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--- pipeline:window:cryolo:picking [2019/09/16 16:48]
twagner
+++ pipeline:window:cryolo:picking [2019/09/17 08:19]
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@@ Line 1: / Line 1: @@
+Select the action prediction and fill all arguments in the //"Required arguments"// tab:
+{{ :pipeline:window:cryolo:cryolo_prediction.png?600 |}}
+<note tip>
+In crYOLO, all particles have a assigned confidence value. By default, all particle with confidence value below 0.3 are discarded. If you want to pick less conservatively or more conservatively you might want to change this confidence threshold to a less conservative value like 0.2 or more conservative value like 0.4 in the //"Optional arguments"// tab.
+However, it is much easier to select the best threshold after picking using the ''CBOX'' files written by crYOLO as described in the next section.
+</note>
+Press the the Start button to run the prediction.
+<hidden **Run prediction from the command line**>
 You can now use the model weights file (//e.g. ''cryolo_model.h5'' in training from scratch or ''gmodel_phosnet_X_Y.h5'' when using the general model//) to pick all your images in the directory ''full_data''. To do this, run:
 <code>
@@ Line 6: / Line 17: @@
 You will find the picked particles in the directory ''boxfiles''.
-If you want to pick less conservatively or more conservatively you might want to change the selection threshold from the default of 0.3 to a less conservative value like 0.2 or more conservative value like 0.4 using the //-t// parameter:
-<code>
+</hidden>
-cryolo_predict.py -c config.json -w cryolo_model.h5 -i full_data/ -g 0 -o boxfiles/ -t 0.2
-</code>
-However, it is much easier to select the best threshold after picking using the ''CBOX'' files written by crYOLO as described in the next section

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