new version of Visium HD data with segmentation from SpaceRanger V4

[KunHHE]

Hi @quentinblampey, for the new new version of Visium HD data with segmentation from SpaceRanger V4, is there any difference when write the .zarr file? there is a new "segmented_outputs" from the spaceranger.

but when check the sdata structure below i can only see "region_of_interest", not sure which one is the cell boundaries?

SpatialData object
├── Images
│ ├── 'Visium_HD_Mouse_Brain_full_image': DataTree[cyx] (3, 23947, 18872), (3, 11973, 9436), (3, 5986, 4718), (3, 2993, 2359), (3, 1496, 1179)
│ ├── 'Visium_HD_Mouse_Brain_hires_image': DataArray[cyx] (3, 6000, 4729)
│ └── 'Visium_HD_Mouse_Brain_lowres_image': DataArray[cyx] (3, 600, 473)
├── Shapes
│ ├── 'Visium_HD_Mouse_Brain_square_002um': GeoDataFrame shape: (6296688, 1) (2D shapes)
│ ├── 'Visium_HD_Mouse_Brain_square_008um': GeoDataFrame shape: (393543, 1) (2D shapes)
│ ├── 'Visium_HD_Mouse_Brain_square_016um': GeoDataFrame shape: (98917, 1) (2D shapes)
│ └── 'region_of_interest': GeoDataFrame shape: (1, 1) (2D shapes)
└── Tables
├── 'square_002um': AnnData (6296688, 19070)
├── 'square_008um': AnnData (393543, 19070)
└── 'square_016um': AnnData (98917, 19070)
with coordinate systems:
▸ 'Visium_HD_Mouse_Brain', with elements:
Visium_HD_Mouse_Brain_full_image (Images), Visium_HD_Mouse_Brain_hires_image (Images), Visium_HD_Mouse_Brain_lowres_image (Images), Visium_HD_Mouse_Brain_square_002um (Shapes), Visium_HD_Mouse_Brain_square_008um (Shapes), Visium_HD_Mouse_Brain_square_016um (Shapes), region_of_interest (Shapes)
▸ 'Visium_HD_Mouse_Brain_downscaled_hires', with elements:
Visium_HD_Mouse_Brain_hires_image (Images), Visium_HD_Mouse_Brain_square_002um (Shapes), Visium_HD_Mouse_Brain_square_008um (Shapes), Visium_HD_Mouse_Brain_square_016um (Shapes), region_of_interest (Shapes)
▸ 'Visium_HD_Mouse_Brain_downscaled_lowres', with elements:
Visium_HD_Mouse_Brain_lowres_image (Images), Visium_HD_Mouse_Brain_square_002um (Shapes), Visium_HD_Mouse_Brain_square_008um (Shapes), Visium_HD_Mouse_Brain_square_016um (Shapes), region_of_interest (Shapes)

[quentinblampey]

Hi @KunHHE,

Currently, we are not loading the cell boundaries produced by SpaceRanger. It will be added soon, see this PR: scverse/spatialdata-io#328

Note that sopa.io.visium_hd directly depends on spatialdata-io, so it all depends on spatialdata-io :)

[KunHHE]

Great! Thank you!