Vesicle models

Vesicle models are appropriate when particles are evenly distributed on surfaces reasonably similar to spheres or ellipsoids. The model can estimate the center and radius provided points provided by the user in the visible part of the object, or the other way round, letting the user provided center and radius.

Important parameters

Radius

Given in pixels. Can be estimated or provided by the user.

Center

Given in pixels. Can be estimated or provided by the user.

Separation

Given in pixels. Defines the mean separation of the cropping positions to be defined in the vesicle surface. When choosing this value, you should think on oversampling the actual distribution of particles that you expect.

Picking vesicles in a tomogram browser

There are different methods for vesicle picking interactively.

Cloud of points

The most robust method requires from the user to pick several points in each vesicle model, and then let Dynamo fit the radius and the center. This procedure can be performed through the browser dtmslice</cc>.

A tomogram with several vesicles shown in dtmslice

Creation of a vesicle model

Click vesicle points on different z levels (use [c] to pick each)

View from a lower z level

Menu options after secondary click on a model point

Menu options after secondary click on a model point

Depiction of the fitted vesicle surface

Command line

Here come some examples of creation and manipulation of vesicle models from the command line

Given user points

Given center and radius

a = dmodels.vesicle(); % creates an empty vesicle model
a.radius = 70;
a.center = [40,100,200];
a.separation = 15;
a.updateCrop();  % here it will some time computing the particles.
t=a.grepTable(); % extracts the table
dtplot(t,'profile','oriented_positions'); % scatter plot of images
axis equal; % for a better visualization, same scale an x,y,z
shg

Table plot of positions and particles generated by a vesicle model