Difference between revisions of "Particle extraction"

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==Using the catalogue==
 
==Using the catalogue==
  
Select the tomograms in which you have models containing particles and click on the menu tab ''Crop particles''. A new GUI will popup, with a list of models. You can then select the models that already contain ''crop points''). Then click on ''Create list'' and ''-> Crop particles''
+
Select the tomograms in which you have models containing particles and click on the menu tab ''Crop particles''. A new GUI will popup, with a list of models. You can then select the models that already contain ''crop points''). Then click on ''Create list''. This will create a text file with extension <tt>.vll</tt> just for information. Click then on ''-> Crop particles'', getting a GUI where you can select the sidelength in pixels, and start the actual cropping.
  
 
==From the command line==
 
==From the command line==
 
 
You might just use the command <tt>dtcrop</tt>.
 
You might just use the command <tt>dtcrop</tt>.
 +
Help on command: [http://{{SERVERNAME}}/w/doc/functions/dynamo_table_crop.html dtcrop]
  
 
==On a single tomogram==
 
==On a single tomogram==
  
==On a single tomogram==
+
==On several tomograms tomogram==
  
 
==On each model separately==
 
==On each model separately==
  
 
When you are manually creating a model in one of the browsers, the real workflow in an actual project involving many tomograms and modeles would be to just click the necessary points to define the user input of the model, store it in the catalogue, and move to the next model.
 
When you are manually creating a model in one of the browsers, the real workflow in an actual project involving many tomograms and modeles would be to just click the necessary points to define the user input of the model, store it in the catalogue, and move to the next model.

Revision as of 15:47, 21 March 2016

Particle extraction is the process of using a set of positions (and possibly orientations) defined on a set of tomograms to create a set of subtomograms files. This set is represented by a data folder containing one file for each cropped subtomogram, and possibly a table retaining the metadata. Data folder and table can directly be used for subtomogram alignment

Using the catalogue

Select the tomograms in which you have models containing particles and click on the menu tab Crop particles. A new GUI will popup, with a list of models. You can then select the models that already contain crop points). Then click on Create list. This will create a text file with extension .vll just for information. Click then on -> Crop particles, getting a GUI where you can select the sidelength in pixels, and start the actual cropping.

From the command line

You might just use the command dtcrop. Help on command: dtcrop

On a single tomogram

On several tomograms tomogram

On each model separately

When you are manually creating a model in one of the browsers, the real workflow in an actual project involving many tomograms and modeles would be to just click the necessary points to define the user input of the model, store it in the catalogue, and move to the next model.