spatialdata
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scverse
An open and interoperable data framework for spatial omics data
Issue: I am trying to load a xenium file from the output from the machine using sdata `sdata = xenium(xenium_path)`. It seems the xenium function expects the morpology names to...
**Is your feature request related to a problem? Please describe.** I am currently unable to install (with pixi) an environment having both spatialdata and rapids because of dependency issues. It...
1. Reproduce using the [`blobs` dataset](https://spatialdata.scverse.org/en/stable/api/datasets.html#spatialdata.datasets.blobs) ```python import numpy as np import pandas as pd import dask.dataframe as dd from spatialdata.datasets import blobs s = blobs() tbl = next(iter(s.tables.values())) df...
The `spatialdata_io.visium_hd()` SpaceRanger 4.0 reader needs to read non-geometry columns from a `.geojson` file and store them to a `GeoDataFrame`. Since `ShapesModel.parse()` ignores such non-geometry columns, @stephenwilliams22 has to write...
I was trying to initialize a spatialdata object directly from S3 as done in the tests here: ```python from upath import UPath import spatialdata as sd test = UPath( "s3://spatialdata/spatialdata-sandbox/merfish.zarr",...
closes #37 This PR adds the capability back of using either `lz4` or `zstd` compression at various compression levels. It is exposed through a `compressor` argument in `write` and `write_element`...
Hello, I have 24 samples with the same elements and names. I'm trying to concatenate them but seems like it doesn't work. It stop at the first sample but I...
Experimental support of z dimension for shapes.
I was trying to rename columns of a spatialdata points object and ran into issues regarding the column that is labeled as feature_key. Some reproducible ways of how I tried...
This PR implements a fix for https://github.com/scverse/spatialdata/issues/947. **Problem summary**: `spatialdata.transform` transforms each of the scales of a multi-scale image and it can happen that (especially lower resolution) scales result in...
