ome-zarr-py
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Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
We are looking to save multiplexing data (⇒ multiple cycles of acquisitions for the same plate) to HCS OME-Zarr files. Reading in the OME-NGFF spec, [plates have the acquisitions key]([https://ngff.openmicroscopy.org/latest/#plate-md](https://ngff.openmicroscopy.org/latest/#plate-md))....
Add changelog 0.6.0. Do we call this `0.6.0rc1`, or should we just go for `0.6.0` release?
updates: - [github.com/psf/black: 22.6.0 → 22.8.0](https://github.com/psf/black/compare/22.6.0...22.8.0)
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The following code example produces an error on the last line. The code does the following: 1) creates a 3D array (cyx axes) and writes it to zarr 2) loads...
Hi there, and thanks for your support. We (me and @mfranzon) encountered some issues while trying to reproduce the behavior of https://github.com/ome/ome-zarr-py/pull/57#issuecomment-722443138, that is, to visualize (in napari) a zarr...
Fixes #65. This refactors `PlateLabels`: - Doesn't assume that a Well exists at `row:0 column:0`. - Doesn't assume that there is a label named `"0"` at `image/labels/0/`. Reads `image/labels/.zattrs` for...
What is the current best practice for generating & saving a multiscale zarr array, given a single resolution of that data? I gather things have changed a lot recently with...
And creates an invalid ome.zarr file! See the minimal example below: ```python import numpy as np import ome_zarr import ome_zarr.scale import ome_zarr.writer import zarr vol = np.random.randint(0, 1000, size=(32, 256,...
Hi, I read and also tried this method: https://ome-zarr.readthedocs.io/en/stable/api/writer.html and from the docu it says the image array must have 5 dimenisons in the following order TCZYX. Which raises some...
Work in progress... I am testing the JSON schemas from ngff repo, downloading them to a cache with https://github.com/allenai/cached_path. This PR adds a `validate` command that validates the JSON at...