# Cellucid documentation

> Cellucid is a free, open-source web app for interactive single-cell data visualization. It renders millions of cells on the GPU in the browser, in 1D, 2D and 3D embeddings such as UMAP, colored by gene expression or cell metadata, and reads AnnData, MuData, Loom, 10x Cell Ranger, MatrixMarket and Seurat or SingleCellExperiment files in place, without uploading them. The cellucid Python package (Scanpy/AnnData, Jupyter) and R package (Seurat, SingleCellExperiment) prepare data for it and show data in it. The app runs at https://www.cellucid.com/.

## Docs

- [Cellucid](https://docs.cellucid.com/en/latest/_sources/index.md.txt)
- [Web App Guide](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/index.md.txt)
- [Landing / Orientation Pages (Start Here)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/a_orientation/index.md.txt)
- [What is Cellucid?](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/a_orientation/01_what_is_cellucid.md.txt)
- [System requirements](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/a_orientation/02_system_requirements.md.txt)
- [Quick tour (60 seconds)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/a_orientation/03_quick_tour_60_seconds.md.txt)
- [UI glossary (terminology)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/a_orientation/04_ui_glossary_terminology.md.txt)
- [“Which workflow is for me?” decision tree](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/a_orientation/05_which_workflow_is_for_me_decision_tree.md.txt)
- [How to visualize single-cell data interactively](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/a_orientation/06_how_to_visualize_single_cell_data_interactively.md.txt)
- [Cellucid and other single-cell viewers](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/a_orientation/07_cellucid_and_other_viewers.md.txt)
- [Data Loading in the Web App (All Paths)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/index.md.txt)
- [Data Loading Overview (Every Route)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/01_loading_options_overview.md.txt)
- [Browser File Picker (No Python Setup)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/03_browser_file_picker_tutorial.md.txt)
- [Server Mode (CLI + Python)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/04_server_tutorial.md.txt)
- [Jupyter Integration (Notebook Embedding)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/05_jupyter_tutorial.md.txt)
- [Open from a link](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/14_open_from_link.md.txt)
- [Google Drive, OneDrive and private sharing](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/16_private_drive_onedrive.md.txt)
- [Data mapping](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/13_data_mapping.md.txt)
- [Subsampled loading: open a share of the cells](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/21_subsampled_loading.md.txt)
- [Share Without Running a Server (Publish a Dataset Catalog)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/02_local_demo_tutorial.md.txt)
- [Dataset identity (why it matters)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/06_dataset_identity_why_it_matters.md.txt)
- [File format expectations](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/07_file_format_expectations.md.txt)
- [Troubleshooting (data loading)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/08_troubleshooting_data_loading.md.txt)
- [Verified data-loading captures](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/09_screenshots.md.txt)
- [Standard Pancreas sample dataset](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/10_standard_pancreas_dataset.md.txt)
- [Publish a Custom Dataset Repository](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/11_custom_dataset_repository.md.txt)
- [Sample dataset provenance and reproducibility](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/12_sample_dataset_provenance.md.txt)
- [Host a Dataset on GitHub](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/15_host_on_github.md.txt)
- [Open R objects and MatrixMarket folders](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/17_open_r_objects.md.txt)
- [Open Loom and 10x Cell Ranger files](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/18_open_loom_and_10x.md.txt)
- [Multimodal data: MuData and the Modality select](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/19_multimodal_mudata.md.txt)
- [Tutorials: open published data as it is](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/b_data_loading/20_tutorials_open_published_data.md.txt)
- [Core Interactions (Viewer Basics)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/c_core_interactions/index.md.txt)
- [Navigation modes (Orbit / Planar / Free-fly)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/c_core_interactions/01_navigation_modes_orbit_planar_free_fly.md.txt)
- [Camera controls (advanced)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/c_core_interactions/02_camera_controls_advanced.md.txt)
- [Render modes: Points or Volumetric smoke](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/c_core_interactions/03_render_modes_points_vs_volumetric_smoke.md.txt)
- [Multiview: Live view and kept snapshots](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/c_core_interactions/04_view_layout_live_snapshots_small_multiples.md.txt)
- [Switching embeddings (1D / 2D / 3D)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/c_core_interactions/05_dimension_switching_1d_2d_3d.md.txt)
