spateo.io.seqfish¶
IO functions for seqFISH-PLUS technology.
Functions¶
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Read a seqFISH cell centroid locations file. |
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Read seqFISH data as AnnData. |
Module Contents¶
- spateo.io.seqfish.read_seqfish_meta_as_dataframe(path: str, fov_offset: pandas.DataFrame = None, accumulate_x: bool = False, accumulate_y: bool = False) pandas.DataFrame[source]¶
Read a seqFISH cell centroid locations file.
- Parameters:
- path
Path to file
- fov_offset
a dataframe contains the x/y offset of each fov (field of view), for example, {‘fov’:[fov_1, ..], ‘x_offset’:[x_offset_1, ..], ‘y_offset’:[y_offset_1, ..]}
- accumulate_x
whether to accumulate x_offset
- accumulate_y
whether to accumulate y_offset
- Returns:
- Pandas DataFrame with the following columns.
fov: ID of field of view
cell_id: ID of cell in each fov
x, y: X, Y coordinates of the cell centroids
region: sample region(tissue)
- spateo.io.seqfish.read_seqfish(path: str, meta_path: str, fov_offset: pandas.DataFrame = None, accumulate_x: bool = False, accumulate_y: bool = False) anndata.AnnData[source]¶
Read seqFISH data as AnnData.
- Parameters:
- path
Path to seqFISH digital expression matrix CSV.
- meta_path
Path to CSV file containing cell centroid locations.
- fov_offset
a dataframe contain offset of each fov, for example, {‘fov’:[fov_1, ..], ‘x_offset’:[x_offset_1, ..], ‘y_offset’:[y_offset_1, ..]}
- accumulate_x
whether to accumulate x_offset
- accumulate_y
whether to accumulate y_offset