Automatic location of microscopic focal planes for computerized stereology

Daniel T. Elozory; Om Pavithra Bonam; Kurt Kramer; Dmitry B. Goldgof; Lawrence O. Hall; Osvaldo Mangual; Peter R. Mouton

doi:10.1117/12.878776

9 March 2011 Automatic location of microscopic focal planes for computerized stereology

Daniel T. Elozory, Om Pavithra Bonam, Kurt Kramer, Dmitry B. Goldgof, Lawrence O. Hall, Osvaldo Mangual, Peter R. Mouton

Author Affiliations +

Proceedings Volume 7963, Medical Imaging 2011: Computer-Aided Diagnosis; 79633C (2011) https://doi.org/10.1117/12.878776
Event: SPIE Medical Imaging, 2011, Lake Buena Vista (Orlando), Florida, United States

Abstract

When applying design-based stereology to biological tissue, there are two primary applications for an auto-focusing function in the software of computerized stereology system. The system must first locate the in-focus optical planes at the upper and lower surfaces of stained tissue sections, thus identifying the top and bottom as well as the thickness of the tissue. Second, the system must find the start and end along the Z-axis of stained objects within a Z-stack of images through tissue sections. In contrast to traditional autofocus algorithms that seek a global maximum or peak on the focus curve, the goal of this study was to find the two "knees" of the focus curve that represent the "just out-of-focus" focal planes. The upper surface of the tissue section is defined as the image just before focus is detected moving down the Z-stack. Continuing down, the lower surface is defined as the first image of the last set of adjacent images where focus is no longer detected. The performance of seven focus algorithms in locating the top and bottom focal planes of tissue sections was analyzed by comparing each algorithm on 34 Z-stacks including a total of 828 images. The Thresholded Absolute Gradient algorithm outperformed all others, correctly identifying the top or bottom focal plane within an average of 1 μm on the training data as well as the test data.

Citation Download Citation

Daniel T. Elozory, Om Pavithra Bonam, Kurt Kramer, Dmitry B. Goldgof, Lawrence O. Hall, Osvaldo Mangual, and Peter R. Mouton "Automatic location of microscopic focal planes for computerized stereology", Proc. SPIE 7963, Medical Imaging 2011: Computer-Aided Diagnosis, 79633C (9 March 2011); https://doi.org/10.1117/12.878776

ACCESS THE FULL ARTICLE

INSTITUTIONAL
Select your institution to access the SPIE Digital Library.

SELECT YOUR INSTITUTION

PERSONAL
Sign in with your SPIE account to access your personal subscriptions or to use specific features such as save to my library, sign up for alerts, save searches, etc.

PERSONAL SIGN IN

No SPIE Account? Create one

PURCHASE THIS CONTENT

SUBSCRIBE TO DIGITAL LIBRARY

50 downloads per 1-year subscription

Members: $195

Non-members: $335 ADD TO CART

25 downloads per 1 - year subscription

Members: $145

Non-members: $250 ADD TO CART

PURCHASE SINGLE ARTICLE

Includes PDF, HTML & Video, when available