Merge pull request #209 from melonora/add_rgb_visiumhd

create rgb images for visiumhd
scverse · Sep 24, 2024 · 9b50d0d · 9b50d0d
2 parents acde579 + 015b0d7
commit 9b50d0d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,7 +16,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Fixed
 
-- Passing `rgb=None` to image model parser, leading to 3-4 channel images being interpreted as RGB(A)
+- Passing `rgb=None` to image model parser for both visium and visiumhd, leading to 3-4 channel images being
+ interpreted as RGB(A)
 
 ## [0.1.4] - 2024-08-07
 

diff --git a/src/spatialdata_io/readers/visium_hd.py b/src/spatialdata_io/readers/visium_hd.py
@@ -385,7 +385,7 @@ def _load_image(
  # dask_image doesn't recognize .btf automatically and imageio v3 throws error due to pixel limit -> use imageio v2
  data = imread2(path, **imread_kwargs).squeeze().transpose(2, 0, 1)
  image = DataArray(data, dims=("c", "y", "x"))
- parsed = Image2DModel.parse(image, scale_factors=scale_factors, **image_models_kwargs)
+ parsed = Image2DModel.parse(image, scale_factors=scale_factors, rgb=None, **image_models_kwargs)
  images[dataset_id + suffix] = parsed
  else:
  warnings.warn(f"File {path} does not exist, skipping it.", UserWarning, stacklevel=2)