Skip to content

Update legacy_anndata.py #320

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
LucaMarconato merged 4 commits into from
Jan 12, 2026
+8 −2
Merged

Update legacy_anndata.py #320

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
f1366bd
Update legacy_anndata.py
Liripo Sep 4, 2025
5aa46df
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 4, 2025
6704bed
add rgb parameter to to_legacy_anndata()
LucaMarconato Jan 12, 2026
ff93890
fix docs
LucaMarconato Jan 12, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 8 additions & 2 deletions src/spatialdata_io/converters/legacy_anndata.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
-------
Expand Down Expand Up @@ -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"))

Expand Down
Loading