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pipeline:window:cryolo:picking_filaments [2019/09/19 15:44]
twagner [3. Configuration]
pipeline:window:cryolo:picking_filaments [2020/03/17 16:58]
twagner [5. Picking]
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 <html> <html>
 <div style="background-color: #cfc ; padding: 10px; border: 1px solid green;">  <div style="background-color: #cfc ; padding: 10px; border: 1px solid green;"> 
-<b>&#9658; You can now press the [Start] button to create you configuration file. </b>+<b>&#9658; You can now press the [Start] button to create your configuration file. </b>
 </div> </div>
 </html> </html>
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 ==== 5. Picking ==== ==== 5. Picking ====
 Select the action prediction and fill all arguments in the “Required arguments” tab:  Select the action prediction and fill all arguments in the “Required arguments” tab: 
-{{ :pipeline:window:cryolo:cryolo_prediction.png?600 |}}+ 
 +{{ :pipeline:window:cryolo:cryolo_prediction_202003.png?700 |}}
  
 Now select the "Filament options" tab and check "Activate filament mode", specifiy the filament width (e.g. 100) and define the box distance (e.g. 20 for 90% overlap when using a box size if 200): Now select the "Filament options" tab and check "Activate filament mode", specifiy the filament width (e.g. 100) and define the box distance (e.g. 20 for 90% overlap when using a box size if 200):
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 The directory ''output_boxes'' will be created and all results are saved there. The format is the eman2 helix format with particle coordinates.  The directory ''output_boxes'' will be created and all results are saved there. The format is the eman2 helix format with particle coordinates. 
 +<note info>
 +**Import into Relion**
  
 You can find a detailed description [[:cryolo_filament_import_relion|how to import crYOLO filament coordinates into Relion here]]. You can find a detailed description [[:cryolo_filament_import_relion|how to import crYOLO filament coordinates into Relion here]].
 +</note>
  
  
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 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>
-cryolo_predict.py -c cryolo_config.json -w cryolo_model.h5 -i full_data --filament -fw 100 -bd 20 -o boxes/ -g 0 -mn 6+cryolo_predict.py -c config_cryolo.json -w cryolo_model.h5 -i full_data --filament -fw 100 -bd 20 -o boxes/ -g 0 -mn 6
 </code> </code>
 </hidden> </hidden>
pipeline/window/cryolo/picking_filaments.txt · Last modified: 2020/06/05 09:04 by twagner