Dear fellow image enthusiasts,

I just recently started doing a lot of confocal fluorescence microscopy imaging and I am getting good images, but I still thought about increasing their quality. I immediately considered deconvolution methods. Only problem is, I have never used a deconvolution tool before.

Could anybody help me out with kind of a "quick start protocol"? I want to use imageJ and donloaded deconvolutionlab 2 (http://bigwww.epfl.ch/deconvolution/deconvolutionlab2/) as well as the PSF generator they recommend (http://bigwww.epfl.ch/algorithms/psfgenerator/).

First thing:

Which method should I chose to generate a PFS which would work for deconvoluting my 2D image?

Which parameters do I have to know (both while taking the image and for generating a proper PSF)?

- I do know the refractive index if my immersion oil, do I also need to consider the refractive index of the NPG used for covering and/or of the glass cover slide?

- I also know, the NA

Which method should I chose for decovoluting the 2D image?

I made a couple of test runs, but the output looked much worse than the input and particularly proper colour information was lost.