Particle picking - Revision history

Daniel Castaño at 11:31, 23 February 2017

2017-02-23T11:31:29Z

Daniel Castaño at 12:49, 4 August 2016

2016-08-04T12:49:52Z

Daniel Castaño: /* Picking particles */

2016-04-27T16:24:09Z

Picking particles

Daniel Castaño at 14:35, 21 March 2016

2016-03-21T14:35:41Z

Daniel Castaño at 14:33, 21 March 2016

2016-03-21T14:33:04Z

Daniel Castaño at 14:32, 21 March 2016

2016-03-21T14:32:35Z

Daniel Castaño at 14:13, 21 March 2016

2016-03-21T14:13:37Z

Daniel Castaño at 14:10, 21 March 2016

2016-03-21T14:10:33Z

Daniel Castaño at 14:10, 21 March 2016

2016-03-21T14:10:17Z

Daniel Castaño at 14:09, 21 March 2016

2016-03-21T14:09:47Z

@@ Line 9: / Line 9: @@
 * Particle picking
 * Particle extraction
 == 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.
 == Picking particles==
 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.

@@ Line 16: / Line 16: @@
 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 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.
+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.
 == 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]]

@@ Line 14: / Line 14: @@
 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==
-Then you would [[tomogram viewing|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.
+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 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.
 == 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]]

@@ Line 1: / Line 1: @@
-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 (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.
+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:
+Whichever the model type is the one that captures the distribution in your particles, the workflow would be the same:
-* Preparing your volumes
+* Prepare your volumes
-* Picking particles
+* Particle picking
-* Extracting particles
+* Particle extraction
 == 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.
+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==
 Then you would [[tomogram viewing|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.

@@ Line 15: / Line 15: @@
 == Picking particles==
 Then you would [[tomogram viewing|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 [[Scripts on sets of models | 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 [[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]]

@@ Line 11: / Line 11: @@
 == Guadalajars==
- You would More tomograms can be incorporated later.
+fsdfd.
 == 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.