organoid_tracker.position_detection_cnn.peak_calling module

organoid_tracker.position_detection_cnn.peak_calling.create_prediction_mask(radius_x_px_float: float, resolution: ImageResolution) → ndarray

Creates a mask that is spherical in micrometers. If the resolution is not the same in the x, y and z directions, this sphere will appear as a spheroid in the images.

For use with the footprint param in scikit-image peak_local_max.

organoid_tracker.position_detection_cnn.peak_calling.reconstruct_volume(multi_im: ndarray, mid_layers_nb: int) → Tuple[ndarray, int]

Reconstructs a volume so that the xy scale is roughly equal to the z scale. Returns the used scale.