This function allows you to build surfaces around points in CytoMAP. This utilizes MATLAB's alphashape() function.
To use this start by clicking the New Figure button in the main interface. Next plot the objects you want to build a surface around. This can be neighborhoods or cells. In the example below we use the example lymph node data and selected the lymphatic spots on LN1.
After plotting the desired objects click the Make Surface button in the top function ribon. This will bring up the surface interface where you can name you surface and select the following creation parameters:
Surface Creation Radius:
This selects the alpha radius, which is the smallest radius that creates a shape enclosing points. Think of this like specifying the size of an ice cream scoop. The smaller this radius the less inclusive the surface will be and the tighter it will surround your points. The larger the radius the bigger and more granular the surface will be.
Volume Exclusion Threshold:
This allows you to exclude any volume smaller than the specified ammount. This is useful if you only are interested in a main volume.
Hole Fill Threshold:
This allows you to fill any holes in your volume.
If you want to make a surface with the same parameters quickly, select the Redefine Surface checkbox and change the plotted sample, then click Plot again. This will make a surface with the same parameters on the newly plotted sample.
If you want to plot a preiously made surface; in the main figure window navigate to Plot -> Plot Surface. Next select the sample for which you want to plot the durface and the surface you want to plot.
Using the surface function you can quickly gate on points, find the intersection between user defined regions, find the distance to region borders, and other useful things.