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Taking the output of `bioformat2raw 0.3.0` which is a collection of OME-Zarr multiscale images as an example:
```bash
bioformats2raw "test&series=2.fake" "test.zarr"
(zarr) [sbesson@pilot-zarr1-…
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BIDS accepts ome-zarr data in its microscopy extension, but not in its main MRI-related specification.
In most cases, MRI volumes are small enough that chunked formats do not make sense, but MRIs…
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On 2 of our servers, we got an error on trying to import ome.zarr into OMERO.
1.
server version 5.6.8 and 5.6.10 tested, same result
M1 aarch64 docker image
BioFormats 6.11.1 revision: 383bac97…
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I just tried validating a local file, and the tool didn't seem to work - the link I used was https://ome.github.io/ome-ngff-validator/?source=file:///Users/dstansby/notebooks/ct-scans/david_ct_scan.za…
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**Describe the bug**
The contents of .extdata don't play nice with R CMD check.
excerpt from check
```
❯ checking for hidden files and directories ... NOTE
Found the following hidden files…
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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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EDIT: The most compelling specific issue is now part of #448. This issue is now to track the broader discussion on how to proceed regarding:
1. scope setting: which use cases will be supported in fra…
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What do you think of having the MDA function automatically handle the writing of data to a zarr on disk that conforms to https://ngff.openmicroscopy.org/latest/ ?
I looked into this a little bit bu…
ianhi updated
3 years ago
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Reviving this old issue on input inference:
We should revisit this in the context of the image list that could store metadata like available channels per Zarr, available labels & tables, number of py…