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I first tried to process visium-hd dataset. In visium-hd, the step of nuclei segmentation is quite important. So, I tried to perform nuclei sengmentation in 10X genomics suggested(using StarDist).
Because it is python-based package, I should convert the format from anndata to seurat object using 'SeuratDisk'.
But it was failed showing this error message.
Convert("stardist_nuclei_segmentation_8um_241116.h5ad", dest = "stardist_nuclei_segmentation_8um_241116.h5Seurat",overwrite=TRUE)
Warning: Unknown file type: h5ad
Warning: 'assay' not set, setting to 'RNA'
Creating h5Seurat file for version 3.1.5.9900
Adding X as data
Adding X as counts
Adding meta.features from var
Error in dfile$obj_copy_from(src_loc = source, src_name = "obs", dst_name = "meta.data") :
HDF5-API Errors:
error #000: ../../../src/H5Ocopy.c in H5Ocopy(): line 233: unable to copy object
class: HDF5
major: Object header
minor: Unable to copy object
Is there anyone who convert the anndata to seurat object after nuclei segmentation?
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Hello :)
I first tried to process visium-hd dataset. In visium-hd, the step of nuclei segmentation is quite important. So, I tried to perform nuclei sengmentation in 10X genomics suggested(using StarDist).
https://www.10xgenomics.com/analysis-guides/segmentation-visium-hd
Because it is python-based package, I should convert the format from anndata to seurat object using 'SeuratDisk'.
But it was failed showing this error message.
Is there anyone who convert the anndata to seurat object after nuclei segmentation?
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