ome-zarr-py
ome-zarr-py copied to clipboard
ome
Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
Dear all, Could you tell me if there is any documentation available for ome-zarr-py? Also, is it possible to straightforwardly parse zarr arrays contained in ome-zarr fileset using original zarr...
The name of fields in the methods in the library are mostly explicit e.g. ``columns``, ``wells``. ``format`` should be used instead of ``fmt``. See https://github.com/ome/ome-zarr-py/pull/153#discussion_r782856448
see: https://github.com/ome/ome-zarr-py/pull/127 Once https://github.com/fsspec/filesystem_spec/issues/819 is closed, the cap can likely be removed.
See https://github.com/ome/ome_zarr_test_suite/pull/11 Currently `ome-zarr-py` doesn't validate data, e.g. checking that essential metadata is present or that data is expected dimensions. Maybe add this functionality to the `info` command by default...
Taking the output of `bioformat2raw 0.3.0` which is a collection of OME-Zarr multiscale images as an example: ```bash bioformats2raw "test&series=2.fake" "test.zarr" (zarr) [sbesson@pilot-zarr1-dev ~]$ ome_zarr info test.zarr/ (zarr) [sbesson@pilot-zarr1-dev ~]$...
We've been working on a remote Zarr workflow that would require the use of a `HTTPFileSystem`. However, the current implementation of `ome-zarr-py` has the `FSStore` kinda baked into it. I've...
Passing `mode=w` to `parse_url` does not truncate existing files as it should. Minimal example: ```python import numpy as np import ome_zarr.writer import zarr file_path = "my.ome.zarr" loc = ome_zarr.io.parse_url(file_path, mode="w")...
With v0.2 released, `ome_zarr` (and likely other libraries) should provide a way for users to upgrade their datasets to nested layout.
The SPW images exported via `omero zarr export` works in napari: ``` $ napari https://minio-dev.openmicroscopy.org/idr/idr0001-graml-sysgro/pr59_nested/2551.zarr/A/5/0 ``` But not the plate itself (visible in vizarr with nested PR): https://deploy-preview-85--vizarr.netlify.app/?source=https://minio-dev.openmicroscopy.org/idr/idr0001-graml-sysgro/pr59_nested/2551.zarr Trying to...
Passing the top-level container from bioformats2raw to `ome_zarr download` leads to the following error: ``` z) ~/opt/ome_zarr_test_suite $./scripts/ome_zarr_downloads data/64x64-fake-v0.2 Traceback (most recent call last): File "/usr/local/anaconda3/envs/z/bin/ome_zarr", line 33, in sys.exit(load_entry_point('ome-zarr',...