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We have a test-dataset which contains all raw data (including metadata files) of a CV acquisition packaged into an hdf5 container. We should test if we can use this as input to our ome-zarr converter.
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Hi,
Nice development on the sopa that we can use. I am a new user and trying to see how sopa cool on spatial data analysis.
I installed sopa in conda (pip install sopa[snakemake,cellpose,baysor,t…
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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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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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We will upload image files to the [Image Data Resource](https://idr.openmicroscopy.org/) and add URL and metadata information to the [Broad Bioimage Benchmark Collection](https://data.broadinstitute.o…
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[idr0035-caie-drugresponse](https://github.com/IDR/idr-metadata/tree/e63515be2e0d201ead634d4b915b68c1f7d2c7d0/idr0035-caie-drugresponse)
Sample plate conversion failed with:
```
(base) [dlindner@…
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[idr0036-gustafsdottir-cellpainting](https://github.com/IDR/idr-metadata/tree/e63515be2e0d201ead634d4b915b68c1f7d2c7d0/idr0036-gustafsdottir-cellpainting)
Sample plate conversion failed with:
```
…
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idr0015-colin-taraoceans
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dropdown with a list of converters to use
.ims to tif
.sld to tif
...
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*This issue captures the requirements as well as the possible implementation choices for a first integration of OME metadata into the OME-NGFF container. The UoD team is targeting the specification as…