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Morphometry of light microscopy images with ImageJ


Morphometric parameters that quantify the shape, size, and orientation of objects in an image are useful for analyzing features of interest while rejecting artifacts or unwanted features. ImageJ can automatically identify objects based on local or global intensity variations (thresholding) and then perform a variety of morphological measurements on them. This workshop will demonstrate how to use these functions of ImageJ to easily quantify information present in 2D biological light microscopy images. Additionally, two simple macros to facilitate the interpretation of morphometric data will be introduced: one for judging the fidelity of object identification by plotting object center points (centroids) onto the original image and another to create scatter plots of morphometric parameters to visualize and quantify relationships between parameters.


morphometry, thresholding, light microscopy

Short CV

G. Esteban Fernandez earned a B.S. in Biology from Harvey Mudd College in 1999 and a Ph.D. in Biological Chemistry from the University of California, Los Angeles in 2006. He has received training in microscopy and digital image analysis and is a biological light microscopy professional working as a core facility manager for the past 5 years. He has extensive experience teaching and utilizing various image processing software packages, including ImageJ, as applied to a diverse range of imaging experiments in biology.

Administrative data

Presenting author: G. Esteban Fernandez, Ph.D.
Organisation: Children's Hospital Los Angeles


Type: Workshop

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