Vesicle models - Revision history

Daniel Castaño: /* Against tomogram data */

2017-02-24T09:00:49Z

Against tomogram data

2017-02-24T08:59:35Z

Against tomogram data

2017-02-24T08:48:41Z

2017-02-22T16:15:18Z

Picking vesicles in a tomogram browser

2017-02-22T16:10:11Z

From dipole det models

2017-02-22T16:08:48Z

Given center and radius

2017-02-22T16:08:34Z

Given center and radius

2017-02-22T16:06:00Z

Given user points

2017-02-22T16:00:42Z

From Dipole Set models

2017-02-22T15:59:13Z

From Dipole Set models

@@ Line 124: / Line 124: @@
 ''Dynamo'' includes some tools for cross correlation based pattern matching. These can be used to fit the center and radius in  a roughly picked vesicle.  The script that we provide below illustrates how to use the low level vesicle finding utilities in a real life example.
-The assumption is that a set of models of approximately picked vesicles (maybe converted from a [[dipole set models |dipole set]]) has been defined in the tomogram with index 1 of a catalogue located in the folder <tt>'../catalogues/ctfCorrected</tt> with relation to the current directory. The script extracts the models whose name follows a pattern as a [[matlab cell array | cell array]] and then loops on them, fitting them to a simulated vesicle.
+The assumption is that a set of models of approximately picked vesicles (maybe [[Vesicle_models#From_dipole_set_models | converted]] from a [[dipole set models |dipole set]]) has been defined in the tomogram with index 1 of a catalogue located in the folder <tt>'../catalogues/ctfCorrected</tt> with relation to the current directory. The script extracts the models whose name follows a pattern as a [[matlab cell array | cell array]] and then loops on them, fitting them to a simulated vesicle.
 The fitting procedure for each vesicle works by first extracting from the tomogram a cube around the vesicle (with {{t| extractEnclosingVolume}}).

@@ Line 122: / Line 122: @@
 === Against tomogram data ===
-''Dynamo'' includes some tools for cross correlation based pattern matching. These can be used to fit the center and radius in  a roughly picked vesicle.
+''Dynamo'' includes some tools for cross correlation based pattern matching. These can be used to fit the center and radius in  a roughly picked vesicle.  The script that we provide below illustrates how to use the low level vesicle finding utilities in a real life example.
   <nowiki>% extracts model files in a catalogued volume of interest.
-files = dynamo_catalogue_models('../test/first','i',1,'nameContains','rawVesicle');
+files = dynamo_catalogue_models('../catalogues/ctfCorrected','i',1,'nameContains','rawVesicle');
 disp(sprintf('Found %d raw vesicle files in the set',length(files)));

@@ Line 95: / Line 95: @@
 Here come some examples of creation and manipulation of vesicle models from the command line
-===Given user points===
+===Creation through user points===
 The method is called <tt>approximateGeometryFromPoints</tt>. If a vesicle object <tt>v</tt> has a set of points stored in the <tt>points</tt
 > property (i.e., <tt>v.points</tt> contains a matrix of Nx3 numbers, each one a 3d coordinate of the vesicle membrane), invoking the order <tt>v.approximateGeometryFromPoints</tt> will write into <tt>v.radius</tt> and <tt>v.center</tt> the codes estimation for radius and center.
-===Given center and radius===
+===Creation through center and radius===
 This code merely explains how to create an uniform distribution of points on a vesicle model. The central idea is to define the distance between points with the <tt>separation</tt> property (in pixels), and then invoke the method <tt>updateCrop</tt> that produces the <tt>crop_point</tt> coordinates.
@@ Line 117: / Line 117: @@
 [[File:vesicle_point_distribution_on_example_with_given_radius.png|thumb|center|400px| Table plot of positions and particles generated by a vesicle model]]

@@ Line 19: / Line 19: @@
 ==Picking vesicles in a tomogram browser==
-There are different methods for vesicle picking interactively.
+There are different methods for vesicle picking interactively, depending on the precision you need. When choosing your method, remember that, if necessary, vesicles can be fitted against the tomogram density map in a later stage. If such a fitting is possible, you don't need to spend too much time trying to make your manual picking too precise, but just reasonable enough to be used as a seed for the automated fitting procedure.
 ===Cloud of points===

@@ Line 50: / Line 50: @@
 [[File:VesicleClickFittingInTomoslice.png|thumb|center|500px|Depiction of the fitted vesicle surface]]
-=== From dipole det models ===
+=== From dipole set models ===
 It is also possible to use other models to define vesicle models. This is useful when you have several vesicles in one tomogram, and you don't want to initiate a vesicle model for each one of them. The [[dipole set models| dipole set model]] allows creating in a single model several 'dipoles', each one of them having a <tt>center</tt>, a <tt>north</tt> and a <tt>south</tt>.
 We can use this model to define each vesicle from a dipole: the <tt>center</tt> property of the dipole can be directly transferred to the vesicle, and the radius of the vesicle can be defined as the distance between the <tt>center</tt> and <tt>north</tt> coordinates registered in the dipole.

@@ Line 103: / Line 103: @@
 This code merely explains how to create an uniform distribution of points on a vesicle model. The central idea is to define the distance between points with the <tt>separation</tt> property (in pixels), and then invoke the method <tt>updateCrop</tt> that produces the <tt>crop_point</tt> coordinates.
 <!--[[File:vesicle_point_distribution_on_example_with_given_radius.png|thumb|right|300px| A screenshot on <tt>dpreview</tt> ]]-->
   <nowiki>
 a = dmodels.vesicle(); % creates an empty vesicle model

← Older revision		Revision as of 16:08, 22 February 2017
Line 101:		Line 101:

	===Given center and radius===		===Given center and radius===
−	~~<!--[[File:vesicle_point_distribution_on_example_with_given_radius.png\|thumb\|right\|300px\| A screenshot on <tt>dpreview</tt> ]]-->~~

		+	This code merely explains how to create an uniform distribution of points on a vesicle model. The central idea is to define the distance between points with the <tt>separation</tt> property (in pixels), and then invoke the method <tt>updateCrop</tt> that produces the <tt>crop_point</tt> coordinates.

		+	<!--[[File:vesicle_point_distribution_on_example_with_given_radius.png\|thumb\|right\|300px\| A screenshot on <tt>dpreview</tt> ]]-->

	<nowiki>		<nowiki>

@@ Line 63: / Line 63: @@
 ds = dread(dipoleSetModelFile);
 disp(sprintf('Found %d dipoles in the set',length(ds.dipoles)));
@@ Line 68: / Line 69: @@
 for i=1:length(ds.dipoles);
+     % selects the i-th individual dipole in the set
      dipole = ds.dipoles{i};
      % creates a vesicle model
      v = dmodels.vesicle();
-     %v.name = sprintf('%sTofittedVesicle_%d',ds.name,i);
      v.name = sprintf('%srawVesicle_%d',ds.name,i);
@@ Line 84: / Line 86: @@
      v.radius = norm(dipole.center - dipole.north);
      v.saveInCatalogue();