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pipeline:window:cryolo [2019/07/11 09:46]
twagner [Data preparation] 		pipeline:window:cryolo [2019/07/11 09:49]
twagner [Configuration]
Line 150: Line 150:
 **Alternative: Using neural-network denoising with JANNI** **Alternative: Using neural-network denoising with JANNI**
  
-Since crYOLO 1.4 you can also use neural network denoising with [[:janni|JANNI]]. The easiest way is to use the JANNI's general model ([[:janni#janni_general_model|Download here]]) but you can also [[:janni_tutorial#training_a_model_for_your_data|train JANNI for your data]]. crYOLO directly uses an interface to JANNI to filter your data, you just have to specify the path to your JANNI model, overlap of the batches (default 24), the batch size (default 16) and a path where the denoised images should be written. +Since crYOLO 1.4 you can also use neural network denoising with [[:janni|JANNI]]. The easiest way is to use the JANNI's general model ([[:janni#janni_general_model|Download here]]) but you can also [[:janni_tutorial#training_a_model_for_your_data|train JANNI for your data]]. crYOLO directly uses an interface to JANNI to filter your data, you just have to specify the path to your JANNI model, overlap of the batches (default 24), the batch size (default 3) and a path where the denoised images should be written. 
  
 To use JANNI's denoising you have to use following entry in your config.json: To use JANNI's denoising you have to use following entry in your config.json:
  
 <code> <code>
-"filter":               ["path/to/janni_model.h5",24,16,"filtered"]+"filter":               ["path/to/janni_model.h5",24,3,"filtered"]
 </code>  </code> 
  
Line 267: Line 267:
         "max_box_per_image":    700,         "max_box_per_image":    700,
         "num_patches":          1,         "num_patches":          1,
-        "filter":               [0.1,"tmp_filtered"]+        "filter":               ["gmodel_janni_20190703.h5",24,3,"tmp_filtered_nn"]
       }       }
     }     }
 </code> </code>
 +
 +You can download the file ''gmodel_janni_20190703.h5'' [[https://github.com/MPI-Dortmund/sphire-janni/tree/master/janni_general_models|here]]
 </hidden> </hidden>
 <html><br></html> <html><br></html>
pipeline/window/cryolo.txt ยท Last modified: 2021/02/19 10:00 by twagner

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