spatialdata
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scverse
An open and interoperable data framework for spatial omics data
When concatenating multiple tables from `spatialdata.aggregrate`, an error is thrown when using a custom region key. Reproducible example: ```python import pathlib import spatialdata as sd import natsort as ns mibitof_zarr_path...
When writing an image to zarr with overwrite=True, I found some unexpected behaviour. Below I give a mimimal example to reproduce the issue. This works, as expected. I can overwrite...
@berombau suggested to be sure to add, when it's available, the units to pixel size value in the OMERO metadata. This number is redundant as it can be computed from...
Hi @LucaMarconato @timtreis said you're already having issues with some relational query functions, just wanted to let you know that I ran into this issue today: ```python from spatialdata._core.query.relational_query import...
Feature that will be implemented as part of the IO refactoring. To make things ergonomic, we should before/at the same time, use `GeoDataFrame` for points https://github.com/scverse/spatialdata/issues/233 and thus unify points...
right now the Shapes model is an anndata. We are just saving the coordinates in `adata.obsm["spatial"]` and the metadata in `uns`. I feel this is overkill and we don't really...
@nilseling is working on extending existing R visualizers to support NGFF and the SpatialData format. He suggested to just add a version number for each element type, but to also...
MRE ``` from spatialdata.datasets import blobs blobs().write("./blob.zarr") ``` fails with ``` FileNotFoundError: [Errno 2] No such file or directory: '/Users/tim.treis/Documents/GitHub/spatialdata-notebooks/notebooks/examples/blob.zarr/images/blobs_image/0/0/0/0' ``` Inspecting the created file shows that it only goes...
Hi @LucaMarconato great work on `spatialdata`! I started playing around with this and noticed and error when cropping an image from the CosMx dataset: ``` import spatialdata as sd data...
Thanks for developing SpatialData! It's been a very ergonomic experience so far trying to convert a small subset of our lab's current multiplexed imaging pipeline as a MVP for testing....