Update recommended sampling in the LS and LF remote refocus paths #69
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Co-Authored-By: Talon Chandler <[email protected]>
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Looks great up to a factor of 2. See my suggested edits after a discussion with @edyoshikun.
Co-authored-by: Talon Chandler <[email protected]>
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* Update recommended sampling in the LS and LF RR paths Co-Authored-By: Talon Chandler <[email protected]> * Drop mirror scan step by half Co-authored-by: Talon Chandler <[email protected]> --------- Co-authored-by: Talon Chandler <[email protected]>
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* adding first prototype of manual registration with napari * adding layer control to hide and show the aligned dataset. * replacing fluor/phase to respective dataset names and saving metadta * fix typo on * fixing channel mixup and adding 3D registration. * z-sampling typo. channels were flipped * fixed focus channel parameters and making this a function to save only the parameters * fixing layer typo * reverting accidental commit with some test * tet for registration.py * adding registration function * adding shape metadata * adding the CLI for applying registration with multiprocessing * adding registration parameter output a more meaningful name * replacing affine transform to similarity transform. this avoids shearing. * adding voxel_size * handle coordinate transformation * formatting isort and black * removing own registration algorithm as scikit image one works * fixes to use only click.echo rather than print * handling float inputs * renaming file to register.py to register and deleting the redundant registration.py * adding refactored register and utils function * renaming chan_1 and chan_2 to phase and fluor * fixing typos to add registration to cli * adding parameters for register.cli that live in utils.py * Fix_deskew_utils (#67) * replacing functinos that live in utils.py * adding utils.py to slurmkit file * adding validation and sorting to parsing.py * update parsing.py for deskew * adding the metadata per position * adding the yaml file writing and parsing * fixing deskew function new utils.py * slurm deskew fixed with new util.py * adding slumkit for registration * Implement O3 autofocus on light-sheet arm (#48) * adding pythonnet and drift correction * removing the pythonnet dependency that should live in copylot * cleanup the demo code * move drift_correction.py to examples * add copylot to dependencies * add O3 stage setup * move serial numbers to acq_engine * rename drift_correction script * add defocus stack acquisition * style * update examples * refactor z stage move * add galvo scanning to acquire_ls_defocus_stack * Update acquire_defocus_stack.py * update examples * switch to pylablib stage and relative moves * add some logging * add KIM101 compensation * fix galvo reset position bug * add find_focus.py example * style * ignore tests in examples dir * move o3 refocus to acq_engine * add checks and logging * debug acq engine o3 refocus * update example * Create separate logs directory * move conda env logger to logs * rename to mantis_acquisition_log * save acquired stacks * implement timed o3 refocus * update kim101 calibration * add relative O3 travel limits * logger fixes * style * add waveorder to deps and format pyproject * update kim101 compensation factor * add threshold and plotting to focus finding * update waveorder dependency * add microscope_operations documentation * update data structure specs * make acquire_ls_defocus_stack MantisAcquisition static method * update examples * rename_kim101 example * rename z_range vars to avoid confusion --------- Co-authored-by: Uditha Velidandla <[email protected]> * Update recommended sampling in the LS and LF remote refocus paths (#69) * Update recommended sampling in the LS and LF RR paths Co-Authored-By: Talon Chandler <[email protected]> * Drop mirror scan step by half Co-authored-by: Talon Chandler <[email protected]> --------- Co-authored-by: Talon Chandler <[email protected]> * Improve autofocus reengagement (#74) wait for autofocus to engage * All CLI calls read from zarr (#71) * read from zarr * Use better colors via `iohub` * isort * `estimate_deskew` read from zarr * first-pass standardize register * remove defunct test * fix readme. * standardize estimate_registration * typo * show `mantis -h` in order * standardize register cli * fix parameter * fix estimate-bleaching bug * fix deskew tests * flake8, isort * add registration tests * Update mantis/analysis/AnalysisSettings.py * reducing parameters in config file * re-adding finding best focus slice and rotate image by 90deg * removing test main calls * fixing apply_affine to perform a rotation first before affine. * renaming cli calls and updating README * renaming files for readability and to match CLI * style fix * adding tests and renaming variables for clarity * missed changin the conftest.py * fixing typo on test for test appy cli * modifying code to pass tests * deleting unsed imports flake8 * fix incorrect click.echo * adding pre-affine 90 deg rotationsa bout z as option for cli and croping ROI for focus finding * swapping config to use the indentity matrix as the affine matrix * return the affine transfrom mapping phase to fluorescence * fixing pre_affine_90degree_rotations_about_z in config * renaming and removing redundant printf() * update slurmkit deskew * adding function to read the voxel size from metadata and updating registration slurmkit * voxel_size retreival and modifing apply_affine to be applied to the labelfree channel. * fix typo * updating slurmkit apply_affine * cleanup slurmkit * pass voxel sizes through apply_affine * scaling passes through apply_affine tested * isort * update readme --------- Co-authored-by: Uditha Velidandla <[email protected]> Co-authored-by: Talon Chandler <[email protected]>
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Fixes #25