visium_hd: no global coordinate system for image

[fbnrst]

I am reading spaceranger outputs like this:

spatialdata_io.visium_hd(
    '../../raw_data/240905_VisiumHD_Periportal_Assembloid/spaceranger/Slide1_phh2_normal1/outs/',
    dataset_id='Slide1_phh2_normal1',
    load_all_images=False,
)

output:

SpatialData object
├── Images
│     ├── 'Slide1_phh2_normal1_cytassist_image': DataArray[cyx] (3, 3000, 3200)
│     ├── 'Slide1_phh2_normal1_hires_image': DataArray[cyx] (3, 4997, 6000)
│     └── 'Slide1_phh2_normal1_lowres_image': DataArray[cyx] (3, 500, 600)
├── Shapes
│     ├── 'Slide1_phh2_normal1_square_002um': GeoDataFrame shape: (326064, 1) (2D shapes)
│     ├── 'Slide1_phh2_normal1_square_008um': GeoDataFrame shape: (20379, 1) (2D shapes)
│     └── 'Slide1_phh2_normal1_square_016um': GeoDataFrame shape: (5279, 1) (2D shapes)
└── Tables
      ├── 'square_002um': AnnData (326064, 18094)
      ├── 'square_008um': AnnData (20379, 18094)
      └── 'square_016um': AnnData (5279, 18094)
with coordinate systems:
    ▸ 'downscaled_hires', with elements:
        Slide1_phh2_normal1_hires_image (Images), Slide1_phh2_normal1_square_002um (Shapes), Slide1_phh2_normal1_square_008um (Shapes), Slide1_phh2_normal1_square_016um (Shapes)
    ▸ 'downscaled_lowres', with elements:
        Slide1_phh2_normal1_lowres_image (Images), Slide1_phh2_normal1_square_002um (Shapes), Slide1_phh2_normal1_square_008um (Shapes), Slide1_phh2_normal1_square_016um (Shapes)
    ▸ 'global', with elements:
        Slide1_phh2_normal1_cytassist_image (Images), Slide1_phh2_normal1_square_002um (Shapes), Slide1_phh2_normal1_square_008um (Shapes), Slide1_phh2_normal1_square_016um (Shapes)

I noticed that the "hires" and "lowres" images do not have a global coordinate system. I manually registered these images before to the CytAssist image using landmarks in the loupe browser, also, when I open the cloupe files in loupe browser the hires image is registered.

This is not what I expected from the tutorial https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/technology_visium_hd.html, there, all images are part of the global coordinate system

[LucaMarconato]

Hi, thanks for reaching out. What you get is expected and is consistent in what is shown in the tutorial (copy-pasting the first print below):

SpatialData object, with associated Zarr store: /Users/macbook/embl/projects/basel/spatialdata-sandbox/visium_hd_3.0.0_io/data.zarr
├── Images
│     ├── 'Visium_HD_Mouse_Small_Intestine_cytassist_image': DataArray[cyx] (3, 3000, 3200)
│     ├── 'Visium_HD_Mouse_Small_Intestine_full_image': DataTree[cyx] (3, 21943, 23618), (3, 10971, 11809), (3, 5485, 5904), (3, 2742, 2952), (3, 1371, 1476)
│     ├── 'Visium_HD_Mouse_Small_Intestine_hires_image': DataArray[cyx] (3, 5575, 6000)
│     └── 'Visium_HD_Mouse_Small_Intestine_lowres_image': DataArray[cyx] (3, 558, 600)
├── Shapes
│     ├── 'Visium_HD_Mouse_Small_Intestine_square_002um': GeoDataFrame shape: (5479660, 1) (2D shapes)
│     ├── 'Visium_HD_Mouse_Small_Intestine_square_008um': GeoDataFrame shape: (351817, 1) (2D shapes)
│     └── 'Visium_HD_Mouse_Small_Intestine_square_016um': GeoDataFrame shape: (91033, 1) (2D shapes)
└── Tables
      ├── 'square_002um': AnnData (5479660, 19059)
      ├── 'square_008um': AnnData (351817, 19059)
      └── 'square_016um': AnnData (91033, 19059)
with coordinate systems:
    ▸ 'downscaled_hires', with elements:
        Visium_HD_Mouse_Small_Intestine_hires_image (Images), Visium_HD_Mouse_Small_Intestine_square_002um (Shapes), Visium_HD_Mouse_Small_Intestine_square_008um (Shapes), Visium_HD_Mouse_Small_Intestine_square_016um (Shapes)
    ▸ 'downscaled_lowres', with elements:
        Visium_HD_Mouse_Small_Intestine_lowres_image (Images), Visium_HD_Mouse_Small_Intestine_square_002um (Shapes), Visium_HD_Mouse_Small_Intestine_square_008um (Shapes), Visium_HD_Mouse_Small_Intestine_square_016um (Shapes)
    ▸ 'global', with elements:
        Visium_HD_Mouse_Small_Intestine_cytassist_image (Images), Visium_HD_Mouse_Small_Intestine_full_image (Images), Visium_HD_Mouse_Small_Intestine_square_002um (Shapes), Visium_HD_Mouse_Small_Intestine_square_008um (Shapes), Visium_HD_Mouse_Small_Intestine_square_016um (Shapes)

As you can see Visium_HD_Mouse_Small_Intestine_hires_image and Visium_HD_Mouse_Small_Intestine_lowres_image are indeed not listed in the global coordinate system.

The difference is that in the tutorial the global coordinate system has the image Visium_HD_Mouse_Small_Intestine_full_image. In your case it seems that the reader could not locate the image, probably because of a naming issue, or because the image is located in a different folder than what the reader expects (we saw this in some datasets in a recent SpaceRanger run).

I would suggest the following:

• please try the latest release of spatialdata-io. We recently fixed a bug with image paths in this PR (and some PRs next): adjust for crc2 dataset #204
• if this doesn't work, please try setting the fullres_image_file argument manually

  spatialdata-io/src/spatialdata_io/readers/visium_hd.py

  Line 43 in bc17abc

  fullres_image_file: str | Path | None = None,

  .

Let me know if it this helps!

[LucaMarconato]

(I closed the issue by accident pressing the wrong key, reopened)

[fbnrst]

Thanks! You are right, not sure why I thought hires and lowres would be part of global. I will try with the fullres image as you suggested. I won't have time to do so soon, so will close this issue for now, and I would only reopen if I cannot make it run. Thanks for looking into this!

[LucaMarconato]

Sounds great! Please be aware of this other bug that has been reported: #216. We are working on it and it does affect only some datasets, so hopefully you will not encounter it.