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--- pipeline:window:cryolo [2019/08/30 13:40]
twagner [Data preparation]
+++ pipeline:window:cryolo [2019/08/30 14:17]
twagner [Configuration]
@@ Line 68: / Line 68: @@
   * CONTROL + LEFT MOUSE BUTTON: Remove a box
-You can change the box size in the main window, by changing the number in the text field labeled //Box size://. Press //Set// to apply it to all picked particles. For picking, you should the use minimum sized square which encloses your particle.
+You can change the box size in the main window, by changing the number in the text field labeled //Box size://. Press //Set// to apply it to all picked particles. __For picking, you should the use minimum sized square which encloses your particle.__
 If you finished picking from your micrographs, you can export your box files with //Files -> Write box files//.
@@ Line 76: / Line 76: @@
 ==== Configuration ====
-You now have to create a config file your picking project. To do this type:
+You now have to create a configuration file your picking project. It contains all important constants and paths and helps you to reproduce your results later on.
+You can either use the commandline to create the configuration file or the GUI.
+**Using the command line:**
+To create an empty file do:
 <code>
 touch config.json
@@ Line 122: / Line 128: @@
 //[[:cryolo_config|Click here to get more information about the configuration file]]//
-Please set the value in the //"anchors"// field to your desired box size. It should be size of the minimum enclosing square in pixels. Furthermore check if the fields //"train_image_folder"// and //"train_annot_folder"// have the correct values. Typically, 20% of the training data are randomly chosen as validation data. If you want to use specific images as validation data, you can move the images and the corresponding box files to the folders specified in //"valid_image_folder"// and //"valid_annot_folder"//. Make sure that they are removed from the original training folder! With the line below, crYOLO automatically filters your images to an absolute frequency 0.1 and write them into a folder "filtered".
+Please set the value in the //"anchors"// field to your desired box size. It should be the same as in your training box files. Furthermore check if the fields //"train_image_folder"// and //"train_annot_folder"// have the correct values. Typically, 20% of the training data are randomly chosen as validation data. If you want to use specific images as validation data, you can move the images and the corresponding box files to the folders specified in //"valid_image_folder"// and //"valid_annot_folder"//. Make sure that they are removed from the original training folder! With the line below, crYOLO automatically filters your images to an absolute frequency 0.1 and write them into a folder "filtered".
 <code>
 "filter":               [0.1,"filtered"].
@@ Line 145: / Line 151: @@
 Please note the wiki entry about the [[:cryolo_config|crYOLO configuration file]] if you want to know more details.
+**Using the GUI:**
 ==== Training ====

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