automate distance measure of uneven surface

Posted by daschneider9 on Feb 25, 2016; 4:55pm
URL: http://imagej.273.s1.nabble.com/automate-distance-measure-of-uneven-surface-tp5015719.html

Greetings,

I need to process a large image set of masks (like the one attached) which represent a tissue cross section (lower white region) and surrounding airspace (upper black region). I've written macros to get me this far but I don't know if there is already an existing automatic way to measure the distance of the surface.

Note, as in this example image, that there are occasional white-black interfaces not to be included. These occur in the non-tissue space (in the image the single white blotch in upper right quadrant) and those holes in the deeper tissue space (one about mid-lower left side, another on low right side). All images are oriented in this way to start. I'm not concerned about not catching the bit of surface that is just below the left edge boundary.  If it will make for a much simpler solution, I could remove the bits of white-in-black and black-in-white not representing the surface to be measured. But as you can see, hand drawing the surface with a line for a hundred or more images is not feasible nor likely to be accurate.

Is there a plugin or function already out there that I can use (preferably in a macro or batch process) to get this done?

Thank you for your assistance,

Dave

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