- [Troubleshooting (core interactions)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/c_core_interactions/06_troubleshooting_core_interactions.md.txt)
- [Verified core-interaction captures](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/c_core_interactions/07_screenshots.md.txt)
- [Fields, Coloring, and Legends (Obs/Var)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/d_fields_coloring_legends/index.md.txt)
- [Field types and sources](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/d_fields_coloring_legends/01_field_types_and_sources.md.txt)
- [Field selector UX](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/d_fields_coloring_legends/02_field_selector_ux.md.txt)
- [Color-by behavior](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/d_fields_coloring_legends/03_color_by_behavior.md.txt)
- [Legend behavior](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/d_fields_coloring_legends/04_legend_behavior.md.txt)
- [Troubleshooting (fields & legends)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/d_fields_coloring_legends/05_troubleshooting_fields_legends.md.txt)
- [Verified coloring and legend captures](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/d_fields_coloring_legends/06_screenshots.md.txt)
- [Which genes the built-in samples publish](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/d_fields_coloring_legends/07_genes_in_the_built_in_samples.md.txt)
- [Cell info](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/d_fields_coloring_legends/08_cell_info.md.txt)
- [Filtering (Visibility, Outliers, and Filter Stacks)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/e_filtering/index.md.txt)
- [Filtering mental model](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/e_filtering/01_filtering_mental_model.md.txt)
- [Outlier filtering (per categorical field)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/e_filtering/02_outlier_filtering_per_active_field.md.txt)
- [Filter stack UI (Filters panel)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/e_filtering/03_filter_stack_ui_active_filters.md.txt)
- [Common filter types](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/e_filtering/04_common_filter_types_document_every_filter_the_ui_exposes.md.txt)
- [Performance considerations](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/e_filtering/05_performance_considerations.md.txt)
- [Edge cases (filtering)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/e_filtering/06_edge_cases_filtering.md.txt)
- [Troubleshooting (filtering)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/e_filtering/07_troubleshooting_filtering.md.txt)
- [Verified filtering captures](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/e_filtering/08_screenshots.md.txt)
- [Highlighting and Selection (Groups, Pages, Tools)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/f_highlighting_selection/index.md.txt)
- [Highlight mental model](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/f_highlighting_selection/01_highlight_mental_model.md.txt)
- [Selection tools (annotation, lasso, proximity, KNN)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/f_highlighting_selection/02_selection_tools_document_each_tool.md.txt)
- [Highlight UI (modes, pages, groups)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/f_highlighting_selection/03_highlight_ui.md.txt)
- [Selection synchronization (views, pages, filters, Python)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/f_highlighting_selection/04_selection_synchronization.md.txt)
- [Edge cases (highlighting and selection)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/f_highlighting_selection/05_edge_cases_highlighting.md.txt)
- [Troubleshooting (highlighting and selection)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/f_highlighting_selection/06_troubleshooting_highlighting.md.txt)
- [Verified highlighting captures](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/f_highlighting_selection/07_screenshots.md.txt)
- [Agents](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/g_agents/index.md.txt)
- [The chat bar (Ask an agent)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/g_agents/01_chat_bar.md.txt)
- [Connect Claude or ChatGPT](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/g_agents/02_connect_claude_and_chatgpt.md.txt)
- [Permissions and what agents see](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/g_agents/03_permissions_and_what_agents_see.md.txt)
- [Analysis (Modes, Outputs, Interpretation)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/index.md.txt)
- [Analysis mental model (Pages, Variables, Scope)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/01_analysis_mental_model.md.txt)
- [Analysis UI overview](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/02_analysis_ui_overview.md.txt)
- [Analysis mode: Quick (automatic composition + stats)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/03_analysis_mode_quick_insights.md.txt)
- [Analysis mode: Detailed (variable + plots + statistical tests)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/04_analysis_mode_detailed_analysis.md.txt)
- [Analysis mode: Correlation (X vs Y across pages)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/05_analysis_mode_correlation_analysis.md.txt)
- [Analysis mode: Differential Expression (DE) (Group A vs Group B)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/06_analysis_mode_differential_expression_de.md.txt)
- [Analysis mode: Gene Signature (Gene Signature Score)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/07_analysis_mode_gene_signature.md.txt)
