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Hi @bugraoezdemir,
Do we already have an activity planned for teaching this?
https://ome.github.io/ome-ngff-validator/
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I'm trying to view Zarr v3 data.
If I enter the OME-Zarr URL:
https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/0.0.5/6001240.zarr/
I get: "Neithre array nor OME multiscale metadata f…
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I am trying to update metadata such as license, organism, and modality in an OME-Zarr filesets converted with bioformats2raw using the ome2024-ngff-challenge tool. Now I am facing an issue where an er…
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Found while running our CI pipeline on this module: https://github.com/TheDeanLab/navigate/blob/develop/test/model/data_sources/test_zarr_data_source.py
The tests work with `pydantic-ome-ngff==0.5.…
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Activity header: **Open OME-Zarr in Java ecosystem**
Implementations:
- Fiji NGFF Viewer
- 3-D EM on S3
- Fiji NGFF BigDataViewer
- 3-D EM on S3
- MoBIE (@tischi)
- Choose datase…
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The spec: https://github.com/ome/ngff
A python library: https://github.com/ome/ome-zarr-py
A viewer: https://github.com/hms-dbmi/vizarr
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Bioformats2raw creates ome.zarrs with "0" top-level directory (`"series" : [ "0" ]` in `OME/.zattr`). These import fine. But when you remove this top level directory, it reports ("no imports found"):
…
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## Context
Tried importing OME NGFF sample at https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457537.zarr
This has a 'translation' in the datasets coordinateTransformations:
```
"data…
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A discussion in the Bioconductor slack channel was wondering whether RBioFormats could already be used to read OME-Zarr format. It seems that with the additional https://github.com/ome/zarrreader jar,…
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