diff --git a/src/spatialdata_io/converters/legacy_anndata.py b/src/spatialdata_io/converters/legacy_anndata.py index 84374700..fbf32aa1 100644 --- a/src/spatialdata_io/converters/legacy_anndata.py +++ b/src/spatialdata_io/converters/legacy_anndata.py @@ -221,7 +221,7 @@ def to_legacy_anndata( return adata -def from_legacy_anndata(adata: AnnData) -> SpatialData: +def from_legacy_anndata(adata: AnnData, rgb: bool | None = None) -> SpatialData: """Convert (legacy) spatial AnnData object to SpatialData object. This is useful for parsing a (legacy) spatial AnnData object, for example the ones produced by Scanpy and older @@ -231,6 +231,9 @@ def from_legacy_anndata(adata: AnnData) -> SpatialData: ---------- adata (legacy) spatial AnnData object + rgb + Argument passed to `spatialdata.models.Image2DModel.parse()`. If `None`, + 3-(4) channels images will be interpreted as RGB(A). Returns ------- @@ -321,7 +324,10 @@ def from_legacy_anndata(adata: AnnData) -> SpatialData: transform_name = f"{dataset_id}_{image_key}" image_name = f"{dataset_id}_{image_key}" images[image_name] = Image2DModel.parse( - image_value, dims=("y", "x", "c"), transformations={transform_name: Identity()} + image_value, + dims=("y", "x", "c"), + transformations={transform_name: Identity()}, + rgb=rgb, ) shapes_transformations[transform_name] = Scale([scalefactor, scalefactor], axes=("x", "y"))