spatialdata
spatialdata copied to clipboard
scverse
An open and interoperable data framework for spatial omics data
I am using `sd.rasterize` on cell polygons of >100k cells and run into the error. ```pytb --------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[14], line 1 ----> 1 sdata["cell_labels"]...
Encountering an issue with missing files when reading BGI's stereo seq data, and there is an inconsistency between the output files from the count command of SAW (a tool under...
I am attempting to read this Visium spatialdata store: https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/technology_visium.html but receive this error, presumably from an Anndata versioning issue: ``` File "/home/admin/anaconda3/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 171, in get_read raise IORegistryError._from_read_parts("read", self.read,...
Hello,I have a error in the follow code： import scanpy as sc import pandas as pd import numpy as np import h5py import anndata as ad import matplotlib.pyplot as plt...
Hi, I noticed the following inconsistencies in the model classes. For some models, e.g. `PointsModel`, `.validate()` is a class method, i.e. I can call it like ``` SomethingModel.validate(obj) ``` However...
## The problem The current point representation does not enforce any spatial ordering. As people are already storing large datasets with tens of millions of points into spatialdata objects, this...
## Problem description Hi all, The problem I am seeing is not something acute at present, but may be become so in the future. The ngff-transformations in this repository are...
Currently, we only test remote read / write for S3, but many companies also use azure. We should add tests for this.
**Describe the bug** I want to split samples by their regions for a Xenium slide. I read the samples' area as `polygon`, but `ArrowInvalid` when I ran `polygon_query`. How to...
