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bioio-devs / bioio

Image reading, metadata management, and image writing for Microscopy images in Python
https://bioio-devs.github.io/bioio/OVERVIEW.html
BSD 3-Clause "New" or "Revised" License
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Feature/ome zarr writer v2 #48

Closed toloudis closed 4 months ago

toloudis commented 5 months ago

Link to Relevant Issue

Resolves #46

We have been developing a new ome-zarr-writer that works better for our long time series data. We want to bring that code into this repo and make it a part of bioio.

Description of Changes

Add new ome zarr writer. Do some code cleanup, and make sure it is well commented and documented. Add unit tests for it.

This PR is intended to be like an "initial add", bringing the new code in without any functional changes, apart from code formatting and commenting, so that it can be a direct replacement in our ome-zarr-conversion codebase.

toloudis commented 4 months ago

Generally all looks good to me! Nice work. My biggest nitpick is to store this in a different location rather than calling it "ome_zarr_writer_2" maybe bioio.experimental.writers.ome_zarr_writer?

Actually I would suggest that this writer code is LESS experimental than the other, since it's been used (from a different repo) to do quite a lot of bulk conversions already.