Re: Chromatin condensation

Posted by Olivier Burri on Aug 03, 2015; 12:49pm
URL: http://imagej.273.s1.nabble.com/Re-Chromatin-condensation-tp5013860p5013864.html

Hi Thomas,

I had some success in calibrating the chromatin condensation using the Texture Analyzer http://rsb.info.nih.gov/ij/plugins/texture.html

On your images:
Cropped the Z stacks to contain slices with nuclei
Ran the GLCM Texture plugin with a step size of 3 pixels

Looked at the Average Contrast output of each image and got these values

Control 229.209
Mid 205.782
Condensed 135.794

What I would suggest is try different step sizes to find the one that maximizes the delta between the conditions and perhaps use that.

You can also try the other metrics from the plugin, which have a similar trend (Except for Correlation, which makes sense);

Best

Oli

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