xenium_to_domain

xenium_to_domain(path_to_xenium_data=None, domain_name='Default_xenium_domain', cells_from_selection_csv=None, load_transcripts=False, selected_transcripts=None, load_nuclei=False, load_cells_as_shapes=True, exclude_no_nuclei_cells=True, print_summary=True)

The function will take a xenium dataset and produce a muspan domain loaded with cell and transcript objects from an xenium output. Each data will be linked using string cell ID from Xenium and given as a label on the object. The function will also load only the cells selected in the cells_from_selection_csv file which is obtained via annotation using Xenium explorer.

Parameters:

path_to_xenium_datastr, optional

String providing the path to the directory to the Xenium data folder, defaults to None.

domain_namestr, optional

Name given to created domain, defaults to ‘Default_xenium_domain’.

cells_from_selection_csvstr, optional

Path to a region csv exported from Xenium Explorer using the ‘download cell states as csv’ functionality, defaults to None.

load_transcriptsbool, optional

Option to load transcripts into the domain, defaults to False.

selected_transcriptslist of str, optional

A list of transcript names to be loaded into the domain. If None, all transcripts will be loaded, defaults to None.

load_nucleibool, optional

Option to load cell nuclei as shape objects into the domain, defaults to False.

load_cells_as_shapesbool, optional

Option to load cells as shapes. If False, cells will be loaded as point objects, defaults to True.

exclude_no_nuclei_cellsbool, optional

Option to exclude any cell object that does not contain a nucleus following segmentation, defaults to True.

print_summarybool, optional

If True, print a summary of the resulting domain, by default True.

Returns:

muspan.domain

A muspan domain object.