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CHANGELOG.md

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[0.2.3] - 2025-03-21

Added

  • New Visium-HD and Visium tutorials
  • Infer default plot size for plots (median neighbors distrance)
  • Can filter by technology in load_dataset

Fixed

  • Fix model.plot_prototype_covariance and model.plot_prototype_weights
  • Edge case: ensure that even negative max-weights are above the prototype threshold

Changed

  • novae.utils.spatial_neighbors can be now called via novae.spatial_neighbors
  • Store distances after spatial_neighbors instead of 1 when coord_type="grid"

[0.2.2] - 2024-12-17

Added

  • load_dataset: add custom_filter and dry_run arguments
  • added min_prototypes_ratio argument in fine_tune to run init_slide_queue
  • Added tutorials for proteins data + minor docs improvements

Fixed

  • Ensure reset clustering if multiple zero-shot (#9)

Changed

  • Removed the docs formatting (better for autocompletion)
  • Reorder parameters in Novae __init__ (sorted by importance)

[0.2.1] - 2024-12-04

Added

  • novae.utils.quantile_scaling for proteins expression

Fixed

  • Fix autocompletion using __new__ to trick hugging_face inheritance

[0.2.0] - 2024-12-03

Added

  • novae.plot.connectivities(...) to show the cells neighbors
  • novae.settings.auto_processing = False to enforce using your own preprocessing
  • Tutorials update (more plots and more details)

Fixed

  • Issue with library_id in novae.plot.domains (#8)
  • Set pandas>=2.0.0 in the dependencies (#5)

Breaking changes

  • novae.utils.spatial_neighbors must always be run, to force the user having more control on it
  • For multi-slide mode, the slide_key argument should now be used in novae.utils.spatial_neighbors (and only there)
  • Drop python 3.9 support (because dropped in anndata)

[0.1.0] - 2024-09-11

First official novae release. Preprint coming soon.