ome-zarr-py
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Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
https://github.com/ome/ome-zarr-py/pull/62 introduced the PlateLabels class which requires some special casing in order to provide 2 nodes from the same URL. One idea for working around this was to use a...
Suggestion by @d-v-b on gitter for wider discussion. See https://github.com/janelia-cosem/fibsem-metadata/blob/master/src/fibsem_metadata/models/metadata.py for an example. In the case of ome-zarr-py, we may want to generate the classes from json-schema rather than the...
* [x] Add Implicit spec to loop over metadata-less "collections" * [x] Add Leaf & Root specs * [x] Support entrypoint-based specs ("ome_zarr.spec") * [x] Use entrypoint to adder suport...
Hello there! I am having some troubles writing an large image using `write_image`. If I understand correctly, as `write_image` takes numpy array as input. It assumes that the image should...
Some general feedback about using the convenience functions from creating an example for converting ome.tiff data to ome.zarr (https://github.com/ome/ome-ngff-prototypes/tree/main/workflows/spatial-transcriptomics-example): - `write_image` is currently very inflexible w.r.t. downsampling functionality: it only...
`ome-zarr-py 0.3.0`includes support for reading/writing datasets compliant with the [OME-NGFF 0.4 specification](ngff.openmicroscopy.org/0.4/) #162 in particular introduced support for writing the `coordinateTransformations` metadata such as the mandatory `scale` at the `multiscales.datasets`...
``` (z) /opt/zarr-python $./ot.py /tmp/a.ome.zarr/OME/METADATA.ome.xml exception on parsing: path exists but is not a directory: %r (stacktrace at DEBUG) Traceback (most recent call last): File "/Users/jamoore/opt/zarr/./ot.py", line 48, in data...
See conversation at https://github.com/ome/ome-zarr-py/pull/161#discussion_r800575583 The `storage_options` keyword introduced in 0.3.0 should support setting the `chunks` to the Zarr dataset. This option also gives the extra flexibility of being able to...
3 of the tests fail with an error which seems to occur as `AssertionError: not a zarr: None` but is then captured as `SystemExit: 2`. I am not entirelly sure...
Current validation implementations throw on the first error, rather than finding all validation errors and listing them. Instead, an exception with all the errors could be raised or alternatively a...