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Methods to stitch a position grid #137

Merged
merged 41 commits into from
Jul 22, 2024
Merged

Methods to stitch a position grid #137

merged 41 commits into from
Jul 22, 2024

Commits on Mar 19, 2024

  1. add image stitcher

    @ieivanov
    ieivanov committed Mar 19, 2024
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Commits on Mar 25, 2024

  1. update stitching scripts

    @ieivanov
    ieivanov committed Mar 25, 2024
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  2. select channel to stich and save as zarr

    @ieivanov
    ieivanov committed Mar 25, 2024
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Commits on Mar 27, 2024

  1. refactor zarr stitching

    @ieivanov
    ieivanov committed Mar 27, 2024
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  2. add cli

    @ieivanov
    ieivanov committed Mar 27, 2024
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Commits on Mar 28, 2024

  1. debug and switch to ndi.shift

    @ieivanov
    ieivanov committed Mar 28, 2024
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  2. refactor stitching into module

    @ieivanov
    ieivanov committed Mar 28, 2024
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  3. refactor stitch cli and add slurmkit option

    @ieivanov
    ieivanov committed Mar 28, 2024
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  4. minor updates

    @ieivanov
    ieivanov committed Mar 28, 2024
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  5. debug timelapse stitching

    @ieivanov
    ieivanov committed Mar 28, 2024
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  6. stitch after shifting with slurm

    @ieivanov
    ieivanov committed Mar 28, 2024
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  7. refactor stitch_shifted_store

    @ieivanov
    ieivanov committed Mar 28, 2024
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Commits on Apr 2, 2024

  1. add config-based stitching

    @ieivanov
    ieivanov committed Apr 2, 2024
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Commits on Apr 28, 2024

  1. fix example stitch settings bug

    @ieivanov
    ieivanov committed Apr 28, 2024
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Commits on Apr 29, 2024

  1. v2 shift estimation

    @ieivanov
    ieivanov committed Apr 29, 2024
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  2. write config file

    @ieivanov
    ieivanov committed Apr 29, 2024
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  3. move write config function

    @ieivanov
    ieivanov committed Apr 29, 2024
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Commits on May 1, 2024

  1. better image shift calculation

    @ieivanov
    ieivanov committed May 1, 2024
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  2. change pre/post processing nomenclature

    @ieivanov
    ieivanov committed May 1, 2024
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  3. v2 stitching

    @ieivanov
    ieivanov committed May 1, 2024
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Commits on May 13, 2024

  1. estimate stitch of multiple wells

    @ieivanov
    ieivanov committed May 13, 2024
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Commits on Jul 15, 2024

  1. better path names

    @ieivanov
    ieivanov committed Jul 15, 2024
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  2. Merge branch 'main' into stitch_images_v2

    @ieivanov
    ieivanov committed Jul 15, 2024
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Commits on Jul 16, 2024

  1. patching the error in our function that parallelizes over t and c.

    @edyoshikun
    edyoshikun committed Jul 16, 2024
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  2. Merge remote-tracking branch 'origin/fix_tc_parallel' into stitch_ima… 

    …ges_v2
    @ieivanov
    ieivanov committed Jul 16, 2024
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  3. multiwell stitching with slurm

    @ieivanov
    ieivanov committed Jul 16, 2024
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Commits on Jul 17, 2024

  1. improvements and bugfixes

    @ieivanov
    ieivanov committed Jul 17, 2024
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  2. remove old scripts

    @ieivanov
    ieivanov committed Jul 17, 2024
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  3. cleanup function names

    @ieivanov
    ieivanov committed Jul 17, 2024
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  4. update output store chunking

    @ieivanov
    ieivanov committed Jul 17, 2024
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  5. refactor and improve documentation

    @ieivanov
    ieivanov committed Jul 17, 2024
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  6. refactor estimate functions into analysis/stitch.py

    @ieivanov
    ieivanov committed Jul 17, 2024
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  7. switch estimate_stitch to use input_position_dirpaths

    @ieivanov
    ieivanov committed Jul 17, 2024
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  8. expand documentation

    @ieivanov
    ieivanov committed Jul 17, 2024
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  9. update example config file

    @ieivanov
    ieivanov committed Jul 17, 2024
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Commits on Jul 18, 2024

  1. add robustness for col shifts

    @ieivanov
    ieivanov committed Jul 18, 2024
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  2. switch to absolute stage error limits

    @ieivanov
    ieivanov committed Jul 18, 2024
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  3. more docs

    @ieivanov
    ieivanov committed Jul 18, 2024
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  4. increase preprocess_and_shift time limit

    @ieivanov
    ieivanov committed Jul 18, 2024
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Commits on Jul 22, 2024

  1. change default temp path

    @ieivanov
    ieivanov committed Jul 22, 2024
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  2. raise warning is SLURM not available, function should still run

    @ieivanov
    ieivanov committed Jul 22, 2024
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