Code

prepare v1#4

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Henley13 merged 47 commits intodevelopfish-quant/big-fish:developfrom prepare_v1fish-quant/big-fish:prepare_v1Copy head branch name to clipboardMay 5, 2020

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Commits

Commits on Jan 22, 2020

• add test for stack.utils

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Commits on Jan 23, 2020

• add mail and licence in a script

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Commits on Jan 27, 2020

• unitary tests for io

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• fix tests utils

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Commits on Feb 12, 2020

• initialize codecov

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• fix test io

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• clean test_utils

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Commits on Feb 13, 2020

• misc with test io

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• add tests for image normalization

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• clean old notebooks

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• clean function to build stack

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Commits on Feb 17, 2020

• add tests for stack.preprocessing and stack.utils

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• refactor tests stack

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Commits on Feb 19, 2020

• tests for image augmentation

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Commits on Feb 24, 2020

• reshape imports and exclude plot folder from pytest config

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Commits on Mar 3, 2020

• misc

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• remove background filter in nuc thresholding

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• add loader for npz files

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• add tests for filtering

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• add tests for projection

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Commits on Mar 4, 2020

• add examples I/O

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• rename notebooks folder -> examples

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• rename notebooks folder -> examples #2

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• rename notebooks folder -> examples #3

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Commits on Mar 6, 2020

• add TODOs

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• improve documentation

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Commits on Mar 11, 2020

• update examples and improve 2D projections

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• update examples and improve 2D projections #2

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• refactor preparation.py

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• refactor stack and detection

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Commits on Mar 26, 2020

• clean and refactor spot detection

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• remove input data

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• remove input test data

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Commits on Apr 14, 2020

• major refactoring and updating of detection + notebooks

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• update TODO

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Commits on Apr 15, 2020

• isolate deep learning code

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Commits on Apr 27, 2020

• misc

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Commits on Apr 29, 2020

• io csv

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• concatenate results detection

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Commits on May 5, 2020

• refactor plots

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• detect_foci returns clustered_spots

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• refactor cell extraction

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• add new examples

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• misc

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• add TODO

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• Smaller fixes for packaging (#6)

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• update requirements

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