Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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 authored Nov 18, 2023
    Configuration menu
    Copy the full SHA
    d5dc804 View commit details
    Browse the repository at this point in the history
  2. napari widget to set cache directory (for model weights and sample da…

    …ta downloads) (#277)
    
    Add napari settings widget
    GenevieveBuckley authored Nov 18, 2023
    Configuration menu
    Copy the full SHA
    d427e9f View commit details
    Browse the repository at this point in the history
  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 and constantinpape authored Nov 18, 2023
    Configuration menu
    Copy the full SHA
    5546343 View commit details
    Browse the repository at this point in the history
  4. Improve device handling (#251)

    Improve device handling to support torch.device as well as string
    constantinpape authored Nov 18, 2023
    Configuration menu
    Copy the full SHA
    1524f4c View commit details
    Browse the repository at this point in the history
  5. Configuration menu
    Copy the full SHA
    1c79323 View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    d8457fc View commit details
    Browse the repository at this point in the history

Commits on Nov 20, 2023

  1. Increase test coverage (#280)

    Add tests for get_sam_model and iterative prediction.
    constantinpape authored Nov 20, 2023
    Configuration menu
    Copy the full SHA
    fe13841 View commit details
    Browse the repository at this point in the history
  2. Fixup typo (#281)

    claydugo authored Nov 20, 2023
    Configuration menu
    Copy the full SHA
    23e974f View commit details
    Browse the repository at this point in the history

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]>
    3 people authored Nov 23, 2023
    Configuration menu
    Copy the full SHA
    c2a4e54 View commit details
    Browse the repository at this point in the history

Commits on Nov 27, 2023

  1. Configuration menu
    Copy the full SHA
    7ad19d3 View commit details
    Browse the repository at this point in the history

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 and constantinpape authored Dec 6, 2023
    Configuration menu
    Copy the full SHA
    c0cdf1a View commit details
    Browse the repository at this point in the history

Commits on Dec 20, 2023

  1. Add Joint Training (#288)

    Implement joint training for interactive and automatic instance segmentation
    anwai98 authored Dec 20, 2023
    Configuration menu
    Copy the full SHA
    cc4fe4b View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    d736b77 View commit details
    Browse the repository at this point in the history

Commits on Dec 21, 2023

  1. Configuration menu
    Copy the full SHA
    4f61c98 View commit details
    Browse the repository at this point in the history

Commits on Dec 22, 2023

  1. Configuration menu
    Copy the full SHA
    c80e8e0 View commit details
    Browse the repository at this point in the history

Commits on Dec 29, 2023

  1. Configuration menu
    Copy the full SHA
    2f397f8 View commit details
    Browse the repository at this point in the history

Commits on Dec 30, 2023

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

    …specialist
    
    Update LiveCELL Specialist Fine-tuning
    constantinpape authored Dec 30, 2023
    Configuration menu
    Copy the full SHA
    d6f1432 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    2f40595 View commit details
    Browse the repository at this point in the history
  3. Remove amg folder

    constantinpape committed Dec 30, 2023
    Configuration menu
    Copy the full SHA
    4670d91 View commit details
    Browse the repository at this point in the history

Commits on Jan 2, 2024

  1. Update livecell evaluation scripts (#296)

    Update livecell evaluation experiments
    constantinpape authored Jan 2, 2024
    Configuration menu
    Copy the full SHA
    88e625c View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    1a2b9d9 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    fce9ca7 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    99395df View commit details
    Browse the repository at this point in the history
  5. Configuration menu
    Copy the full SHA
    915e66b View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    a9c3d37 View commit details
    Browse the repository at this point in the history
  7. Configuration menu
    Copy the full SHA
    c91bac1 View commit details
    Browse the repository at this point in the history
  8. Update dependencies

    constantinpape committed Jan 2, 2024
    Configuration menu
    Copy the full SHA
    19126ed View commit details
    Browse the repository at this point in the history
  9. Configuration menu
    Copy the full SHA
    db21189 View commit details
    Browse the repository at this point in the history
  10. Update livecell evaluation scripts (#296)

    Update livecell evaluation experiments
    constantinpape committed Jan 2, 2024
    Configuration menu
    Copy the full SHA
    52b0cb7 View commit details
    Browse the repository at this point in the history
  11. Configuration menu
    Copy the full SHA
    352d361 View commit details
    Browse the repository at this point in the history
  12. Merge pull request #297 from computational-cell-analytics/new-instanc…

