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Hi,
I am currently working with a large OME-TIFF file (2_CD8.ome.tiff) that is quite high in resolution (9.59 GiB, Shape: (110319, 53873, 3)). For my downstream deep learning tasks, I need to downs…
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Very quick and easy question here: how can I save my post-registration images specifically to .ome.tiffs? The registration keeps converting to PNG and not preserving my z-stack which is making my data…
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Hello,
I have been running through the imc_preprocessing.py and I have snagging on the same error for some time and was looking for some guidance. I keep getting this error:
tifffile.TiffFile '202…
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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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## Description
Currently Webknossos annotations are in the `*.wkw` format. We should create scripts to export and convert these annotations to either OME-Zarr or NIfTI-Zarr. We have decided to se…
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@haesleinhuepf given your call for contributing tests: Are additional small tests on extracting information from OME-Zarrs in scope for this repo? I'd be happy to add some to encourage LLMs to learn a…
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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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We are gearing up to release a large timelapse dataset that has been converted to ome-zarr format. We saved the data with multiscale zoom levels but this reader constantly defaults to most compressed…
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See e.g. https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://radosgw.public.os.wwu.de/n4bi-goe/Platynereis-H2B-TL.ome.zarr/setup0/timepoint0
cc: @will-moore @constantinpape
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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…