SerialEM Note: Adding Mesh Polygon by a Single Click¶

Author: Chen Xu
Contact: <chen.xu@umassmed.edu>
Date Created: Nov. 22, 2024
Last Updated: Nov. 22, 2024

Abstract

Sometimes, one wishes to be able to add a mesh polygon to LMM map quickly. It is alright to just add a few point items to the centers of wanted meshes, and then define a single polygon montage file to cover them all. However, this is not ideal when the multiple meshes are at different sizes. SerialEM can fit montage for each polygon to deals with different sizes, but you have to have polygons defined already. One can manually add polygon for each of the meshes wanted, but it needs to click multiple times to add a polygon.

Recently, a new feature was implemented to add mesh polygon from a single mouse click. Here I show you how.

Autocontour¶

You perhaps already know SerialEM has Autocontour function to find multiple meshes and add polygons. The end result is like below.

Fig.1 Autocontour Result

The dialog for autocontour is shown here.

Fig.2 Autocontour Dialog

If this all works, then you can ask the same program to add a single mesh polygon. First you make sure to check the box “Make single polygons by clicking in images”. And then you use Ctrl+SHIFT+middle to click in a mesh area. The single mesh polygon will be generated. You don’t have to accurtely click on the very center of a mesh, anywhere inside the mesh will work.

This is a special case for Autocontour function which utlize statistics info from multiple meshes. In this special case, there is a property internally to control how big areas to help.

AutocontSubareaSizeFac
   Follow with the linear size of the region to extract for making a single polygon around
   a grid square by clicking, as a multiple of the current setting for the maximum grid square
   size in the Autocontouring Grid Squares dialog; the default is 6.  A smaller value will make
   it run faster.

If you want to change from default, you can add a line in your property file

AutocontSubareaSizeFac   3

Or you can temporarily control it via script command, since this is a scriptable property

SetProperty AutocontSubareaSizeFac 3

Below is an image shown the result.

Fig.3 Autocontour Single Click