Colocalization

Match colocalized spots over two different channels:

• bigfish.multistack.detect_spots_colocalization()

Visualize the impact of distance threshold to discriminate between the colocalized spots and the distant ones:

• bigfish.multistack.get_elbow_value_colocalized()

bigfish.multistack.detect_spots_colocalization(spots_1, spots_2, voxel_size, threshold=None, return_indices=False, return_threshold=False)

Detect colocalized spots between two arrays of spot coordinates ‘spots_1’ and ‘spots_2’. Pairs of spots below a specific threshold are defined as colocalized.

Parameters:

spots_1np.ndarray

Coordinates of the spots 1 with shape (nb_spots_1, 3) or (nb_spots_1, 2).

spots_2np.ndarray

Coordinates of the spots 2 with shape (nb_spots_2, 3) or (nb_spots_2, 2).

voxel_sizeint, float, Tuple(int, float), or List(int, float)

Size of a voxel, in nanometer. One value per spatial dimension (zyx or yx dimensions). If it’s a scalar, the same value is applied to every dimensions.

thresholdint, float or None

A threshold to discriminate colocalized spots from distant ones. If None, an optimal threshold is selected automatically.

return_indicesbool

Return the indices of the colocalized spots within ‘spots_1’ and ‘spots_2’.

return_thresholdbool

Return the threshold used to detect colocalized spots.

Returns:

spots_1_colocalizednp.ndarray

Coordinates of the colocalized spots from ‘spots_1’ with shape (nb_colocalized_spots,).

spots_2_colocalizednp.ndarray

Coordinates of the colocalized spots from ‘spots_2’with shape (nb_colocalized_spots,).

distancesnp.ndarray, np.float64

Distance matrix between spots with shape (nb_colocalized_spots,).

indices_1np.ndarray, np.int64

Indices of the colocalized spots in ‘spots_1’ with shape (nb_colocalized_spots,). Optional.

indices_2np.ndarray, np.int64

Indices of the colocalized spots in ‘spots_2’ with shape (nb_colocalized_spots,). Optional.

thresholdint or float

Threshold used to discriminate colocalized spots from distant ones. Optional.

bigfish.multistack.get_elbow_value_colocalized(spots_1, spots_2, voxel_size)

Get values to plot the elbow curve used to automatically set the threshold to detect colocalized spots.

Parameters:

spots_1np.ndarray

Coordinates of the spots with shape (nb_spots, 3) or (nb_spots, 2).

spots_2np.ndarray

Coordinates of the spots with shape (nb_spots, 3) or (nb_spots, 2).

voxel_sizeint, float, Tuple(int, float), or List(int, float)

Size of a voxel, in nanometer. One value per spatial dimension (zyx or yx dimensions). If it’s a scalar, the same value is applied to every dimensions.

Returns:

thresholdsnp.ndarray, np.float64

Candidate threshold values.

nb_colocalizednp.ndarray, np.float64

Colocalized spots count.

optimal_thresholdfloat or None

Threshold automatically set.