Find Focused Slices

Downloads

You can download this plugin here, and put it into ImageJ's plugins folder.

The java source code: Find_focused_slices.java

Sample image stacks could be downloaded here

Description

This ImageJ plugin will pick up focused slices from a Z stack. Focus quality of each slice is evaluated by autofocus algorithm "Normalized variance"  (Groen et al., 1985; Yeo et al., 1993).

Applications

• • You can use this plugin to first select out slices with acceptable focus quality within a stack which covered a large range of Z (e.x. automatically acquired images). Then run simply a maximum projection or use plugins like Extended Depth of Field to get a single focused image. It is similar to the "Best focus" function in Metamorph, but give better result in my experience. 

  • It could be used to find out the focus plane of a given object within a Z stack. For example the z coordinate of centrosome position within the cell. (The slice number being selected is recorded in the "Label" field of the new stack, which could be easily retrieved by using the macro function getMetadata("Label") )

  • It could be used to find the height of a cell provided that the membrane is fluorescent labeled.

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This plugin was inspired by the "Select Frames With Best Edges" plugin from Jennifer West (http://www.umanitoba.ca/faculties/science/astronomy/jwest/plugins.html).

The Normalized Variance autofocus algorithm has also been implemented as an ImageJ macro by Andy Weller.

System Requirement

Tested on ImageJ 1.44 and above. But should be compatible with earlier version.

Installation

Download the Find_focused_slices.class and put it into ImageJ's plugins folder.

Then restart ImageJ or run "Refresh Menus".

Contact

Any question or comment, please contact Qingzong TSENG (qztseng at gmail.com).

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