ome-zarr-py
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Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
I am trying to save a multidimensional image using ome-zarr, however saving fails with the following error: ``` FileNotFoundError: [Errno 2] No such file or directory: '/path/to/input_image.ome.zarr/0/0/0/0' ``` I am...
Various scaling issues have been reported. These are due to the initial Scaler designed to scale planes (or a series of planes) in 2D and to work with numpy arrays...
Hello! I'm trying to write an ome-zarr for a small-ish dataset — ~90MB compressed. Because it's much easier to share single files than folders I want to try using a...
Based on this - https://github.com/scikit-image/scikit-image/issues/4294 multichannel=False nees to be changed to channel_axis=None on lines 190 & 201. In writer.py line 885 mip = scaler.nearest(image) should be mip = getattr(scaler, scaler.method)(image)...
Dear ome team, I recently came across an interesting use case. I have couple of microscopy software tools that export very large images as a series of .tiff (or .bpm,...
write_multiscale() writes to local path on Linux instead of cloud bucket when using dask>=2023.1.0
Please see this issue https://github.com/dask/dask/issues/10324 , which is the source of this problem Here is an MRE: ```python import numpy as np import dask.array as da import zarr from ome_zarr.writer...
Addresses https://github.com/ome/ome-zarr-py/issues/240, see there for a description of the issue This PR adds a second code path to the `get_pyramid_lazy` function. Its goal is to load the metadata of each...
A workflow which tests mainline builds of Zarr was removed in #251. Some infrastructure, either in this repo or elsewhere, is needed to test upstream changes before they appear in...
Right now `parse_url` does not allow to add any storage_options. In my case I'd like to be able of adding `headers` to the HTTP request for authentication purposes but the...
