Autofocus per FOV

[guiwitz]

Here

Squid/software/control/core/core.py

Line 1710 in 86216a2

and (self.af_fov_count % Acquisition.NUMBER_OF_FOVS_PER_AF == 0)

autofocus is only performed every Nth field of view as set by NUMBER_OF_FOVS_PER_AF whose default is 3. This seems to mean that only every third FOV will have images in focus? It doesn't look like the updated focus information from that FOV is propagated to other FOVs. Is there a logic behind that or is it just a bug?

[hongquanli]

It was a historical implementation to speed things up. The UX part for autofocus needs improvement.

Below are the options we should support:

• Focus map alone
  • option 1: imported focus map
  • option 2: manually defined focus map
  • option 3: focus map auto-generated by contrast autofocus or focus map auto-generated by laser af
• Contrast AF every FOV (on top of focus map - if focus map enabled)
• Laser AF (on top of focus map - if focus map enabled)

With Nt > 1, we should give user the option to offset the focus map (for each region, optionally) with laser AF or contrast AF.

To implement the above I think we need to add an acquisition configuration dialog window to present the different options.

[hongquanli]

@Alpaca233

[mpiersonsmela]

I was also just running into this problem. Can this setting be adjusted to do a new autofocus on every well (instead of a fixed number of FOVs)?

More generally it would be good to have settings like this one able to be changed in the GUI instead of hardcoded.

[hongquanli]

@mpiersonsmela for "every well" do you want to use center of the well or first FOV of the well?

[mpiersonsmela]

Probably the center of the well would have better results.