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.
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Particle picking (sometimes referred to as ''Volume annotation'') 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.  
  
Whichever the model type is that capture the distribution in your particles, the workflow would be the same:  
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Whichever the model type is the one that captures the distribution in your particles, the workflow would be the same:  
  
* Preparing your volumes
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* Prepare your volumes
* Picking particles
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* Particle picking
* Extracting particles
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* Particle extraction
  
== Guadalajars==
 
You would start putting  all your tomograms in one single catalogue, maybe asking ''Dynamo'' to [[Viewing tomograms#Prebinned tomograms| prepare binned]] copies of them. More tomograms can be incorporated later.
 
 
== Preparing your volumes==
 
== Preparing your volumes==
You would start putting  all your tomograms in one single catalogue, maybe asking ''Dynamo'' to [[Viewing tomograms#Prebinned tomograms| prepare binned]] copies of them. More tomograms can be incorporated later.
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You would start putting  all your tomograms in one single [[catalogue]], maybe asking ''Dynamo'' to [[Viewing tomograms#Prebinned tomograms| 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 one or models that capture the geometry of the particle distribution. The models will be also kept in the catalogue.
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Then you would [[Viewing tomograms|visit]] each tomogram in the catalogue, and would define in them one or models that capture the geometry of the particle distribution. The models will be also kept in the catalogue.
Sometimes, models carry parameters that need to be tuned for your case (for instance, the radius of filament models, or the particle density in surface models). When you have many models defined on the same data set, which will have the same parameter values, it is a good idea to define each individual model with the minimal amount of user input, save it and proceed to the next one. Then, when all the models in the catalogue have been defined, one can define XXXX
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Sometimes, models carry parameters that need to be tuned for your case (for instance, the radius of [[filament model]]s, or the particle density in surface models). When you have many models defined on a set of tomograms, and you want them to have the same, non-default parameter values, it is a good idea to define each individual model with the minimal amount of user input, save it and proceed to the next one. Then, when all the models in the catalogue have been defined, one can write a [[Scripts on sets of models | script]] to visit in one loop all the models and operate on them.
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== Extracting particles==
 
== 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]]
 
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]]

Latest revision as of 12:31, 23 February 2017

Particle picking (sometimes referred to as Volume annotation) 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 class.

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

  • Prepare your volumes
  • Particle picking
  • Particle extraction

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 one or models that capture the geometry of the particle distribution. The models will be also kept in the catalogue.

Sometimes, models carry parameters that need to be tuned for your case (for instance, the radius of filament models, or the particle density in surface models). When you have many models defined on a set of tomograms, and you want them to have the same, non-default parameter values, it is a good idea to define each individual model with the minimal amount of user input, save it and proceed to the next one. Then, when all the models in the catalogue have been defined, one can write a script to visit in one loop all the models and operate on them.

Extracting particles

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