Hi, and thanks for maintaining spatialdata-io!
When the Visium HD files have no filename prefix (e.g. feature_slice.h5) and dataset_id is not provided, visium_hd() falls back to dataset_id="".
Since dataset_id is used both as element prefix and as coordinate-system name, this yields an empty coordinate system that is problematic downstream: for instance, napari-spatialdata silently ignores it and shows it as a blank row, so the full-resolution image can't be displayed at all. This was reported as a Sopa bug in prism-oncology/sopa#446 before we traced it here.
That could be avoided by either defaulting to a non-empty identifier, or keeping "" but naming the coordinate system "global" when dataset_id is empty.
Thanks!
Hi, and thanks for maintaining spatialdata-io!
When the Visium HD files have no filename prefix (e.g.
feature_slice.h5) anddataset_idis not provided,visium_hd()falls back todataset_id="".Since
dataset_idis used both as element prefix and as coordinate-system name, this yields an empty coordinate system that is problematic downstream: for instance, napari-spatialdata silently ignores it and shows it as a blank row, so the full-resolution image can't be displayed at all. This was reported as a Sopa bug in prism-oncology/sopa#446 before we traced it here.That could be avoided by either defaulting to a non-empty identifier, or keeping
""but naming the coordinate system"global"whendataset_idis empty.Thanks!