[ ] Move the functions from /mantis/cli/stabilization to /mantis/analysis/stablize
[ ] Test the stabilization calculations
[ ] Update slurmkit call for CLI
This PR has the code for:
[x] Calculating the z-drift and returning a z-translation matrix for timelapses estimate_stabilization_affine()
[x] Calculating the xy-translation and returning a xy-translation matrices for timelapses stabilize_timalpse()
[x] CLI call for running the stabilization
[x] Save the translation matrices for XY and Z drift as yml
[x] 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
commented
6 months ago
TODO (01/19/24):
registration_v2/mantis/cli/stabilizationto/mantis/analysis/stablizeThis PR has the code for:
estimate_stabilization_affine()stabilize_timalpse()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.zarrFor 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