Difference between revisions of "Particle picking"

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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.
 
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 [[Model|model class]].  
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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 [[Model|model]]class.  
  
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Whichever the model type is that capture the distribution in your particles, the workflow would be the same:
  
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* Preparing your volumes
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  This is fun.
 +
* Picking particles
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* Extracting particles
  
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]
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You would start putting  all your tomograms in one single catalogue.
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 +
 
 +
 
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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.
 +
 
 +
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 14:50, 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
 This is fun.
  • Picking 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.

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