Aligner class for StackReg strategy.

Calculated rigid translational shifts using PyStackReg. PyStackReg is a Python port of the StackReg plugin for ImageJ which uses a pyramidal approach to minimize the least-squares difference in image intensity between a source and target image. StackReg is described in: P. Thevenaz, U.E. Ruttimann, M. Unser. A Pyramid Approach to Subpixel Registration Based on Intensity, IEEE Transactions on Image Processing vol. 7, no. 1, pp. 27-41, January 1998. https://doi.org/10.1109/83.650848

start¶

Position in tilt series to use as starting point for the alignment. If None, the slice closest to the midpoint will be used.

show_progressbar¶

Enable/disable progress bar

Returns:¶

shifts – The X- and Y-shifts to be applied to each image

Return type:¶

ndarray

Constructors¶

StackRegAligner(stack: TomoStack, start: int | None = 0, ...)[source]

Initialize self. See help(type(self)) for accurate signature.

Methods¶

calculate_shifts() → ndarray[source]

Calculate shifts using PyStackReg.

align(shift_method: 'interp' | 'fourier' = 'fourier') → TomoStack[source]

Perform stack alignment.