Difference between revisions of "Particle picking"

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* Preparing your volumes
 
* Preparing your volumes
  This is fun.
+
You would start putting  all your tomograms in one single catalogue, maybe asking ''Dynamo'' to prepare binned copies of them. More tomograms can be incorporated later.
 
* Picking particles
 
* Picking particles
 +
Then you would visit each tomogram in the catalogue, and would define in them models that capture the geometry of the particle distribution. The models will be also kept in the catalogue.
 
* Extracting particles
 
* Extracting particles
  
  
You would start putting  all your tomograms in one single catalogue.
 
  
  
 +
  
Then you would visit each tomogram in the catalogue, and would define in them models that capture the geometry of the particle distribution. The models will be also kept in the catalogue.
+
Sometimes, models  
  
 
After the stage of particle picking, we normally need to [[Particle extraction|extract particles]], an operation that crops the particles from inside the annotated tomograms and puts all the subtomogram files inside a single [[data folder]] that can be used to design an [[alignment project|alignment project]]
 
After the stage of particle picking, we normally need to [[Particle extraction|extract particles]], an operation that crops the particles from inside the annotated tomograms and puts all the subtomogram files inside a single [[data folder]] that can be used to design an [[alignment project|alignment project]]

Revision as of 15:56, 21 March 2016

Particle picking consists in all the interactive operations on the tomograms towards the definition of 3d positions (and possibly) euler angles that roughly correspond to the presence of a particle.

In some cases, the on-screen interaction simply consists in the user directly clicking the centers of the individual particles. But in many other geometries, the user will rather design supporting objects, like filaments, vesicles, pseudo-crystals or freely-shaped membranes. For each different geometry type, Dynamo provides a different modelclass.

Whichever the model type is that capture the distribution in your particles, the workflow would be the same:

  • Preparing your volumes

You would start putting all your tomograms in one single catalogue, maybe asking Dynamo to prepare binned copies of them. More tomograms can be incorporated later.

  • Picking particles

Then you would visit each tomogram in the catalogue, and would define in them models that capture the geometry of the particle distribution. The models will be also kept in the catalogue.

  • Extracting particles




Sometimes, models

After the stage of particle picking, we normally need to extract particles, an operation that crops the particles from inside the annotated tomograms and puts all the subtomogram files inside a single data folder that can be used to design an alignment project