omicverse.io.read_nanostring

omicverse.io.read_nanostring#

omicverse.io.read_nanostring(path, *, counts_file, meta_file, fov_file=None)[source]#

Read Nanostring formatted dataset.

This follows the Squidpy nanostring reader layout: - obsm['spatial']: local cell center coordinates. :rtype: AnnData

  • obsm['spatial_fov']: global cell center coordinates.

  • uns['spatial'][fov]['images']: hires and segmentation images from CellComposite and CellLabels.

  • uns['spatial'][fov]['metadata']: optional FOV-level metadata.

  • If geometry-like columns exist in metadata, writes obs['geometry'] as WKT strings to match read_visium_hd_seg format for ov.pl.spatialseg.

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