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pipeline:window:cryolo [2019/04/16 11:05]
twagner [Configuration] 		pipeline:window:cryolo [2019/07/09 21:00]
twagner [Data preparation]
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 ==== Data preparation ==== ==== Data preparation ====
 CrYOLO supports MRC, TIF and JPG files. It can work with 32 bit data, 8 bit data and 16 bit data. CrYOLO supports MRC, TIF and JPG files. It can work with 32 bit data, 8 bit data and 16 bit data.
-It will work on original MRC files, but it will probably improve when the data are filtered. Therefore you should low-pass filter them to a reasonable level. Since Version 1.2 crYOLO can automatically do that for you. You just have to add+It will work on original MRC files, but it will probably improve when the data are denoised. Therefore you should low-pass filter them to a reasonable level. Since Version 1.2 crYOLO can automatically do that for you. You just have to add
 <code> <code>
 "filter":               [0.1,"filtered"] "filter":               [0.1,"filtered"]
 </code>  </code> 
 +
 to the model section in your config file to filter your images down to an absolute frequency of 0.1. The filtered images are saved in folder ''filtered''. to the model section in your config file to filter your images down to an absolute frequency of 0.1. The filtered images are saved in folder ''filtered''.
 +
 +<hidden Alternative: Using neural-network denoising with JANNI> 
 +<code>
 +"filter":               [model.h5,1,2,"filtered"]
 +</code> 
 +</hidden> 
 +
  
 If you followed the installation instructions, you now have to activate the cryolo virtual environment with If you followed the installation instructions, you now have to activate the cryolo virtual environment with
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 ===== Picking particles - Without training using a general model ===== ===== Picking particles - Without training using a general model =====
 +Here you can find how to apply the general models we trained for you. If you would like to train your own general model, please see our extra wiki page: [[:cryolo_train_general_model|How to train your own general model]]
  
-The general models can be found and downloaded here: [[howto:download_latest_cryolo|Download and Installation]]. +Our general models can be found and downloaded here: [[howto:download_latest_cryolo|Download and Installation]]. 
 ==== Configuration==== ==== Configuration====
 The next step is to create a configuration file. Type: The next step is to create a configuration file. Type:
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 ==== Training ==== ==== Training ====
-In comparision to the training from scratch, you can skip the warm up training. Moreover you have to add the //--fine_tune// flag:+In comparision to the training from scratch, you can skip the warm up training. Moreover you have to add the //%%--%%fine_tune// flag:
  
 <code> <code>
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   * //%%--%%num_cpu NUMBER_OF_CPUS//: Number of CPU cores used during prediction   * //%%--%%num_cpu NUMBER_OF_CPUS//: Number of CPU cores used during prediction
   * //%%--%%gpu_fraction FRACTION//: Number between 0 -1 quantifying the fraction of GPU memory that is reserved by crYOLO   * //%%--%%gpu_fraction FRACTION//: Number between 0 -1 quantifying the fraction of GPU memory that is reserved by crYOLO
 +  * //-sr SEARCH_RANGE_FACTOR//: (FILAMENT MODE) The search range for connecting boxes is the box size times this factor. Default is 1.41
  
 ===== Help ===== ===== Help =====
pipeline/window/cryolo.txt ยท Last modified: 2021/02/19 10:00 by twagner

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