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Feature request: Option for multiscale images opened with aszarr to be valid OME-Zarr #335
Right now using aszarr returns zarr that are almost valid OME-Zarr, but not quite.
For example, for a multiscale (pyramidal) image, the multiscales metadata follows ome-zarr. But, the arrays after level 0 have axes names like Y1, X1 (where 1 is the level) that don't follow:
The âdimension_namesâ attribute MUST be included in the zarr.json of the Zarr array of a multiscale level and MUST match the names in the âaxesâ metadata.
Also, for the case of an RGB image, the axis order is returned as YXC, which is unfortunately invalid, as C needs to be before spatial axes:
The order of the entries MUST correspond to the order of dimensions of the zarr arrays. In addition, the entries MUST be ordered by âtypeâ where the âtimeâ axis must come first (if present), followed by the âchannelâ or custom axis (if present) and the axes of type âspaceâ.
yes. I'll have to review xarray and OME-Zarr to see if this can be resolved.
as C needs to be before spatial axes
The OME-XML model has a SamplesPerPixel property but I don't see that in OME-Zarr. Am I missing something? That means interleaved RGB images (the most common image type in the world by far) cannot be represented in OME-Zarr? Bummer. Anyway, series in TIFF files may have many dimension types and orders that are not supported by the 5D OME models. You'll have to use transpose or other workarounds (or just fail) for those files.
I agree the axes restrictions are pretty frustrating. There is an RFC to improve this, but I'm not sure on the status.
I totally understand if you want to close this as no-thanks. Might help the next person who gets a bit confused like me!
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cgohlke commentedon Oct 6, 2026
yes. I'll have to review xarray and OME-Zarr to see if this can be resolved.
The OME-XML model has a
SamplesPerPixelproperty but I don't see that in OME-Zarr. Am I missing something? That means interleaved RGB images (the most common image type in the world by far) cannot be represented in OME-Zarr? Bummer. Anyway, series in TIFF files may have many dimension types and orders that are not supported by the 5D OME models. You'll have to use transpose or other workarounds (or just fail) for those files.psobolewskiPhD commentedon Oct 6, 2026
I agree the axes restrictions are pretty frustrating. There is an RFC to improve this, but I'm not sure on the status.
I totally understand if you want to close this as no-thanks. Might help the next person who gets a bit confused like me!