Thinking in Three Dimensions: An Exploration of Analytical Methods for Optical Sections from Confocal Microscopy Using ImageJ

 

Michael J. Keller

Tested Studies in Laboratory Teaching, 2011, Volume 32

Abstract

The microscope has long been a key piece of laboratory equipment, and in modern research fluorescence microscopy has become the dominant technology. Confocal microscopy has gained prominence through image clarity and the ability to generate three dimensional image data through optical sectioning. This exercise uses the open-source software package ImageJ to explore the analysis and representation of fluorescent images in two- and three-dimensions using confocal image stacks. Manipulations by students include merging color stacks, making a two-dimensional image montage, generating a two-dimensional z-projection of a three-dimensional stack, and rotating stacks in three dimensions.

Keywords:  image analysis, ImageJ, confocal microscopy

Dalhousie University (2010)