Code

Finalize segmentation#6

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Draft

MikeLippincott wants to merge 51 commits intoWayScience:mainWayScience/NF1_3D_organoid_profiling_pipeline:mainfrom MikeLippincott:finalize_segmentationMikeLippincott/GFF_3D_organoid_profiling_pipeline:finalize_segmentationCopy head branch name to clipboard

+6,733-2,786

Commits

Commits on Dec 2, 2024

• Initial commit

  MikeLippincott

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  6cdb987

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Commits on Dec 4, 2024

• inital commit + preprocessing (WayScience#1)

  Show description for 007c4ca
  MikeLippincott

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  007c4ca

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Commits on Dec 12, 2024

• gitignore

  MikeLippincott

  committed
  e438dd0

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• Merge remote-tracking branch 'upstream/main'

  MikeLippincott

  committed
  aa116ed

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Commits on Dec 20, 2024

• Merge remote-tracking branch 'upstream/main'

  MikeLippincott

  committed
  8b7f04b

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• Merge remote-tracking branch 'upstream/main'

  MikeLippincott

  committed
  be53653

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Commits on Dec 23, 2024

• progress capture

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  committed
  74584fc

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Commits on Dec 24, 2024

• test on alpine

  MikeLippincott

  committed
  dcfc868

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Commits on Dec 25, 2024

• testing on alpine

  MikeLippincott

  committed
  9d5a1b2

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• alpine errors fixed?

  MikeLippincott

  committed
  94ddb5d

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• add fix

  MikeLippincott

  committed
  cf33dea

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• run again

  MikeLippincott

  committed
  92ca33e

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• run on alpine

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  committed
  d61ed99

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• init segs

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  committed
  8415ea6

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• run all

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  0d19755

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Commits on Dec 26, 2024

• test running all

  MikeLippincott

  committed
  9877a77

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• fix slurm script

  MikeLippincott

  committed
  fffdf32

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• update runs

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  c53a001

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Commits on Dec 27, 2024

• fix run

  MikeLippincott

  committed
  43dc6c1

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• prep segmentations for cellprofiler

  MikeLippincott

  committed
  74d335c

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• run all segs

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  committed
  f7b34dd

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• rerun_pipe in the correct order

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  committed
  c1ea7f1

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• rerun

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  committed
  24b218b

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Commits on Dec 29, 2024

• fix slurm timing

  MikeLippincott

  committed
  9e37507

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• spelling fixes

  MikeLippincott

  committed
  6ef9854

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Commits on Dec 30, 2024

• progress capture

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  committed
  7a6a93e

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• update file checker

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  committed
  5cbf1df

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Commits on Dec 31, 2024

• run on HPC

  MikeLippincott

  committed
  1a6b7f8

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• testing on HPC

  MikeLippincott

  committed
  6cd2557

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• fix slurm workflow

  MikeLippincott

  committed
  2f41427

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• fix slurm workflow

  MikeLippincott

  committed
  2184d17

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• test dir testing

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  committed
  6067b93

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• test dir testing

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  committed
  35e48de

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• process all on HPC please

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  committed
  be736ac

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Commits on Jan 1, 2025

• testing on HPC

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  committed
  1a1e115

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• testing continues

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  committed
  fbeb16e

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• run attempt

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  b1086cc

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• attempting success

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  committed
  1a6ab56

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• run on HPC

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  committed
  8f98173

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Commits on Jan 2, 2025

• run again

  MikeLippincott

  committed
  ebbf4b0

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• rerun on HPC

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  committed
  9ae4e8b

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Commits on Jan 4, 2025

• rerun the bad runs

  MikeLippincott

  committed
  dc79637

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Commits on Jan 7, 2025

• attempt to run all on alpine again

  MikeLippincott

  committed
  1413ebc

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• add todo

  MikeLippincott

  committed
  2848d7c

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Commits on Jan 9, 2025

• progress capture

  MikeLippincott

  committed
  9d62760

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• rerun segmentations

  MikeLippincott

  committed
  0d1edb4

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• segmentation on HPC

  MikeLippincott

  committed
  425e9ec

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• fixing segmentaiton

  MikeLippincott

  committed
  d393fa4

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Commits on Jan 12, 2025

• fix child scripts

  MikeLippincott

  committed
  1d9f5e7

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• edit organoid compatibility

  MikeLippincott

  committed
  5bc41dc

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Commits on Jan 16, 2025

• rerun example segmentations

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  committed
  ec6ac2c

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