XY and Z drift stabilization; replaces #108

[ieivanov]

TODO (01/19/24):

• Merge main after registration_v2
• Move functions between /mantis/cli/stabilization and /mantis/analysis/stabilize
• fix tests @edyoshikun
• Test the stabilization calculations @ieivanov , use verbose mode
• Update slurmkit call for CLI @edyoshikun
• estimate_xy_stabilization should use the z indices calculated by estimate_z_stabilization @ieivanov
• estimate_stabilization should use channel_name rather than channel_index, like estimate_affine. Is there ever a case where we'd want to use different channels for focus finding and xy stabilization? In not, the config can have just "channel_name" rather than focus_finding_channel_index @ieivanov
• Can we try to reduce the number of CLI input parameters of estimate_stabilization? Should we collect them using input or is it useful for this function to be non-interactive? - These should be CLI options
• Can we reuse process_single_position and apply_function_to_zyx_and_save in apply_stabilization?
• remove analysis/stabilize.py if not used
• Optional: can we estimate the XY stabilization in parallel across timepoints? See discussion here: Parallel image registration glichtner/pystackreg#14. Can we supply the algorithm with pairs of (t_{n}, t_{n+1}) images? Does this computation take a lot of time and is it worth parallelizing? - limiting step is z stabilization, no need to parallelize for now
• Add optional argument to estimate_stabilization to specify which position name is used for xy stabilization @ieivanov

This PR has the code for:

• Calculating the z-drift and returning a z-translation matrix for timelapses estimate_stabilization_affine()
• Calculating the xy-translation and returning a xy-translation matrices for timelapses stabilize_timalpse()
• CLI call for running the stabilization
• Save the translation matrices for XY and Z drift as yml
• add tests

For the XY stabilization, you can use:
/hpc/projects/comp.micro/mantis/2023_09_22_A549_0.52NA_illum/3-registration/A549_MitoViewGreen_LysoTracker_W3_FOV5_1_phase.zarr

For Z drift, any of the timelapses:
/hpc/projects/comp.micro/mantis/2023_11_01_OpenCell_infection/4-registration/timelapse_7/timelapse_7_phase_registered.zarr

[ieivanov]

I am happy with this PR. The Z stabilization is well-tested. The XY stabilization is not used as much and not tested quite as well.