SOAPy_st.pp.read_dsp2adata

SOAPy_st.pp.read_dsp2adata(information_file: str | PathLike, slide_name: str | list | None = None, xml_file: dict | None = None, polygon_key: str = 'Polygon', point_attribute: str = 'Points') → AnnData

Read spatial transcriptomics data of NanoString GeoMx DSP.

The Export3_BiologicalProbeQC.xlsx or Export4_NormalizationQ3.xlsx file in DSP is used to build adata data. If the information of each AOI(ROI) sampling point needs to be placed, the dictionary is used to pass in the xml file of each slide.

Parameters

information_fileUnion[str, PathLike]

The path of Export3_BiologicalProbeQC.xlsx or Export4_NormalizationQ3.xlsx file.

slide_nameUnion[str, list], optional

The name or names list of used slides. By default, all slides are read.

xml_filedict, optional

If sampling points inside each AOI are needed, pass in the xml file using the dictionary. e.g.: {‘mu_dev_E13_011’: ‘./mu_dev_E13_011.ome.xml’}

polygon_keystr

Polygon Tag in .xml file

point_attributestr

Point attribute in polygon Tag.

Returns

anndata.Anndata object