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Changes for new release #327

Merged
merged 54 commits into from
Jan 17, 2024
Merged

Changes for new release #327

merged 54 commits into from
Jan 17, 2024

Commits on Nov 18, 2023

  1. Merge pull request #279 from computational-cell-analytics/master 

    Keep master and dev in sync
    @constantinpape
    constantinpape authored Nov 18, 2023
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  2. napari widget to set cache directory (for model weights and sample da… 

    …ta downloads) (#277)

Add napari settings widget
    @GenevieveBuckley
    GenevieveBuckley authored Nov 18, 2023
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  3. Run github actiosns CI tests on Windows, Mac and Linux (#267) 

    Add CI for windows and mac

---------

Co-authored-by: Constantin Pape <[email protected]>
    @GenevieveBuckley @constantinpape
    GenevieveBuckley and constantinpape authored Nov 18, 2023
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  4. Improve device handling (#251) 

    Improve device handling to support torch.device as well as string
    @constantinpape
    constantinpape authored Nov 18, 2023
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  5. Update examples to use cache directory

    @constantinpape
    constantinpape committed Nov 18, 2023
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  6. Ensure embedding cache dir exists in examples and fix typo

    @constantinpape
    constantinpape committed Nov 18, 2023
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Commits on Nov 20, 2023

  1. Increase test coverage (#280) 

    Add tests for get_sam_model and iterative prediction.
    @constantinpape
    constantinpape authored Nov 20, 2023
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  2. Fixup typo (#281)

    @claydugo
    claydugo authored Nov 20, 2023
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Commits on Nov 23, 2023

  1. Download models with pooch (#276) 

    Use pooch to download model weights and simplify some other functionality
---------

Co-authored-by: Constantin Pape <[email protected]>
Co-authored-by: Constantin Pape <[email protected]>
    @GenevieveBuckley @constantinpape
    3 people authored Nov 23, 2023
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Commits on Nov 27, 2023

  1. Add xxh128 version of hashes for model (#284)

    @hmaarrfk
    hmaarrfk authored Nov 27, 2023
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Commits on Dec 6, 2023

  1. Update Rescaling Inputs (#286) 

    Implement identity transform and input check for SAM training

---------

Co-authored-by: Constantin Pape <[email protected]>
    @anwai98 @constantinpape
    anwai98 and constantinpape authored Dec 6, 2023
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Commits on Dec 20, 2023

  1. Add Joint Training (#288) 

    Implement joint training for interactive and automatic instance segmentation
    @anwai98
    anwai98 authored Dec 20, 2023
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  2. Fix load_checkpoint encoder prefix (#290)

    @anwai98
    anwai98 authored Dec 20, 2023
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Commits on Dec 21, 2023

  1. Update livecell specialist fine-tuning

    @anwai98
    anwai98 committed Dec 21, 2023
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Commits on Dec 22, 2023

  1. Update livecell_finetuning.py - Add trainer desc.

    @anwai98
    anwai98 authored Dec 22, 2023
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Commits on Dec 29, 2023

  1. Update livecell evaluation

    @constantinpape
    constantinpape committed Dec 29, 2023
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Commits on Dec 30, 2023

  1. Merge pull request #291 from computational-cell-analytics/u-livecell-… 

    …specialist

Update LiveCELL Specialist Fine-tuning
    @constantinpape
    constantinpape authored Dec 30, 2023
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  2. Update livecell experiments

    @constantinpape
    constantinpape committed Dec 30, 2023
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  3. Remove amg folder

    @constantinpape
    constantinpape committed Dec 30, 2023
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Commits on Jan 2, 2024

  1. Update livecell evaluation scripts (#296) 

    Update livecell evaluation experiments
    @constantinpape
    constantinpape authored Jan 2, 2024
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  2. Start implementing new instance segmentation WIP

    @constantinpape
    constantinpape committed Jan 2, 2024
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  3. Update grid search for instance segmentation

    @constantinpape
    constantinpape committed Jan 2, 2024
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  4. Implement grid search for instance segmentation with decoder WIP

    @constantinpape
    constantinpape committed Jan 2, 2024
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  5. Update training to always resize input

    @constantinpape
    constantinpape committed Jan 2, 2024
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  6. Update livecell specialist fine-tuning

    @anwai98 @constantinpape
    anwai98 authored and constantinpape committed Jan 2, 2024
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  7. Simplify embedding precomputation in sam training

    @constantinpape
    constantinpape committed Jan 2, 2024
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  8. Update dependencies

