fishtank.io.read_fov

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fishtank.io.read_fov#

fishtank.io.read_fov(path, fov, series=None, colors=None, channels=None, file_pattern='{series}/Conv_zscan_{fov}.dax', z_slices=None, z_project=False, ref_series=None)#

Read FOV from MERFISH experiment.

Parameters:

  • path (str | Path) – Path to image files.

  • fov (int | str) – Field of view number.

  • series (Union[int, str, list, None] (default: None)) – List of series names to read.

  • colors (Union[int, str, list, None] (default: None)) – List of color indices to read.

  • channels (Optional[DataFrame] (default: None)) – DataFrame with “series” and “color” columns specifying the channels to read.

  • file_pattern (str (default: '{series}/Conv_zscan_{fov}.dax')) – Pattern for image files.

  • z_slices (Optional[list] (default: None)) – List of z-slice indices to read.

  • z_project (bool (default: False)) – If True, z-project the image.

Return type:

tuple[ndarray, dict]

Returns:

img

a numpy array, such that a gray image is (Y,X), a 3D gray image is (Z,Y,X), and 3D multi-channel image is (C,Z,Y,X).

attrs

a dictionary of image attributes.

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