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ARBO 1.0.1

Release highlights

  • Added Zenodo DOI information for software citation.
  • Added image origin and usage notes for the artificially constructed MSI dataset Miss Teng.

DOI

ARBO 1.0.0

Release highlights

  • First stable 1.0.0 release of ARBO.
  • Finalized the main spatial clustering workflow for Cardinal MSI objects.
  • Completed package documentation, examples, and vignette materials.
  • Consolidated support for two UMAP preprocessing strategies:
    • "scaled": min-max scaled spectra
    • "l2_pca": row-wise L2-normalized spectra followed by PCA with irlba
  • Stabilized integration of clustering results back into Cardinal MSI objects.
  • Finalized utilities for spatially enriched metabolite screening and MSI image visualization.

Improvements

  • Improved robustness of clustering result attachment to MSI objects.
  • Refined README and workflow documentation for package release.

ARBO 0.5.1

Improvements

  • Improved compatibility when writing clustering results back to Cardinal MSI objects.
  • Updated SEMs_screen() to better handle different output structures returned by Cardinal::colocalized().
  • Removed unnecessary use of magrittr pipe import.
  • Refined workflow documentation and examples.

ARBO 0.5.0

New features

  • Added two UMAP input strategies in spatial_clustering_workflow():
    • "scaled" for min-max scaled spectra
    • "l2_pca" for row-wise L2-normalized spectra followed by PCA with irlba
  • Added pca_n_components to control the number of retained principal components in the "l2_pca" workflow.
  • Enforced metric = "euclidean" when umap_input_method = "l2_pca".

Package changes

  • Added irlba as a package dependency for PCA-based preprocessing.

ARBO 0.4.1

New features

  • Added parallel execution support for Python UMAP via n_jobs.
  • run_umap_py() now allows random_state = NULL for non-deterministic parallel UMAP.
  • spatial_clustering_workflow() now supports n_jobs and umap_seed = NULL.

Improvements

  • Improved documentation for the interaction between UMAP random seeds and parallel execution.
  • Clarified that n_jobs only affects the Python UMAP step, not downstream clustering in R.

ARBO 0.4.0

  • Renamed the package to ARBO.
  • Updated package metadata and documentation.
  • Refined clustering workflows and result integration into Cardinal MSI objects.

spatMetaCluster 0.3.1

  • Updated vignettes.

spatMetaCluster 0.3.0

  • Added SEMs_screen() for spatially enriched metabolite screening.
  • Added image2ggplot() to reconstruct Cardinal::image() output with ggplot2.
  • Added msi_img_overlay() for layered MSI image overlay with internal legend handling.
  • Updated cherry_tomato_msi with additional m/z annotations and regenerated data.

spatMetaCluster 0.2.0

  • Added a unified clustering interface via run_clustering().
  • Renamed spatial_kmeans_workflow() to spatial_clustering_workflow().
  • Replaced minmax_normalize() with apply_feature_scaling(method = "minmax").
  • Updated UMAP-related documentation and parameter descriptions.