spatialdata

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Added parameter to `sd.concatenate` to control whether to merge coordinate systems with the same name

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timtreis

module 'spatialdata' has no attribute 'match_sdata_to_table'

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Hello, I wanted to filter my Xenium data but I have an error with the function `match_sdata_to_table`. Here an reproducible example ```python import spatialdata as spd from spatialdata.datasets import blobs...

bellenger-l

**Is your feature request related to a problem? Please describe.** I'm trying to get the result of 3D segmentation back into the SpatialData world in order to use sopa but...

lguerard

Remove reference cycle within SpatialData to fix memory leak in bounding_box_query

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# Introduction Hi, my name is Nick, and I'm part of the SciPy issue triage team, and I was looking into high memory usage within spatialdata as part of my...

nickodell

cannot import spatialdata

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Dear : I am running to process the Xenium data. When I try to import the spatialdata package, there always exists such error . The error shows something like the...

bozhangstat

Geopandas benchmarks

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This is a work-in-progress for testing performance of [`geopandas`](https://geopandas.org/en/stable/) compared to [`dask-geopandas`](https://dask-geopandas.readthedocs.io/en/stable/). I used the `asv` framework to add benchmarks for geopandas [nearest](https://geopandas.org/en/stable/docs/reference/api/geopandas.sindex.SpatialIndex.nearest.html) and [query](https://geopandas.org/en/stable/docs/reference/api/geopandas.sindex.SpatialIndex.query.html). Unfortunately, dask-geopandas doesn't implement these...

aeisenbarth

Geopandas vs pandas for points

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Points now use lazy dataframes (Dask `DataFrame`). We talked about allowing having in-memory both as dataframes and lazy dataframes. https://github.com/scverse/spatialdata/issues/153 What about using `GeoDataFrame` and Dask `GeoDataFrame` instead? This will...

LucaMarconato

[pre-commit.ci] pre-commit autoupdate

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updates: - [github.com/rbubley/mirrors-prettier: v3.5.1 → v3.5.3](https://github.com/rbubley/mirrors-prettier/compare/v3.5.1...v3.5.3) - [github.com/astral-sh/ruff-pre-commit: v0.9.6 → v0.11.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.6...v0.11.2)

pre-commit-ci[bot]

Added `filter_table_by_query`

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Added filtering by a table query as discussed in #626. Added both a standalone function `sd.filter_table_by_query` and a method `sd.SpatialData.filter_table_by_query`. Function signature ```python class SpatialData: ... def filter_by_table_query( self, table_name:...

srivarra

Rename SpatialData elements

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**Is your feature request related to a problem? Please describe.** The spatialdata_io.merscope reader has the two arguments 'region_name' and 'slide_name'. If set to None, file path directory is used. If...

Fritze