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--- pipeline:window:cryolo:picking_filaments [2019/09/19 08:15]
twagner [3. Configuration]
+++ pipeline:window:cryolo:picking_filaments [2020/03/17 17:00]
twagner [5. Picking]
@@ Line 32: / Line 32: @@
 ==== 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
@@ Line 42: / Line 38: @@
 </code>
+{{page>pipeline:window:cryolo:start_cryolo}}
+==== 3. Configuration ====
 {{page>pipeline:window:cryolo:configuration}}
@@ Line 47: / Line 47: @@
 <html>
 <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>
 </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}}
+<html>
+<div style="background-color: LightCyan ; padding: 10px; border: 1px solid Black;">
+<b> </b>
+</div>
+</html>
 ==== 4. Training ====
@@ Line 58: / Line 69: @@
 ==== 5. Picking ====
 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):
-{{ :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.
+<note info>
+**Import into Relion**
+You can find a detailed description [[:cryolo_filament_import_relion|how to import crYOLO filament coordinates into Relion here]].
+</note>
@@ Line 71: / Line 90: @@
 </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:
 <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>
 </hidden>
+<html>
+<div style="background-color: LightCyan ; padding: 10px; border: 1px solid Black;">
+<b> </b>
+</div>
+</html>

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