aeisenbarth

Following issue https://github.com/scverse/napari-spatialdata/issues/150, the logic to decide whether channels should be visualized as RGB has been moved from the viewer `napari-spatialdata` to the parser in [spatial-image](https://github.com/spatial-image/spatial-image/pull/21), which in the case...

Creating flow run from deployment fails with Pydantic 2 parameters

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### First check - [X] I added a descriptive title to this issue. - [X] I used the GitHub search to find a similar issue and didn't find it. -...

moments_weighted_normalized causes warning "invalid value encountered in double_scalars"

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### Description: When measuring region properties on image data that may have negative values (background subtracted), a warning is thrown. This is because `sum(powers) / nu.ndim + 1` can be...

Draft SpatialData.filter()

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(In reference to https://github.com/scverse/spatialdata/pull/620) This PR imlements an more advanced filtering options than `subset`, allowing to create a new SpatialData object that contains only specific tables, layers, obs keys, var...

Naming constraints break compatibility with existing datasets

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[`_check_valid_name`](https://github.com/scverse/spatialdata/blame/95d69ff7138305ee2a530bcc45f8460a06e8118b/src/spatialdata/_core/_elements.py#L34-L40) implemented stricter naming constraints in https://github.com/scverse/spatialdata/commit/137e1e06c946800599d55c45f18fe8a6a1fb06eb. We already have existing SpatialData datasets where `.` is used as separator for naming components with different meanings, like `Slide1.A2.0.pre_maldi`. When loading them...

When METASPACE login fails in the constructor, the error is silently caught and printed, which goes unnoticed if not using an interactive console/notebook. When checking `logged_in()`, an AttributeError is raised...

Coordinate systems widget not sorted

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Coordinate systems are displayed non-alphabetically. With a large number of coordinate systems, this makes it hard to find and select a specific one.  If things are unordered, it usually...

Sort elements in widgets

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Closes #284

Fix transformed labels with outline

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Outlines are rendered on an axis separate from the filled labels. The transformation was only applied to the filled labels, so that the outlines had an identity transform. This was...

It seems `outline=True` takes a code path that causes labels to have a wrong scale. It is important for the images that I render to not have filled labels, but...