Document recommended pixel size and crop size

[tibuch]

From #61:

I also would like to ask about recommendation of voxel size.
I tried several test by using the original image of 20x20x100nm, then downsampled the image using Fiji to 40x40x100 and I found the fit way more convincing on the second stack. I was wondering if you have recommendation to what the ratio between axial and lateral step size should be to get a good fit.

[rdemets]

Please allow me to add an image as an example. Both fits are coming from the exact same beads acquired at the same time. The fit on the left is with a 20x20x100nm acquisition. The one of the right is the same image downsampled at 40x40x100nm.

[lgelman]

Hi there!
the ratio between axial and lateral should somehow reflect the difference in resolution in both directions, i.e. approx 3 times.
20x20x100 is oversampling for most regular light microscopes (i.e. with no super-resolution capability), because that would mean an expected reoslution of approx. 50nm in XY and 250 in Z. I recommend to at least double these numbers. For toutine assessment of microscopes (no PSF distillation) we use at least 60-70nm in XY and 200 in Z. Anything below will just add some noise and will reduce the precision of the fit.
Cheers!
Laurent.