Deconvolution

Deconvolution#

Deconvolution is a method of denoising a microscopy image using information about the optical setup. In this case, we estimate a point spread function for the deconvolution using the user input parameters of numerical aperture, resolution, emission wavelength, and refractive index.

A Fiji macro developed by Ed Evans is available in the “Scripts” directory of the Google Drive. It is called “decon.groovy”.

More background on the algorithm (Richardson-Lucy + Total Variation Regularization):
https://doi.org/10.1002/jemt.20294

  1. Copy-paste the code into the script editor (File > New > Text Window, Ctrl-Shift-N), or open the .groovy file. Change the script language to Groovy by going to Language > Groovy in the Editor window, then run the script on the selected image.

Deconvolution macro editor

  • A dialog will prompt for the experimental parameters. Enter the known parameters from the experiment (or for the demo use the default values).

Deconvolution prompt

Example: Try with Cell Colony (FIJI Sample) and default parameters to see a demonstration.
You’ll notice sharper edges and reduced background noise — even though the parameters may not match the real imaging conditions.

Deconvolution PSF