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lexical error when reading SpatialData example OME-NGFFs #59
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Thanks for the issue. Pizzarr should definitely produce a better error in this case, but there are ultimately no attributes at that location at the root of the store. This is arising because SpatialData does not store a
https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zarr/.zattrs |
There is a zattrs file at
|
Thanks Mark. Yes it seems that only the image part of SpatialData is stored as OME-NGFF within the overall SpatialData zarr store. |
Yes, there will also be zattrs files at other places within a SpatialData object such as within the |
Great, closing, this does the trick. Thanks! |
Hi @keller-mark,
@lee-t and I were just playing around with pizarr and tried to use it to load some of the SpatialData example datasets from here:
https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html
However, we encountered the following problems:
It seems
crul
is inSuggests
but it would rather need to go intoImports
. Or alternatively keep it inSuggests
if it is not considered essential functionality for the package and throw an error with a prompt for the user to install thecrul
package. But here it seems to be an essential part as it is part of creating a newHttpStore
object.Ok, proceeding after installing
crul
:The same happens when using another dataset as
root
eg, when usingThe text was updated successfully, but these errors were encountered: