are in the ''full_data'' directory. Than the picking command would be: Let's assume you want to pick a filament with a width of 100 pixels (-fw 100). The box size is 200x200 and you want a 90% overlap (-bd 20). Moreover, you wish that each filament has at least 6 boxes (-mn 6). The micrographs are in the ''full_data'' directory. Than the picking command would be:
 <code> <code>
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 </code> </code>
 </hidden> </hidden>
 +<html>
 +<div style="background-color: LightCyan ; padding: 10px; border: 1px solid Black;"> 
 +<b> </b>
 +</div>
 +</html>
  
  
pipeline/window/cryolo/picking_filaments.txt · Last modified: 2020/06/05 09:04 by twagner

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