dexp.processing.deskew.yang_deskew

dexp.processing.deskew.yang_deskew(image: numpy.ndarray, depth_axis: int, lateral_axis: int, flip_depth_axis: bool, dx: float, dz: float, angle: float, camera_orientation: int = 0, num_split: int = 4, internal_dtype=None, padding: None = None)

‘Yang’ Deskewing as done in Yang et al. 2019 ( https://www.biorxiv.org/content/10.1101/2020.09.22.309229v2 )

Parameters

imageinput image (skewed 3D stack)

depth_axisDepth axis.

lateral_axisLateral axis.

flip_depth_axisFlips image to deskew in the opposite orientation (True for view 0 and False for view 1)

dzfloat, scanning step (stage or galvo scanning step, not the same as the distance between the slices)

dxfloat, pixel size of the camera

anglefloat, incident angle of the light sheet, angle between the light sheet and the optical axis in degrees

camera_orientationCamera orientation correction expressed

as a number of 90 deg rotations to be performed per 2D image in stack.

num_splitnumber of splits to break down the data into pieces (along y, axis=2) to fit into the memory of GPU

internal_dtypeinternal dtype to perform computation

paddingdummy argument for compatibility

Returns

Deskewed image