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pipeline:window:cryolo [2019/03/17 10:03]
twagner [Data preparation] 		pipeline:window:cryolo [2019/03/17 19:58]
twagner [Picking]
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 You can find more technical details in our paper: You can find more technical details in our paper:
  
-[[https://www.biorxiv.org/content/10.1101/356584v1|SPHIRE-crYOLO: A fast and well-centering automated particle picker for cryo-EM]]+[[https://www.biorxiv.org/content/10.1101/356584v2|SPHIRE-crYOLO: A fast and accurate fully automated particle picker for cryo-EM 
 +]]
  
 <html> <html>
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 [{{ :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.}}] [{{ :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.}}]
  
-Right now, this filtering does not work for filaments.+Right now, **this filtering does not yet work for filaments**.
  
  
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 Picking is identical as with a model trained from scratch, so we will skip it here. Just follow the description given [[pipeline:window:cryolo#Picking|above]] Picking is identical as with a model trained from scratch, so we will skip it here. Just follow the description given [[pipeline:window:cryolo#Picking|above]]
  
- +==== Training on CPU ==== 
 +[[downloads:cryolo_1|License]] 
 +The fine tune mode is especially useful if you want to train crYOLO on the CPU. On my local machine it reduced the time from 12-15 hours to 4-5 hours.
 ===== Picking filaments - Using a model trained for your data ===== ===== Picking filaments - Using a model trained for your data =====
 Since version 1.1.0 crYOLO supports picking filaments. Since version 1.1.0 crYOLO supports picking filaments.
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 ===== Advanced parameters ===== ===== Advanced parameters =====
-During **training** (//cryolo_train//), there is the following advanced parameter:+During **training** (//cryolo_train//), there are the following advanced parameters:
   * //%%--%%warm_restarts//: With this option the learning rate is decreasing after each epoch and then reset after a couple of epochs.   * //%%--%%warm_restarts//: With this option the learning rate is decreasing after each epoch and then reset after a couple of epochs.
   * //%%--%%num_cpu NUMBER_OF_CPUS//: Number of CPU cores used during training   * //%%--%%num_cpu NUMBER_OF_CPUS//: Number of CPU cores used during training
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   * //%%--%%skip_augmentation//: Set this flaq, if crYOLO should skip the data augmentation (not recommended).   * //%%--%%skip_augmentation//: Set this flaq, if crYOLO should skip the data augmentation (not recommended).
  
-During **picking** (//cryolo_predict//), there are two advanced parameters:+During **picking** (//cryolo_predict//), there are five advanced parameters:
   * //-t CONFIDENCE_THRESHOLD//: With the -t parameter, you can let the crYOLO pick more conservative (e.g by adding -t 0.4 to the picking command) or less conservative (e.g by adding -t 0.2 to the picking command). The valid parameter range is 0 to 1.   * //-t CONFIDENCE_THRESHOLD//: With the -t parameter, you can let the crYOLO pick more conservative (e.g by adding -t 0.4 to the picking command) or less conservative (e.g by adding -t 0.2 to the picking command). The valid parameter range is 0 to 1.
   * //-d DISTANCE_IN_PIXEL//: With the -d parameter you can filter your picked particles. Boxes with a distance (pixel) less than this value will be removed.   * //-d DISTANCE_IN_PIXEL//: With the -d parameter you can filter your picked particles. Boxes with a distance (pixel) less than this value will be removed.
pipeline/window/cryolo.txt · Last modified: 2021/02/19 10:00 by twagner

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