rasterize_bins(value_key=None) declares dtype=uint32 while blocks hold X.dtype; writing the result silently zeroes non-integer values

[!NOTE]
This whole message is AI-generated. The issue was automatically discovered and reported by an AI agent (Claude) during an autonomous bug hunt on the spatialdata code base. It has not been verified or triaged by a human yet; the needs: triage label is set so that a maintainer can confirm it. The reproduction script below was executed by the agent in an isolated environment (see Environment) and its output is pasted verbatim.

Summary

The lazy (all-genes) path reports img.dtype == uint32 but the computed blocks are float32 (the table's X.dtype). Writing the element to Zarr creates a uint32 array, so values in (0, 1) become 0. Raw integer counts stored as floats survive the cast, which is why this went unnoticed. The explicit value_key=[...] path uses the right dtype.

Severity (agent's assessment): high — silent data loss for normalised/log-transformed tables

Where: src/spatialdata/_core/operations/rasterize_bins.py (da.map_blocks(channel_rasterization, chunks=..., dtype=np.uint32) while channel_rasterization allocates np.zeros(..., dtype=table.X.dtype))

Expected behaviour

The declared dtype equals the block dtype and the written data equals the in-memory data.

Reproduction

Save as repro.py and run uv run repro.py (the PEP 723 header pins spatialdata to the commit the bug was found on; replace the URL fragment with @main to test the current main branch).

# /// script
# requires-python = ">=3.12"
# dependencies = [
#     "spatialdata @ git+https://github.com/scverse/spatialdata.git@ccf1ea048d054b6624214bf618008a9f9ae223e0",
# ]
# ///
"""rasterize_bins(value_key=None) declares dtype=uint32 while blocks hold X.dtype; writing zeroes float values."""
import os
import shutil
import tempfile
import warnings
import numpy as np
import pandas as pd
import geopandas as gpd
from anndata import AnnData
from scipy.sparse import csc_matrix
from shapely.geometry import box
from spatialdata import SpatialData, rasterize_bins, read_zarr
from spatialdata.models import ShapesModel, TableModel

warnings.simplefilter("ignore")
n = 6
rows, cols = np.meshgrid(range(n), range(n), indexing="ij")
rows, cols = rows.ravel(), cols.ravel()
bins = ShapesModel.parse(gpd.GeoDataFrame({"geometry": [box(c, r, c + 1, r + 1) for r, c in zip(rows, cols)]}, index=np.arange(n * n)))
X = csc_matrix(np.random.default_rng(0).uniform(0.1, 0.9, (n * n, 3)).astype(np.float32))  # e.g. normalised expression
obs = pd.DataFrame({"region": pd.Categorical(["bins"] * (n * n)), "instance_id": np.arange(n * n), "row": rows, "col": cols})
table = TableModel.parse(AnnData(X=X, obs=obs, var=pd.DataFrame(index=["g1", "g2", "g3"])), region="bins", region_key="region", instance_key="instance_id")
sdata = SpatialData(shapes={"bins": bins}, tables={"table": table})
img = rasterize_bins(sdata, "bins", "table", col_key="col", row_key="row", value_key=None)
computed = img.data.compute()
print(f"declared dtype: {img.dtype} | computed block dtype: {computed.dtype} | computed max: {float(computed.max()):.3f}")
tmp = tempfile.mkdtemp()
sdata.images["raster"] = img
sdata.write(os.path.join(tmp, "store.zarr"))
back = read_zarr(os.path.join(tmp, "store.zarr"))["raster"].data.compute()
print(f"after write + read: dtype {back.dtype} | max {float(back.max()):.3f} | all zero: {bool((back == 0).all())}   (expected: floats ~0.9)")
shutil.rmtree(tmp)
bug = str(img.dtype) != str(computed.dtype) or bool((back == 0).all())
print("VERDICT:", "BUG REPRODUCED" if bug else "NOT REPRODUCED")

Observed output

declared dtype: uint32 | computed block dtype: float32 | computed max: 0.898
after write + read: dtype uint32 | max 0.000 | all zero: True   (expected: floats ~0.9)
VERDICT: BUG REPRODUCED

Possible fix direction (unverified)

Pass dtype=dtype (the table's X.dtype) and a matching meta to da.map_blocks; add a round-trip test with non-integer values.

Environment

uv run repro.py with the PEP 723 metadata in the script (fresh, isolated environment; spatialdata built from main @ ccf1ea0 (2026-08-28); Python 3.13, latest releases of the dependencies at run time: pandas 3.0, anndata 0.13, zarr 3.3, dask 2026.8, numpy 2.5, geopandas 1.1, shapely 2.1). macOS (arm64). Also reproduced in a second environment with pandas 2.3.3 / anndata 0.12.11 / numpy 2.4.4 / zarr 3.2.1.

Automatically generated; discovered by an AI agent (Claude) and not yet reviewed by a human.

Start by running repro.py and inspect src/spatialdata/_core/operations/rasterize_bins.py, especially the lazy all-genes path and its dtype declaration. Done means the computed block dtype matches the table's X.dtype and the write/read round trip preserves non-integer values instead of producing zeros; add or update a regression test if the project provides a suitable test location.