Correct for jittering

[brunicardoso]

I am not sure if Ultrack has a function to correct for jittering? In may dataset, when there is a little jitter (usually occurs in the first to the second frame and when a treatment is added), the tracks are messed up.

[JoOkuma]

Hi, Alexandre

We have a more sophisticated and (brittle) approach to register different frames using a flow field; it's used on this example.

If your jitter is mostly a translation shift, using skimage to register when pre-processing your image will be more robust.

This function is a good starting point:

import numpy as np
import scipy.ndimage as ndi
from skimage.registration import phase_cross_correlation
from tqdm import tqdm

def _register(video: np.ndarray) -> np.ndarray:
    # registration using channel 1
    reg_channel = 1
    for t in tqdm(range(video.shape[0] - 1), "register"):
        shift, error, _ = phase_cross_correlation(
            video[t, reg_channel],
            video[t + 1, reg_channel],
            normalization=None,
            overlap_ratio=0.25,
        )
        video[t+1] = ndi.shift(video[t+1], (0, *shift), order=1)
    return video

[brunicardoso]

Thank, Jordao! I will try it