spatialdata
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scverse
An open and interoperable data framework for spatial omics data
Hi @giovp and @LucaMarconato, I'm new to spatialdata and thinking about using it. Just wanted to know - does spatialdata have a way to take distance measurements from one point...
Reported by @timtreis
Here are the linked issues **Incremental IO** https://github.com/scverse/spatialdata/issues/186 https://github.com/scverse/spatialdata/issues/222 (old PR containing discussion) https://github.com/scverse/spatialdata/pull/138 **Lazy vs non-lazy** https://github.com/scverse/spatialdata/issues/243 https://github.com/scverse/spatialdata/issues/153 https://github.com/scverse/spatialdata/issues/297
I think this was mentioned before, but I couldn't find it back. When adding columns with annotation to the shapes layer, these aren't saved. I have different types of shapes...
If incompatible versions of `pygeos`, `geopandas` and `shapely` are installed one may encounter bugs with `geopandas` or reduced performance. In an extreme case I just saw `sjoin` fail with the...
The geometry argument is used to select which kind of shapes to create when using `ShapesModel.parse`. The possible arguments are 0, 3 and 6 which map to `Circles`, `Polygon` and...
Idea for enhancement: Add a filter option to the spatialdata object, where it is possible to filter out certain cells, based on a column in the table. This can be...
Currently `value_key` of `aggregate()` is either a list of names of numerical columns, either a single categorical column. It is not currently possible to mix numerical and categorical columns, or...
In the [Xenium + Visium notebook 01](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/paper_reproducibility/01_xenium_and_visium.ipynb) This block of code, that performs an aggregation of cell types (cells) by visium circles (with `fractions=True`) could be simplified. Here we aggregate...
Test the case when two squares (one in shapes and one in by) touch in a side or a vertex but not overlap. For the `overlay()` case we will get...