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--- pipeline:window:cryolo:picking_filaments [2019/09/18 10:19]
twagner [5. Picking]
+++ pipeline:window:cryolo:picking_filaments [2019/09/18 14:07]
twagner [1. Data preparation]
@@ Line 1: / Line 1: @@
 ===== Picking filaments - Using a model trained for your data =====
-When picking filaments, it is important to identify each filament individually. This allows to place the boxes a specific distance apart (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.
 Filament mode on actin:
@@ Line 22: / Line 22: @@
 The first step is to create the training data for your model. Right now, you have to use the e2helixboxer.py for this:
 <code>
-e2helixboxer.py --gui my_images/*.mrc
+e2helixboxer.py --gui train_image/*.mrc
 </code>
-After tracing your training data in e2helixboxer, export them using //File -> Save//. Make sure that you export particle coordinates, as this the only format supported right now (see screenshot). In the following example, it is expected that you exported into a folder called "train_annotation".
+After tracing your training data in e2helixboxer, export them using //File -> Save//. Unfortunately you have to do that with each image separately.
+<note important>
+**Adapt the file saving options**
+Make sure that you uncheck the boxes "Write Helices" and "Particle Images" and check the box "Particle Coordinates", as this the only format supported right now (see screenshot). Also remove the "_helix_ptcl_coords" suffix in the path field. The coordinate files have to have the same name as the micrographs.
+</note>
+In the following example, it is expected that you exported into a folder called "train_annot".
 For projects with roughly 20 filaments per image we successfully trained on 40 images (=> 800 filaments).

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