Automatic Section Thickness Determination

Theory. The determination of section thickness is required for accurate object (cell) counting.  Two sharp ‘knees’ exists on the focus curve during the transition from unfocused to focused optical planes. We developed a thresholded absolute gradient function for finding detectable bends that closely correspond to the bounding optical planes at the upper and lower tissue surfaces. This critical step requires a trained user to estimate the section thickness by manually locating the upper and lower surfaces of tissue sections.

Practice. This algorithm provides an accurate method for automatically finding the top and bottom planes on a stained tissue section.

Reference: Elozory, D.T., Bonam, O.P., Kramer, K., Goldgof, D., Hall, L., Mangual, O., Mouton, P.R. Automatic Section Thickness Determination Using An Absolute Gradient Focus FunctionJournal of Microscopy, 248: 245-59, 2012.