fishtank.decode.spot_intensities

fishtank.decode.spot_intensities#

fishtank.decode.spot_intensities(img, x, y, z=None, radius=5, agg=<function max>)#

Get spot intensities.

Parameters:

  • img (ndarray) – A (Y,X), (C,Y,X) or (C,Z,Y,X) image.

  • x (ndarray) – A numpy array of x coordinates.

  • y (ndarray) – A numpy array of y coordinates.

  • z (Optional[ndarray] (default: None)) – A numpy array of z coordinates. If None, the image is assumed to be 2D.

  • radius (int (default: 5)) – The radius of the spot in pixels.

  • agg (Callable (default: <function max at 0x75ac4d56ceb0>)) – The aggregation function to use.

Return type:

ndarray

Returns:

intensities a N x C numpy array of intensities where N is the number of spots and C is the number of channels.

Contents