Save HCS position label in NDTiff dataset axes

[ieivanov]

This PR enables using HCS position labels as indices of the NDTiff dataset "position" axis. This will allow us to parse them using iohub (czbiohub-sf/iohub#166) and propagate them to downstream processed results using infrastructure developed in czbiohub-sf/iohub#159.

Example datasets available in https://github.com/micro-manager/NDTiffStorage/pull/124/files and cm.automaton/mantis_HCS_acq_1

Closes #32.

Requires micro-manager/AcqEngJ#95 and #39

This PR should be used with caution until micro-manager/NDStorage#124 is resolved. Using iohub to read the data is robust to sorting issues discussed in that PR.

EDIT: micro-manager/NDStorage#124 has merged. iohub is also robust to reading data with unordered position labels.

Other related PRs: micro-manager/AcqEngJ#95, micro-manager/pycro-manager#640

[ziw-liu]

I'm a bit confused, czbiohub-sf/iohub#166 requires ndtiff>2.2.1, but c07ad15 requires ndtiff<2.0?

[ieivanov]

I'm a bit confused, czbiohub-sf/iohub#166 requires ndtiff>2.2.1, but c07ad15 requires ndtiff<2.0?

Right, this is a temporary restriction until #39 merges, hopefully very soon

[ieivanov]

@talonchandler @edyoshikun can I get a review on this PR? In summary it switches the position axis of mantis datasets from integers, e.g. [0, 1, 2], to strings, e.g. ['Pos0', 'Pos1', 'Pos2'] or more likely ['A1_Site0', 'A1_Site1', 'A1_Site2']. This is a simple change to the acquisition engine, but downstream processing of this data has been a bit more involved. After czbiohub-sf/iohub#171 merges we'll be in good shape to take these datasets and convert them to zarr, preserving the HCS site labels in the zarr store.

[talonchandler]

LGTM! Nice inter-library metadata wrangling 🤠 .

[edyoshikun]

LGTM! This makes more sense. Thanks for this

[ziw-liu]

Does this require iohub==0.1.0dev5?