Image processing for nice pictures

Good time of a day, friends.
We have faced a temporary (I HOPE) difficulties in our laboratory: our confocal microscope is broken.
So we are switching to fluorescent one, which is not really good.
Some examples of images (not best, not worst) are attached. (somewhy they are not loading dropbox link)

So I want to ask for advices:

  1. What can we do on the software level to make them better in scientifical part. My guess is to take short time series and marge “average” image, but maybe you can give some other ideas. Or maybe tips how to do it better.

  2. What can we do on software level to make them nice. Even if not scientifically correct - for some presentations. I perfectly know, that there are some processings, which will dramatically change “information”, and it is not appropriate to calculate data after such processing. But sometimes just beautifull image is needed.

Mainly noise and resolution are the problem. Should I invest some times in deconvolution? Or anything else? I am experimenting myself, but some tips would be nice. There are quite a lot of approaches and as always its hard to understand without help are you doing something wrong or you should use another approach.

Thank you a lot for your time.


The most important question: what information do you want to get from the images?

Some general remarks –

I don’t think noise is the problem, so averaging won’t help.

The punctate structures look a bit blurry. They could be simply out of focus. You can reduce blur from out-of-focus light by collecting a z series and doing deconvolution.

If you can’t find any focal plane that looks in focus, then you may have dirty or misaligned optics. In that case there is no reputable processing method that will help.

To improve spatial resolution (assuming optics are clean and set up properly):

  • use a lens with high magnification AND high numerical aperture (at least 1.3 or 1.4)
  • use 1x1 binning (that is, no binning) in the camera

Let’s say, that for now task is to get “nice” picture for presentation. Not scientific information.
And the question is about software solutions, not hardware.

Here are examples of my attempts. I consider one of them “better”. dropbox link to original files

and 2 more

What do you want to show with these images – what is the message to the reader?

A background subtraction with a radius based on the punctate objects should eliminate the blurring. CLAHE may also be of interest for this also.

Hope this helps