User Tools

Site Tools

janni_tutorial

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
Next revision Both sides next revision
janni_tutorial [2019/07/10 10:05]
twagner [Training a model for your data] 		janni_tutorial [2019/07/10 10:37]
twagner [Denoise]
Line 11: Line 11:
 ==== Training a model for your data ==== ==== Training a model for your data ====
 In case you want to use the general model ([[janni#Download|Download here]]) you can skip this part and directly [[janni_tutorial#denoise|denoise]] your images.  In case you want to use the general model ([[janni#Download|Download here]]) you can skip this part and directly [[janni_tutorial#denoise|denoise]] your images. 
 +
 In case you would like to train a model for your data, the first thing you have to do is to create a configuration file for JANNI. In the following I assume you named it //config.json//. It should look like this: In case you would like to train a model for your data, the first thing you have to do is to create a configuration file for JANNI. In the following I assume you named it //config.json//. It should look like this:
 <code json config.json> <code json config.json>
Line 51: Line 52:
 ==== Denoise ==== ==== Denoise ====
  
-After you trained your model, you can denoise either your movies or denoise your averages directly. In our experience, denoising the motion corrected averages works better.+With a trained model (either trained by you or the general model) you can directly denoise either your movies or averages. In our experience, denoising the motion corrected averages works better.
  
 To denoise a set if images you have to tell JANNI three **mandatory** arguments: To denoise a set if images you have to tell JANNI three **mandatory** arguments:
Line 66: Line 67:
  
 Here is now how you do the actual denoising: Here is now how you do the actual denoising:
-It is assumed that you run the command in a directory with the with your model file ''mymodel.h5'' (might have a different name in case of the [[janni#Download|general model]]). Furthermore, it is assumed that your would like denoise averages in the folder ///my/averages/// and want to write results in the folder ///my/outputdir/denoised///+It is assumed that you run the command in a directory with your model file ''mymodel.h5'' (might have a different name in case of the [[janni#Download|general model]]). Furthermore, it is assumed that your would like denoise averages in the folder ///my/averages/// and want to write results in the folder ///my/outputdir/denoised///
  
 The following command will run the denoising on GPU 0: The following command will run the denoising on GPU 0:
janni_tutorial.txt ยท Last modified: 2020/09/24 14:46 by twagner

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: GNU Free Documentation License 1.3
GNU Free Documentation License 1.3 Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki