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pipeline:window:cryolo:picking_filaments [2019/09/19 08:16]
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 ====
 +If you followed the installation instructions, you now have to activate the crYOLO virtual environment with
 +
 +<code>
 +source activate cryolo
 +</code>
 +
 {{page>pipeline:window:cryolo:start_cryolo}} {{page>pipeline:window:cryolo:start_cryolo}}
  
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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;">  
-You can find a detailed description [[:cryolo_filament_import_relion|how to import crYOLO filament coordinates into Relion here]].+<b> Alternative: Run prediction in commmand line</b> 
 +</div> 
 +</html>
  
-<hidden **Alternative:** Run prediction in commmand line>+<hidden>
 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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