Merging autotracker (#156)

* initial test of the multiotsu

* adding working pcc, template matching and multiotsu. borrowing funcs from dexv2

* adding autotracker shrimpy backbone and tracking methods

* this runs on demo mode without updating the events for the stage. Assumes that there are shifts computed and returned.

* autotracker with demo mode working

* adding autotracker parameters to the mantis config

* add notes

* add back isort on/off

* implement shift limits

* fix bug in template matching validator

* debug autotracker

* change from tuple to list

* adding normalization flag

* Update autotracker.py

small fix on phase cross corr

* Update autotracker.py

printing positions in the same order

* Update autotracker.py

Update printing positions and logging

* Update acq_engine.py

* Update autotracker.py

use t=0 as reference

* update O3 refocus to use new piezo stage

* style

* add autotracker stall debugging

* move autotracker logs to /logs (#176)

* move autotracker logs to /logs

* Update author metadata labeling in CITATION.cff (#188)

Update author metadata format in CITATION.cff

* Add CLI to stir plate before acquisition (#189)

* add stir_plate CLI

* docs and check for empty pos list

* use logging instead of click.echo

* style

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Co-authored-by: Mandy Chen <[email protected]>

* Update MM position list when using autotracker (#197)

* update MM position list

* bugfixes

* update positions at last timepoint

* from pycromanager import JavaObject

* add autotracker stall debugging

* abort stalled O3 autofocus

* add phase reconstruction

* update pcc removing padding

* bug fix

* clean gpu

* keep track of gpu vars

* autotracker debug

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* clip shift_zyx

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* update limits

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* remove log transform from PCC and adding max shift

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* add vs to autotracker

* adding viscy and correcting bugs

* correct config indentation

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* add vs to pydantic acquisition settings model

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* debug

* remove device log and tif file writes

* Autotracker based on phase reconstruction (#198)

* add autotracker stall debugging

* abort stalled O3 autofocus

* add phase reconstruction

* update pcc removing padding

* bug fix

* clean gpu

* keep track of gpu vars

* autotracker debug

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* clip shift_zyx

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* update limits

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* remove log transform from PCC and adding max shift

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

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Co-authored-by: Taylla Theodoro <[email protected]>

* Revert "Autotracker based on phase reconstruction" (#201)

Revert "Autotracker based on phase reconstruction (#198)"

This reverts commit d295f36.

* abort stalled O3 autofocus

* add phase reconstruction

* update pcc removing padding

* bug fix

* clean gpu

* keep track of gpu vars

* autotracker debug

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* clip shift_zyx

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* update limits

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* remove log transform from PCC and adding max shift

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* debug - don't use PM for O3 autofocus

* if shift reaches the max value, use max

Co-Authored-By: Taylla Milena Theodoro <[email protected]>

* working stage with autotracker instanciated once, buffer=100

* limit shifts function

* autotracker settings in classs init

* adding data preprocessing label free function

* Autotracker refactor instantiation and shifit limits (#209)

* instanciate autotracker once

* refactor shift lim

* add logging

* debug

* tracker in autotracker

* arguments from tracker to init

* zyx_shape as parameter

* tf in autotracker

* push last updates from mantis microscope

* remove extra print statements

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Co-authored-by: Ivan Ivanov <[email protected]>

* remove python-no-eval hook

* style

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Co-authored-by: Ivan Ivanov <[email protected]>
Co-authored-by: [email protected] <[email protected]>
Co-authored-by: Mandy Chen <[email protected]>

On-mantis-debug-late-2025 (#210)

* remove position/time chunking/chunking from examples yamls

* fix previously ommitted zarr-config reading in cli code

* how am I still hitting camel-case issues?

* fix plate argument

* fix zarr store initialzation so that position_settings can be accesed

* pass output_path directly to initialize_zarr_store

* fix incorrect StreamSettings constructor arg

* fix zarr compression configuration

* add .zarr suffix to output file if one does not exist

Update README.md (#155)

* Update README.md

* Update README.md

* Update README.md

Co-authored-by: Talon Chandler <[email protected]>

* update manuscript link

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Co-authored-by: Talon Chandler <[email protected]>