scverse / scverse/squidpy

Nothing is displayed in the image, but I can display it normally using official data in the same environment.

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Dominant language
Python
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Forks
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Avg merge
3d 11h
Merged PRs (30d)
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Description

%reset -f
import scanpy as sc
import squidpy as sq
adata = sc.read("data/MCAO_1d.h5ad")
sq.pl.spatial_scatter(
    adata,
    color="Gfap",
    library_id="MCAO_1d",
    img=True,                 # 打开底图
    img_res_key="lowres",     # 指定用 lowres
    spatial_key="spatial",    # 你的坐标键
    # size=1.0,                 # 点大小(可调)
    cmap="magma",
    frameon=False
)
Image

What puzzles me most is that I can display spot very smoothly on Squidpy's official data.

%reset -f
import numpy as np
import pandas as pd

import anndata as ad
import scanpy as sc
import squidpy as sq

display(sc.logging.print_header())
print(f"squidpy=={sq.__version__}")

# load the pre-processed dataset
img = sq.datasets.visium_hne_image(path="data/hne_image")
adata = sq.datasets.visium_hne_adata(path="data/hne_adata")

sq.pl.spatial_scatter(
    adata,
    color="Gfap",
    use_raw=False,
    library_id="V1_Adult_Mouse_Brain",
    img=True,                 # 打开底图
    img_res_key="lowres",     # 指定用 lowres
    spatial_key="spatial",    # 你的坐标键
    size=1.0,                 # 点大小(可调)
    cmap="magma",
    frameon=False
)
Image

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce the report with data/MCAO_1d.h5ad using sq.pl.spatial_scatter, then compare its spatial metadata and image entries with the official visium_hne_image and visium_hne_adata datasets. Check the img_res_key, library_id, spatial_key, and coordinate/image metadata first; done means identifying the data difference that prevents the background image from rendering and confirming the behavior with the supplied examples.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data-visualization
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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