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Add ViM-UNet #236

Merged
merged 55 commits into from
Apr 12, 2024
Merged

Add ViM-UNet #236

merged 55 commits into from
Apr 12, 2024

Commits on Jan 23, 2024

  1. Add vision mamba + decoder experiments

    @anwai98
    anwai98 committed Jan 23, 2024
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Commits on Jan 25, 2024

  1. Fix checkpoint loading issue

    @anwai98
    anwai98 committed Jan 25, 2024
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  2. Update repo installation

    @anwai98
    anwai98 committed Jan 25, 2024
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  3. Update save_root

    @anwai98
    anwai98 committed Jan 25, 2024
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  4. Add inference script

    @anwai98
    anwai98 committed Jan 25, 2024
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Commits on Jan 26, 2024

  1. Update inference + add all instance segmentation setups

    @anwai98
    anwai98 committed Jan 26, 2024
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Commits on Feb 3, 2024

  1. Refactor Vim backbone + Add more vision mamba configs

    @anwai98
    anwai98 committed Feb 3, 2024
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Commits on Feb 4, 2024

  1. Add class token

    @anwai98
    anwai98 committed Feb 4, 2024
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  2. Fix imports

    @anwai98
    anwai98 committed Feb 4, 2024
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  3. Fix more imports

    @anwai98
    anwai98 committed Feb 4, 2024
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  4. Fix vim imports

    @anwai98
    anwai98 committed Feb 4, 2024
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Commits on Feb 5, 2024

  1. Update result saving

    @anwai98
    anwai98 committed Feb 5, 2024
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  2. Fix missing updates

    @anwai98
    anwai98 committed Feb 5, 2024
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  3. Add plotting script

    @anwai98
    anwai98 committed Feb 5, 2024
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  4. Update installation

    @anwai98
    anwai98 committed Feb 5, 2024
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Commits on Feb 7, 2024

  1. Add training for longer + use class tokens as default

    @anwai98
    anwai98 committed Feb 7, 2024
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Commits on Feb 8, 2024

  1. Merge branch 'main' into vision-mamba

    @anwai98
    anwai98 committed Feb 8, 2024
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  2. Update vimunet training - with new unetr backbone

    @anwai98
    anwai98 committed Feb 8, 2024
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Commits on Feb 10, 2024

  1. Merge branch 'main' into vision-mamba

    @anwai98
    anwai98 committed Feb 10, 2024
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  2. Update livecell training

    @anwai98
    anwai98 committed Feb 10, 2024
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Commits on Feb 11, 2024

  1. Check result outputs

    @anwai98
    anwai98 committed Feb 11, 2024
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Commits on Feb 15, 2024

  1. Merge branch 'main' into vision-mamba

    @anwai98
    anwai98 committed Feb 15, 2024
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Commits on Feb 16, 2024

  1. Add plotting for unetr

    @anwai98
    anwai98 committed Feb 16, 2024
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Commits on Mar 19, 2024

  1. Merge branch 'main' into vision-mamba

    @anwai98
    anwai98 committed Mar 19, 2024
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Commits on Mar 30, 2024

  1. Add CREMI experiments using ViMUNet (#12) 

    CREMI experiments for benchmarking instance segmentation using UNet, UNETR and ViMUNet
    @anwai98
    anwai98 committed Mar 30, 2024
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  2. Update NeurIPS CellSeg - to allow download from zenodo links (#14)

    @anwai98
    anwai98 committed Mar 30, 2024
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Commits on Mar 31, 2024

  1. Add NeurIPS CellSeg experiments for ViMUNet (#15)

    @anwai98
    anwai98 committed Mar 31, 2024
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  2. Refactor LIVECell experiments for UNETR setup

    @anwai98
    anwai98 committed Mar 31, 2024
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Commits on Apr 1, 2024

  1. Add LIVECell benchmarking experiments (#16)

    @anwai98
    anwai98 committed Apr 1, 2024
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  2. Add scripts for training all benchmarking experiments (#17)

    @anwai98
    anwai98 committed Apr 1, 2024
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Commits on Apr 4, 2024

  1. Add LM training for ViMUNet (#18)

    @anwai98
    anwai98 committed Apr 4, 2024
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Commits on Apr 5, 2024

  1. Update inference scripts (#19)

    @anwai98
    anwai98 committed Apr 5, 2024
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  2. Expose learning rate parameter for vimunet experiments

    @anwai98
    anwai98 committed Apr 5, 2024
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  3. Expose lr for vit and unet-based methods

    @anwai98
    anwai98 committed Apr 5, 2024
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  4. Add neurips cellseg inference

    @anwai98
    anwai98 committed Apr 5, 2024
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Commits on Apr 7, 2024

  1. Add resource efficient limited data training (#20)

    @anwai98
    anwai98 committed Apr 7, 2024
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  2. Update ViMUNet documentation

    @anwai98
    anwai98 committed Apr 7, 2024
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  3. Update README.md

    @anwai98
    anwai98 committed Apr 7, 2024
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  4. Update README.md

    @anwai98
    anwai98 committed Apr 7, 2024
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  5. Minor fix to limited data training

    @anwai98
    anwai98 committed Apr 7, 2024
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  6. Update multicut for livecell

    @anwai98
    anwai98 committed Apr 7, 2024
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Commits on Apr 11, 2024

  1. Cleanup scripts

    @anwai98
    anwai98 committed Apr 11, 2024
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  2. Cleanup code2

    @anwai98
    anwai98 committed Apr 11, 2024
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  3. Merge branch 'main' into vision-mamba

    @anwai98
    anwai98 committed Apr 11, 2024
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  4. Cleanup vision mamba directory

    @anwai98
    anwai98 committed Apr 11, 2024
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  5. Refactor scripts

    @anwai98
    anwai98 committed Apr 11, 2024
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  6. Simplify scripts with helper arguments

    @anwai98
    anwai98 committed Apr 11, 2024
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  7. Final refactor for vimunet scripts

    @anwai98
    anwai98 committed Apr 11, 2024
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  8. Refactor unet and unetr benchmarking scripts

    @anwai98
    anwai98 committed Apr 11, 2024
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  9. Update documentation for using unetr

    @anwai98
    anwai98 committed Apr 11, 2024
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  10. Update vimunet documentation

    @anwai98
    anwai98 committed Apr 11, 2024
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  11. Update documentation

    @anwai98
    anwai98 committed Apr 11, 2024
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  12. Fix pip install scripts

    @anwai98
    anwai98 committed Apr 11, 2024
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  13. Minor doc fix

    @anwai98
    anwai98 committed Apr 11, 2024
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  14. Minor cuda-related mention

    @anwai98
    anwai98 committed Apr 11, 2024
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