Changelog#

All notable changes to Cellucid will be documented here.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased#

0.9.0 - 2026-01-01#

This release graduates Cellucid Python out of alpha (still pre-1.0).

Added#

  • AnnData-first viewing and serving with .h5ad and .zarr support (lazy/backed loading where possible).

  • Unified cellucid serve CLI with auto-detection for .h5ad, .zarr, and pre-exported dataset directories.

  • Jupyter notebook integration (CellucidViewer, AnnDataViewer, show(), show_anndata()) with event hooks and session export.

  • Session bundle support (.cellucid-session) including CellucidSessionBundle and apply_cellucid_session_to_anndata() for round-tripping highlights and user-defined fields back into AnnData.

  • Multi-dimensional embedding exports (1D/2D/3D/4D) and vector-field overlays (RNA velocity / drift) via prepare() and vector_fields helpers.

  • Hosted web UI proxy mode with on-disk caching helpers (get_web_cache_dir(), clear_web_cache()).

Changed#

  • Export format now includes explicit dataset identity metadata (dataset_identity.json) for reproducible sharing and session compatibility checks.

  • Reduced export size and improved load performance with optimized manifests, improved connectivity edge export, and optional quantization + gzip compression knobs.

Security#

  • Session bundles are treated as untrusted input with bounds checks and dataset mismatch policies when applying to AnnData.

Documentation#

  • Major Read the Docs expansion and restructuring (Python package + web app guides), plus new publishing and contributing documentation.

0.0.1a2 - 2025#

Added#

  • Initial alpha release

  • AnnData visualization with UMAP embeddings (1D, 2D, 3D)

  • Gene expression overlays with sparse matrix support

  • Cell metadata coloring (categorical and continuous)

  • Interactive filtering and cell selection

  • KNN connectivity visualization

  • Multiple deployment modes:

    • Local demo (browser-only)

    • Browser file picker (h5ad and exported formats)

    • Server CLI (cellucid serve)

    • Python API (serve(), serve_anndata())

    • Jupyter integration (show(), show_anndata())

  • Export functionality for web deployment