Differences

This shows you the differences between two versions of the page.

--- pipeline:window:cryolo [2019/02/13 17:46]
twagner [Data preparation]
+++ pipeline:window:cryolo [2019/02/26 08:13]
twagner [Configuration]
@@ Line 181: / Line 181: @@
 Open the file with your preferred editor.
-For the general **[[:cryolo_nets#network_3_phosaurusnet|Phosaurus network]]** enter the following inside:
+There are two general **[[:cryolo_nets#network_3_phosaurusnet|Phosaurus networks]]** available. One for cryo em images and one for negative stain data.
+=== CryoEM images ===
+For the general **[[:cryolo_nets#network_3_phosaurusnet|Phosaurus network]]** trained for **cryo images** enter the following inside:
 <code json config.json>
     {
@@ Line 191: / Line 193: @@
         "num_patches":          1,
         "filter":               [0.1,"tmp_filtered"]
+      }
+    }
+</code>
+Please set the value in the //"anchors"// field to your desired box size. It should be size of the minimum particle enclosing square in pixel.
+=== Negative stain images ===
+For the general model for **negative stain data** please use:
+<code json config.json>
+    {
+    "model" : {
+        "architecture":         "PhosaurusNet",
+        "input_size":           1024,
+        "anchors":              [205,205],
+        "max_box_per_image":    700,
+        "num_patches":          1
       }
     }