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pipeline:window:cryolo:picking_filaments [2019/09/19 15:44]
twagner [3. Configuration]
pipeline:window:cryolo:picking_filaments [2020/05/25 10:15]
twagner [Picking filaments - Using a model trained for your data]
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 +<note important>
 +
 +**DOCUMENTATION OUTDATED**
 +
 +The documentation has moved to https://cryolo.readthedocs.io/en/latest/
 +
 +</note>
 +
 ===== Picking filaments - Using a model trained for your data ===== ===== Picking filaments - Using a model trained for your data =====
 When picking filaments, it is important to identify each filament individually. This allows specific spacing of the boxes (i.e., the helical rise) to maximize the number of particles. CrYOLO supports this method of picking filaments. When picking filaments, it is important to identify each filament individually. This allows specific spacing of the boxes (i.e., the helical rise) to maximize the number of particles. CrYOLO supports this method of picking filaments.
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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):
  
-{{ :pipeline:window:cryolo_filament.png?700 |}}+{{ :pipeline:window:cryolo:cryolo_filament_202003.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.  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