spateo.io.merfish#

IO functions for MERFISH technology.

Module Contents#

Functions#

read_merfish_as_anndata(→ anndata.AnnData)

Read MERFISH matrix as AnnData.

read_merfish_positions_as_dataframe(→ pandas.DataFrame)

Read MERFISH cell positions CSV as dataframe.

read_merfish(→ anndata.AnnData)

Read MERFISH data as AnnData.

spateo.io.merfish.read_merfish_as_anndata(path: str) anndata.AnnData[source]#

Read MERFISH matrix as AnnData.

Parameters:
matrix_dir

Path to matrix file.

Returns:

AnnData of cell x genes.

spateo.io.merfish.read_merfish_positions_as_dataframe(path: str) pandas.DataFrame[source]#

Read MERFISH cell positions CSV as dataframe.

Parameters:
path

Path to file

Returns:

DataFrame containing cell positions.

spateo.io.merfish.read_merfish(path: str, positions_path: str) anndata.AnnData[source]#

Read MERFISH data as AnnData.

Parameters:
path

Path to matrix files

positions_path

Path to xlsx containing spatial coordinates