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Several of the IDR studies are now also available on S3 see https://idr.github.io/ome-ngff-samples/. Note that some from the BioImageArchive are also available at https://uk1s3.embassy.ebi.ac.uk/bia-z…
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* Create a ``conda`` environment with the required dependencies
* Run the example below
```
from zarr.storage import FSStore
from itkwidgets import view
import zarr
fsstore = FSStore('https…
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An attendee at TiM2023 (Dr. Sarah Schweighofer) had issues when both when importing her OBF file into OMERO as well as when converting it to OME-TIFF with NGFF-Converter. The same behavior is seen in …
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Currently, when viewing an NGFF Plate in vizarr or napari, the pyramid is created by using 1 down-sampled tile from the first Image of every Well.
In vizarr (https://github.com/hms-dbmi/vizarr/pull…
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Here is an overview of current MoBIE projects, which have ome.zarr data and samples:
## Spatial Transcriptomics Data
https://github.com/mobie/mouse-embryo-spatial-transcriptomics-project
This…
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@will-moore @joshmoore @bogovi @bogovicj (also please tag eventually missing relevant contributors).
Giovanni (@giovp) and I have implemented a first draft of the [coordinate systems](https://githu…
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idr0001 has 192 x 96-Well Plates, 6 acquisitions each.
1 Plate converted [below](https://github.com/IDR/idr-metadata/issues/683#issuecomment-1886903270) is 47 GB.
Approx 4.5 TB in total.
bioformats…
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Workflow:
1. Convert the ``...downloads.openmicroscopy.org/images/OME-TIFF/2016-06/binaryonly`` images into zarr using bf2raw version 0.4.0, using the command
2. ``bioformats2raw binaryonly/multi…
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See e.g. https://github.com/IDR/idr-metadata/issues/652#issuecomment-1505229546
The reordering of Wells seen there is hard to work with since it needs `.pattern` files, which can't be easily import…
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I generated an ome.zarr file using the example image from ome-zarr-py:
https://gist.github.com/constantinpape/69e3cb8e0401621365d814b4d6fda0bc
However, in Windows 10, the file explorer views this …