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--- pipeline:window:cryolo:visualize [2019/09/14 10:18]
twagner created
+++ pipeline:window:cryolo:visualize [2020/03/18 08:35]
twagner
@@ Line 1: / Line 1: @@
-To visualize your results you can use the box manager:
+To visualize your results you can use the boxmanager:
-<code>
-cryolo_boxmanager.py
-</code>
-Now press //File -> Open image// folder and the select the ''full_data'' directory. The first image should pop up. Then you import the box files with //File -> Import box files// and select in the ''boxfiles'' folder the ''EMAN'' directory.
-Since version 1.3.0 crYOLO writes cbox files in a separate ''CBOX'' folder. You can import them into the box manager, change the threshold easily using the live preview and write the new box selection into new box files.
+{{ :pipeline:window:cryolo:cryolo_visualize_202003.png?700 |}}
+As image_dir you select the ''full_data'' directory. As box_dir you select the ''CBOX'' folder (or ''EMAN_HELIX_SEGMENTED'' in case of filaments).
-[{{ :pipeline:window:ezgif-1-3b966b0324d1.gif?400 |This example shows how to filter particle boxes using the cryolo boxmanager. It is an animated gif. Click on it to see it playing.}}]
 <note warning>
-Right now, **this filtering does not yet work for filaments**.
+**The following does not yet work for filaments**.
 </note>
+CBOX files contain besides the particle coordinates more information like the confidence and the estimated size of each particle. When importing .cbox files into the box manager, it enables more filtering options in the GUI. You can plot size- and confidence distributions. Moreover, you can change the confidence threshold, minimum and maximum size and see the results in a live preview. If you are done with the filtering, you can then write the new box selection into new box files. The video below shows an example.
+[{{ :pipeline:window:cryolo:cryolo_size_adjustment_5.gif?700 |This example shows how to filter particle boxes using the crYOLO boxmanager. It is an animated GIF. Click on it to see it playing.}}]

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