EMC2 Stitcher

Stiching/gap closing with EMC2 algorithm (See tps propagation from propagation module)

class byotrack.implementation.refiner.stitching.emc2.EMC2Stitcher(method: str | DirectedPropagate = 'tps', eta: float = 5.0, **kwargs)

Bases: DistStitcher

Implements Elastic Motion Correction and Concatenation (EMC2)

Stitch tracks using motion corrected positions following the paper: T. Lagache, A. Hanson, J. Perez-Ortega, et al., “Tracking calcium dynamics from individual neurons in behaving animals”, PLoS computational biology, vol. 17, pp. e1009432, 10 2021.

method

Method to use for position propagation. Either “constant”, “tps” or “flow” (see constant_directed_propagate, tps_directed_propagate or optical_flow_directed_propagate) or a user defined Callable following the DirectedPropagate protocol. Default: “tps”

Type:

str | DirectedPropagate

eta

Soft threshold in LAP solving (See DistStitcher) Default: 5.0 (Pixels)

Type:

float

kwargs

Additional parameters given to method. For instance for “tps”, you can set alpha (float) which is the regularization parameter of the interpolation (see tps_propation module and torch_tps librarie). We advise to use alpha > 5.0 (alpha = 10 by default). For “flow” propagation, you should provide optflow (byotrack.OpticalFlow) to correctly estimate optical flows.

Type:

Dict[str, Any]

max_overlap

Cannot stitch tracks that overlap more than max_overlap Default: 5

Type:

int

max_dist

Cannot stich track i and track j if the last position of i and first position of j are farther than max_dist (ignored if max_dist <= 0) Default: 100.0

Type:

float

max_gap

Cannot stich track i and track j if i ended more than max_gap frame before j started (ignored if max_gap <= 0) Default: 250

Type:

int

compute_dist(video: Sequence[ndarray] | ndarray, tracks: Collection[Track]) → ndarray

Compute EMC2 distance between tracks

Compute the mininum distance between each track propagation (only in the temporal gap between them).

Parameters:

• video (Sequence[np.ndarray] | np.ndarray) – Video of the tracked particles

• tracks (Collection[Track]) – Input tracks

Returns:

Distance between each track. (Contains np.inf)

Shape: (N, N), dtype: float32

Return type:

np.ndarray