Code

XY and Z drift stabilization#108

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edyoshikun wants to merge 74 commits intomainczbiohub-sf/shrimPy:mainfrom stabilization_ymlczbiohub-sf/shrimPy:stabilization_ymlCopy head branch name to clipboard

+1,137

Commits

Commits on Sep 22, 2023

• initial commit adding tools for cropping and registering with ants

  edyoshikun

  committed
  b78a3c3

Commits on Sep 26, 2023

• adding lir crop

  edyoshikun

  committed
  6c1ce18

Commits on Oct 4, 2023

• starting cleanup for registration

  edyoshikun

  committed
  0b71192

Commits on Oct 5, 2023

• converting nan to zero

  edyoshikun

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  f11874d

Commits on Oct 24, 2023

• ants estimate affine

  edyoshikun

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  1df5d66

• adding config file for estimate_transform

  edyoshikun

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  b2e38e1

• cleaning up some redundancies

  edyoshikun

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  7819ec4

• fix edge case of input not being float32

  edyoshikun

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  9fc7df8

• channel is an int

  edyoshikun

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  957fc49

• typo in napari add image for vs ants optimzer

  edyoshikun

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  ccde02e

• adding utils yaml

  edyoshikun

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  ee1845f

Commits on Oct 30, 2023

• separated the manual estimation from the optimizer

  edyoshikun

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  e617ffc

• added ants to numpy and viceversa

  edyoshikun

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  d019bf6

• adding input at the end to prevent from closing

  edyoshikun

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  a76d70c

Commits on Nov 1, 2023

• replacing the reading of .mat to matrix from yaml

  edyoshikun

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  0d39cbe

Commits on Nov 3, 2023

• added changes to ants to numpy from Jordaos input

  edyoshikun

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  362e7a7

• cannot have recOrder as dependency given different pycromanager versions

  edyoshikun

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  9d25d1a

• format

  edyoshikun

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  caa84dc

• add test for optimize_affine and update readme

  edyoshikun

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  6d6504a

• adding docstring

  edyoshikun

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  f2c56fb

• removed the config dependency

  edyoshikun

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  8ed961d

• removing the focus_finding svg

  edyoshikun

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  7a7b20d

• removing the estimate_affine.yml and making flags to choose channels and verbose

  edyoshikun

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  ac4a5fc

• added comment and code to use scipy.

  edyoshikun

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  2d13d4d

• -ls and -lf to -s and -t

  talonchandler

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  58175d0

• document FOCUS_SLICE_ROI_WIDTH

  talonchandler

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  3b9d5eb

• estimate-source-to-target-affine -> estimate-affine

  talonchandler

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  8acad5c

• standardize optimize-affine arguments

  talonchandler

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  3fabc8a

• cleaner docs

  talonchandler

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  52c21ad

• update RegistrationSettings

  talonchandler

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  66d8990

• fix tests

  talonchandler

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  98089b2

• remove duplicate

  talonchandler

  committed
  c34bad0

• write indices to output config

  talonchandler

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  a35153f

• read channels from file

  talonchandler

  committed
  36f0b7e

Commits on Nov 4, 2023

• test fix

  talonchandler

  committed
  9bfbd20

• echo improvments

  talonchandler

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  2ca449c

• black

  talonchandler

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  5bf0ba0

• stabilization draft

  edyoshikun

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  bbbaf97

• slurm z drift correction

  edyoshikun

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  558e0ce

• pystackreg

  edyoshikun

  committed
  01b180b

Commits on Nov 6, 2023

• functions for estimating the z_drift and xy translation over time

  edyoshikun

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  b6366ea

• Merge branch 'registration_v2' of github.com:czbiohub/mantis into stabilization

  edyoshikun

  committed
  3ea70f7

Commits on Nov 9, 2023

• style

  ieivanov

  committed
  3e236f9

• remove duplicate cli call

  ieivanov

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  6226786

Commits on Nov 10, 2023

• more intuitive manual registration

  ieivanov

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  9137527

• Merge branch 'main' into registration_v2

  ieivanov

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  4f709ba

Commits on Nov 13, 2023

• stabilization cli

  edyoshikun

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  d3eb2b2

• patch for deskewing

  edyoshikun

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  ca75078

Commits on Nov 14, 2023

• fixing CLI calls and docstrings

  edyoshikun

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  70f0c13

• addine more comments to doctring

  edyoshikun

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  4ffe820

• stabilize_timalapse cli typo

  edyoshikun

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  dcc6e5f

• stabilize_timalapse cli typo

  edyoshikun

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  ada50f2

• Merge branch 'stabilization' of github.com:czbiohub/mantis into stabilization

  edyoshikun

  committed
  c7fc544

• removing some args in doctring.

  edyoshikun

  committed
  0bd70ae

Commits on Nov 15, 2023

• testing slurmkit

  edyoshikun

  committed
  df53a74

• fix apply affine example

  ieivanov

  committed
  cd698d6

• matrix multiplication bugfix

  ieivanov

  committed
  fdae716

• updating the lir_crop using new registration

  edyoshikun

  committed
  ebc8b04

Commits on Nov 16, 2023

• adding lir crop to the apply affine and modifying the manual estimation and the optimizer to output the input zyx shape to yaml

  edyoshikun

  committed
  94761c8

• convert nans to zeros

  edyoshikun

  committed
  a29811a

• updating the output saving scheme taking zarrs and saving the verbose in the parent directory.

  Show description for a4d1589
  edyoshikun

  committed
  a4d1589

Commits on Nov 17, 2023

• Merge branch 'registration_v2' of github.com:czbiohub/mantis into stabilization

  edyoshikun

  committed
  5a6d59f

Commits on Nov 22, 2023

• add affine test

  edyoshikun

  committed
  0762001

• fixing z-shift error

  edyoshikun

  committed
  998b714

• remove saving intermediate z-shifts

  edyoshikun

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  903df4d

• save to yml

  edyoshikun

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  804b3f9

Commits on Dec 5, 2023

• prototype to change to v2

  edyoshikun

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  769d8ff

Commits on Dec 7, 2023

• fixing the xy drift calculation. refactoring placed xy order instead of yx

  edyoshikun

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  548c9a2

Commits on Dec 8, 2023

• adding option to fill the zeroes with previous value.

  edyoshikun

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  5be1323

• adding tests

  edyoshikun

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  5cad1eb

• adding one more test

  edyoshikun

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  4ec9f0c

Commits on Dec 14, 2023

• add slurmkit

  edyoshikun

  committed
  1a6a59e

Commits on Jan 20, 2024

• Merge branch 'main' of github.com:czbiohub/mantis into stabilization_yml

  edyoshikun

  committed
  d867ff8

Commits on Jan 23, 2024

• formatting

  edyoshikun

  committed
  ec38003