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base repository: mehta-lab/VisCy
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base: v0.2.0
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head repository: mehta-lab/VisCy
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compare: v0.2.1
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  • 7 commits
  • 44 files changed
  • 8 contributors

Commits on Aug 8, 2024

  1. version lighting CLI example (#128)

    * version lighting CLI example
    
    * add some documentation
    
    * ignore slurm output
    
    * add more tips
    mattersoflight authored Aug 8, 2024

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Commits on Aug 9, 2024

  1. Updated code (contrastive learning) (#130)

    * updated prediction code to test specific cells
    
    * updated kernel and stride
    
    * updated kernel and stride
    
    * new training script and predict takes in output path as parameter
    
    * passing ci requirements
    
    * fixed error for output path
    
    * fixed error for output path
    
    * fixed formatting
    
    * format resolved
    
    * docstrings for methods that parse tracks
    
    ---------
    
    Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org>
    alishbaimran and mattersoflight authored Aug 9, 2024

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  2. Configurable drop path rate in contrastive models (#131)

    * log instead of print
    
    * configurable drop path rate
    
    * fix docstring
    ziw-liu authored Aug 9, 2024

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Commits on Aug 14, 2024

  1. Config-based prediction with Xarray-based output format (#132)

    * use callback to write prediction embeddings
    
    * moving over the script to compute infection score from contrastive_update
    
    * delete unused stem module
    
    * organize scripts and CLIs for contrastive phenotyping
    
    * add dependencies for prediction
    
    * export embedding dataset reader function
    
    * add more plots to script
    
    * use real paths in predict config
    
    * do not require seaborn and umap-learn for base install
    
    * use relative path in example job script
    
    * add docstrings for embedding writer and reader
    
    * don't assign unused grid object
    
    * show time and id as hover data in interactive plot
    
    * fix typo
    
    * fix script to test data i/o
    
    * ignore accidental lightning_logs
    
    * add plotly and nbformat to visual dependencies
    
    * tweak predict cli example
    
    * add another plot type - raw features of random samples
    
    * comment on speed of clustermap
    
    * add prediction config example to specify log path
    
    * simplify env var in job script
    and match cpu count with config
    
    * vectorize string concatenation
    
    ---------
    
    Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org>
    ziw-liu and mattersoflight authored Aug 14, 2024

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Commits on Aug 17, 2024

  1. Plot tracks in latent space and real space (#135)

    * slice by FOV and track
    
    * proper indexing
    
    Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
    
    * plot features of a single track
    
    * rename (dataset -> embedding_dataset)
    
    * trying to read patches of a track
    
    * display cells from the chosen track in napari
    
    * project a track on umap computed from all features
    
    * Animated latent space (#137)
    
    * animated latent space
    
    * delete duplicate umap calculation
    
    ---------
    
    Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org>
    
    * PCA of features and projections
    
    ---------
    
    Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
    mattersoflight and ziw-liu authored Aug 17, 2024

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Commits on Aug 31, 2024

  1. Fix deprecated custom forward method (#151)

    * fix deprecated custom forward method
    
    * specify device type
    ziw-liu authored Aug 31, 2024

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Commits on Sep 6, 2024

  1. updating the notebook after running it at DLMBL2024 (#149)

    * updating the notebook after running it at DLMBL2024
    
    Co-authored-by: Diane Adjavon <diane.adjavon@icloud.com>
    Co-authored-by: AlbertDominguez <albert.dominguezmantes@epfl.ch>
    Co-authored-by: Anna Foix <afoix@ebi.ac.uk>
    
    * adding template for the phase contrast demo
    
    * adding custom viscy["examples"]
     installation
    
    * updating the DLMBL2024 exercise and solution ipynb
    
    * updating image2image example
    
    * adding nbconvert and updating ipynb img2img example
    
    * fixing the img2img outline
    
    * update structure and links of main README
    
    * updating readme links for the pngs
    
    * - removing the 'redundant' readme.md
    - adding the phase contrast example
    - saving the PhC notebook with images
    
    * update setup.sh to handle 0.2 versions only
    
    * collapse citations, ignore slurm
    
    * clean up citations
    
    * addressing Ziwen's comments
    
    * cleanup the img2img notebook after testing
    
    * updating the inference demo scripts
    
    * - making absolute paths on root readme.
    - description on docstrings for inference demo scripts
    
    ---------
    
    Co-authored-by: Diane Adjavon <diane.adjavon@icloud.com>
    Co-authored-by: AlbertDominguez <albert.dominguezmantes@epfl.ch>
    Co-authored-by: Anna Foix <afoix@ebi.ac.uk>
    Co-authored-by: Shalin Mehta <2934183+mattersoflight@users.noreply.github.com>
    Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org>
    6 people authored Sep 6, 2024

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