This post is a duplication of one from the Image.sc forum, because it may be more relevant here.
I am curious about what is expected for a focus map produced by commercial microscope software and whether there is anything like a consensus in the field. For instance, should one expect that the software can produce a flat plane that is angled and tilted to compensate for a stage or holder that is at a slight angle to the imaging device, or should the software also be able to produce a more complex surface to compensate for tissue that is not completely flat?
In your experience which vendors produce software of just the tilted plane type and which can deal with an undulating surface? Do your expectations differ between confocal and widefield? Between ‘standard’ microscopes and slide scanning devices?
I will be happy to receive direct responses as well as replies on this list.