    …e-seg
    
    New instance segmentation
    constantinpape authored Jan 2, 2024
    Configuration menu
    Copy the full SHA
    ae46a20 View commit details
    Browse the repository at this point in the history

Commits on Jan 3, 2024

  1. Fix Resizing Input Prompts (#299)

    Fix input resizing for prompts in training
    anwai98 authored Jan 3, 2024
    Configuration menu
    Copy the full SHA
    56a94cd View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    b539648 View commit details
    Browse the repository at this point in the history
  3. Simplify training implementations (#301)

    Simplify interactive training and implement box distortion
    constantinpape authored Jan 3, 2024
    Configuration menu
    Copy the full SHA
    80463da View commit details
    Browse the repository at this point in the history
  4. Make grid search functionality more flexible (#300)

    Make grid search more flexible to enable external re-use
    constantinpape authored Jan 3, 2024
    Configuration menu
    Copy the full SHA
    fda8148 View commit details
    Browse the repository at this point in the history

Commits on Jan 4, 2024

  1. Update box distortion

    constantinpape committed Jan 4, 2024
    Configuration menu
    Copy the full SHA
    5eef3ce View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    a19f432 View commit details
    Browse the repository at this point in the history

Commits on Jan 5, 2024

  1. Update LM Generalists (#292)

    Update training for LM datasets
    anwai98 authored Jan 5, 2024
    Configuration menu
    Copy the full SHA
    e2e04a9 View commit details
    Browse the repository at this point in the history

Commits on Jan 7, 2024

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

    Update LM Generalist experiments
    anwai98 authored Jan 7, 2024
    Configuration menu
    Copy the full SHA
    e4219a1 View commit details
    Browse the repository at this point in the history

Commits on Jan 8, 2024

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

    Implement EM organelle model training
    anwai98 authored Jan 8, 2024
    Configuration menu
    Copy the full SHA
    3c984c5 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    733a220 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    a13341e View commit details
    Browse the repository at this point in the history

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 authored Jan 9, 2024
    Configuration menu
    Copy the full SHA
    a135c33 View commit details
    Browse the repository at this point in the history

Commits on Jan 10, 2024

  1. Add EM Boundaries Generalist (#312)

    Add fine-tuning for EM boundary generalist model
    anwai98 authored Jan 10, 2024
    Configuration menu
    Copy the full SHA
    5983045 View commit details
    Browse the repository at this point in the history

Commits on Jan 14, 2024

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

    Minor updates in finetuning scripts.
    anwai98 authored Jan 14, 2024
    Configuration menu
    Copy the full SHA
    8ec6df9 View commit details
    Browse the repository at this point in the history
  2. Update LiveCELL inference scripts (#315)

    * Update livecell inference
    anwai98 authored Jan 14, 2024
    Configuration menu
    Copy the full SHA
    ca7e02c View commit details
    Browse the repository at this point in the history

Commits on Jan 15, 2024

  1. Configuration menu
    Copy the full SHA
    46e6a08 View commit details
    Browse the repository at this point in the history
  2. Add livecell specialist results (#317)

    * Add livecell specialist results
    anwai98 authored Jan 15, 2024
    Configuration menu
    Copy the full SHA
    a8910fe View commit details
    Browse the repository at this point in the history
  3. Add livecell (lm) generalist results (#319)

    * Add livecell results from lm generalists
    anwai98 authored Jan 15, 2024
    Configuration menu
    Copy the full SHA
    8eac7f9 View commit details
    Browse the repository at this point in the history
  4. Minor fix to livecell eval. scripts (#316)

    * Fix evaluation script
    
    * Update precomputing embeddings for val + other minor fixes
    anwai98 authored Jan 15, 2024
    Configuration menu
    Copy the full SHA
    ac211b7 View commit details
    Browse the repository at this point in the history

Commits on Jan 17, 2024

  1. Configuration menu
    Copy the full SHA
    c0e5f54 View commit details
    Browse the repository at this point in the history
  2. Refactor files in scripts (#321)

    * Refactor path convention for scripts
    
    * Add EM generalist results (#322)
    
    * Add EM generalist results
    
    * Add snemi results
    anwai98 authored Jan 17, 2024
    Configuration menu
    Copy the full SHA
    93f7b22 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    3fda1d9 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    102c4a4 View commit details
    Browse the repository at this point in the history