Upgrade PM and MM

[talonchandler]

The current pycromanager==0.25.40 is not compatible with recOrder, so this PR suggests an upgrade to pycromanager==0.27.2. See mehta-lab/recOrder#373.

You might try upgrading pycromanager without upgrading MM, but I expect you'll need to upgrade MM to 2023-04-26 at the same time. I've updated the docs to reflect this, but feel free to change.

These upgrades should be tested on the scope before merging.

[ieivanov]

Thanks @talonchandler, I think this will be good, we'll test and merge soon

[ieivanov]

I find that when using pycromanager==0.27.2 ndtiff also needs to be pinned to 1.12.2. I recommend using MM nightly build 2023-03-12 rather than 2023-04-26 - I expect the pycromanager storage_monitor_fn will not work with 2023-04-26.

TODO: update the readme to reflect the correct MM version

[talonchandler]

Sounds good, MM recommendation fixed.

Feel free to merge when you're ready.

[ieivanov]

I ran into a bug with the mantis acquisition that I'm trying to trace down before merging this PR. If the bug is in the java AnqEngJ then we'll need to upgrade to a newer PM version after I fix it.

[ieivanov]

We'll need to upgrade to the latest pycromanager and MM nightly build after micro-manager/AcqEngJ#94 and micro-manager/pycro-manager#623 get merged.

[ieivanov]

@talonchandler @edyoshikun this PR is ready to merge, pending one more test on the microscope. Can I get a quick review of the code?

[edyoshikun]

This LGTM. The most important change I think was the iohub to 0.1.0.dev4for making sure that the datasets created have the proper dtype and LUT when loaded into napari, and the pycromanager version which is the one on mantis at the moment. Thanks guys!

[ieivanov]

Thanks! As far as the acquisition goes, there is no real dependency on iohub. For the next few acquisitions I will keep two conda environments and two MM versions, just in case we need a quick fallback.

[talonchandler]

LGTM, thanks Ivan.

[ieivanov]

Before this PR, the mantis acquisition used MM nightly build 2023-02-08 with NDTiffStorage 2.10.0 for the LF acquisition and MM nightly build 2023-03-12 for the LS acquisition. A clone of the conda environment used before this PR is available as mantis_pm02540.