基础脚本更新--10X HD的bin模式与细胞分割模式的数据读取与基础分析

path_to_data <- "/brahms/shared/vignette-data/visium_hd_human_kidney"

kidney_obj <- Load10X_Spatial(data.dir = path_to_data,
                              bin.size = c(8, "polygons"),
                              image.name = "tissue_hires_image.png")

adata =  Load10X_Spatial(data.dir = './',bin.size = c(16, "polygons"),image.name = "tissue_hires_image.png")
> adata
An object of class Seurat 
77212 features across 373881 samples within 2 assays 
Active assay: Spatial.Polygons (38606 features, 0 variable features)
 1 layer present: counts
 1 other assay present: Spatial.016um
 2 spatial fields of view present: slice1.016um slice1.polygons

import spatialdata_io as sdio

spaceranger_path = "/visium_hd/output"

# 使用spatialdata-io读取Visium HD数据
# 这里设置了加载细胞分割的关键参数
sdata = sdio.visium_hd(
    path=spaceranger_path,
    load_segmentations_only=True,  # 只加载细胞分割，跳过binned数据
    load_nucleus_segmentations=True # 同时加载细胞核分割
)

# 查看加载的数据结构，确认包含了shapes和tables
print(sdata)

# 将SpatialData对象保存为Zarr格式
# 这会创建一个名为 'visium_hd.zarr' 的文件夹，里面包含了所有数据
sdata.write("./visium_hd.zarr")

visium_hd_zarr_path = "./visium_hd.zarr"

import spatialdata as sd
import spatialdata_plot

sdata = sd.read_zarr(visium_hd_zarr_path)
sdata

SpatialData object, with associated Zarr store:./visium_hd.zarr
├── Images
│     ├── 'Visium_HD_3prime_Mouse_Brain_hires_image': DataArray[cyx] (3, 5492, 6000)
│     └── 'Visium_HD_3prime_Mouse_Brain_lowres_image': DataArray[cyx] (3, 549, 600)
├── Shapes
│     ├── 'Visium_HD_3prime_Mouse_Brain_cell_segmentations': GeoDataFrame shape: (84031, 2) (2D shapes)
│     └── 'Visium_HD_3prime_Mouse_Brain_nucleus_segmentations': GeoDataFrame shape: (83153, 2) (2D shapes)
└── Tables
      ├── 'cell_segmentations': AnnData (84031, 33696)
      └── 'nucleus_segmentations': AnnData (83153, 33696)
with coordinate systems:
    ▸ 'Visium_HD_3prime_Mouse_Brain', with elements:
        Visium_HD_3prime_Mouse_Brain_hires_image (Images), Visium_HD_3prime_Mouse_Brain_lowres_image (Images), Visium_HD_3prime_Mouse_Brain_cell_segmentations (Shapes), Visium_HD_3prime_Mouse_Brain_nucleus_segmentations (Shapes)
    ▸ 'Visium_HD_3prime_Mouse_Brain_downscaled_hires', with elements:
        Visium_HD_3prime_Mouse_Brain_hires_image (Images), Visium_HD_3prime_Mouse_Brain_cell_segmentations (Shapes), Visium_HD_3prime_Mouse_Brain_nucleus_segmentations (Shapes)
    ▸ 'Visium_HD_3prime_Mouse_Brain_downscaled_lowres', with elements:
        Visium_HD_3prime_Mouse_Brain_lowres_image (Images), Visium_HD_3prime_Mouse_Brain_cell_segmentations (Shapes), Visium_HD_3prime_Mouse_Brain_nucleus_segmentations (Shapes)