    @constantinpape
    constantinpape committed Jan 2, 2024
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  9. Remove deprecated instance segmentation functionality

    @constantinpape
    constantinpape committed Jan 2, 2024
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  10. Update livecell evaluation scripts (#296) 

    Update livecell evaluation experiments
    @constantinpape
    constantinpape committed Jan 2, 2024
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  11. Merge branch 'dev' into new-instance-seg

    @constantinpape
    constantinpape authored Jan 2, 2024
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  12. Merge pull request #297 from computational-cell-analytics/new-instanc… 

    …e-seg

New instance segmentation
    @constantinpape
    constantinpape authored Jan 2, 2024
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Commits on Jan 3, 2024

  1. Fix Resizing Input Prompts (#299) 

    Fix input resizing for prompts in training
    @anwai98
    anwai98 authored Jan 3, 2024
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  2. Minor fix to image embeddings (#302)

    @anwai98
    anwai98 authored Jan 3, 2024
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  3. Simplify training implementations (#301) 

    Simplify interactive training and implement box distortion
    @constantinpape
    constantinpape authored Jan 3, 2024
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  4. Make grid search functionality more flexible (#300) 

    Make grid search more flexible to enable external re-use
    @constantinpape
    constantinpape authored Jan 3, 2024
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Commits on Jan 4, 2024

  1. Update box distortion

    @constantinpape
    constantinpape committed Jan 4, 2024
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  2. Update livecell finetuning (#303)

    @anwai98
    anwai98 authored Jan 4, 2024
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Commits on Jan 5, 2024

  1. Update LM Generalists (#292) 

    Update training for LM datasets
    @anwai98
    anwai98 authored Jan 5, 2024
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Commits on Jan 7, 2024

  1. Update LM Generalist Dist. Trafo. (#306) 

    Update LM Generalist experiments
    @anwai98
    anwai98 authored Jan 7, 2024
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Commits on Jan 8, 2024

  1. Add EM Mito-Nuc Generalist (#295) 

    Implement EM organelle model training
    @anwai98
    anwai98 authored Jan 8, 2024
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  2. Implement train grid search and update instance segmentation grid sea… 

    …rch (#308)
    @constantinpape
    constantinpape authored Jan 8, 2024
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  3. Update patch shape argument (#309)

    @anwai98
    anwai98 authored Jan 8, 2024
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Commits on Jan 9, 2024

  1. Minor typo in em mito nuc (#311) 

    * Update train_mito_nuc_em_generalist.py

* Update obtain_mito_nuc_em_datasets.py
    @anwai98
    anwai98 authored Jan 9, 2024
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Commits on Jan 10, 2024

  1. Add EM Boundaries Generalist (#312) 

    Add fine-tuning for EM boundary generalist model
    @anwai98
    anwai98 authored Jan 10, 2024
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Commits on Jan 14, 2024

  1. Minor updates to finetuning desc. (#314) 

    Minor updates in finetuning scripts.
    @anwai98
    anwai98 authored Jan 14, 2024
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  2. Update LiveCELL inference scripts (#315) 

    * Update livecell inference
    @anwai98
    anwai98 authored Jan 14, 2024
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Commits on Jan 15, 2024

  1. Add custom pickler to handle generalists (#318)

    @anwai98
    anwai98 authored Jan 15, 2024
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  2. Add livecell specialist results (#317) 

    * Add livecell specialist results
    @anwai98
    anwai98 authored Jan 15, 2024
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  3. Add livecell (lm) generalist results (#319) 

    * Add livecell results from lm generalists
    @anwai98
    anwai98 authored Jan 15, 2024
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  4. Minor fix to livecell eval. scripts (#316) 

    * Fix evaluation script

* Update precomputing embeddings for val + other minor fixes
    @anwai98
    anwai98 authored Jan 15, 2024
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Commits on Jan 17, 2024

  1. Minor fix to path convention (#323)

    @anwai98
    anwai98 authored Jan 17, 2024
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  2. Refactor files in scripts (#321) 

    * Refactor path convention for scripts

* Add EM generalist results (#322)

* Add EM generalist results

* Add snemi results
    @anwai98
    anwai98 authored Jan 17, 2024
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  3. Add mitonet quantitative results (#325)

    @anwai98
    anwai98 authored Jan 17, 2024
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  4. Update to new finetuned models (#326)

    @constantinpape
    constantinpape authored Jan 17, 2024
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