- [Analysis mode: Marker Genes (Genes Panel)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/08_analysis_mode_genes_panel.md.txt)
- [Exporting analysis results](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/09_exporting_analysis_results.md.txt)
- [Troubleshooting (analysis)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/10_troubleshooting_analysis.md.txt)
- [The analysis lifecycle, end to end](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/11_screenshots.md.txt)
- [Analysis mode: Composition](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/12_analysis_mode_composition.md.txt)
- [Analysis mode: Dot plot](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/h_analysis/13_analysis_mode_dot_plot.md.txt)
- [Vector Field / Velocity Overlay (GPU Particle Overlay)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/i_vector_field_velocity/index.md.txt)
- [What vector fields are (user-facing)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/i_vector_field_velocity/01_what_vector_fields_are_user_facing.md.txt)
- [Enable the overlay and select a field](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/i_vector_field_velocity/02_enabling_overlay_and_selecting_field.md.txt)
- [Core particle-flow controls](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/i_vector_field_velocity/03_core_parameters_document_exact_ui_labels.md.txt)
- [Advanced parameters](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/i_vector_field_velocity/04_advanced_parameters_document_every_setting.md.txt)
- [Performance and quality](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/i_vector_field_velocity/05_performance_and_quality.md.txt)
- [Vector field edge cases](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/i_vector_field_velocity/06_edge_cases.md.txt)
- [Troubleshooting (velocity overlay)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/i_vector_field_velocity/07_troubleshooting_velocity_overlay.md.txt)
- [Verified vector-field captures](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/i_vector_field_velocity/08_screenshots.md.txt)
- [Community Annotation (Voting + Consensus; GitHub Sync)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/j_community_annotation/index.md.txt)
- [Community Annotation — Annotator Guide (UI + Voting)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/j_community_annotation/01_annotator_guide.md.txt)
- [Community Annotation — Author Guide (Repo Setup + Operations)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/j_community_annotation/02_author_guide.md.txt)
- [Community Annotation — UI Reference + Troubleshooting](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/j_community_annotation/03_ui_reference.md.txt)
- [Lifecycle Walkthrough (Screens, Step by Step)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/j_community_annotation/04_lifecycle_walkthrough.md.txt)
- [Figure Export (Publication-Grade SVG/PNG)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/k_figure_export/index.md.txt)
- [Figure export goals (WYSIWYG and reproducibility)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/k_figure_export/01_figure_export_goals_wysiwyg_and_reproducibility.md.txt)
- [Export UI walkthrough](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/k_figure_export/02_export_ui_walkthrough.md.txt)
- [Export formats and renderers](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/k_figure_export/03_export_formats_and_renderers.md.txt)
- [Quality knobs and best practices](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/k_figure_export/04_quality_knobs_and_best_practices.md.txt)
- [Metadata and provenance](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/k_figure_export/05_metadata_and_provenance.md.txt)
- [Figure export edge cases](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/k_figure_export/06_edge_cases.md.txt)
- [Troubleshooting (figure export)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/k_figure_export/07_troubleshooting_figure_export.md.txt)
- [Verified figure-export captures](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/k_figure_export/08_screenshots.md.txt)
- [Reference (implementation notes)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/k_figure_export/09_reference_implementation_notes.md.txt)
- [Session Saving, Restoring, and Sharing](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/index.md.txt)
- [Session mental model](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/01_session_mental_model.md.txt)
- [What gets saved and restored](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/02_what_gets_saved_and_restored.md.txt)
- [Save/restore UX (manual save + restore)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/03_save_restore_ux.md.txt)
- [Starting views named by a catalog](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/04_official_sample_states.md.txt)
- [Share workflows (links, session files and data files)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/05_share_workflows_links_sessions_data_files.md.txt)
- [Collaboration best practices](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/06_collaboration_best_practices.md.txt)
- [Current format and dataset identity](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/07_versioning_compatibility_and_dataset_identity.md.txt)
- [Security, privacy, and trust](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/08_security_privacy_and_trust.md.txt)
- [Edge cases: sessions](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/09_edge_cases.md.txt)
- [Troubleshooting sessions](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/10_troubleshooting_sessions.md.txt)
- [Verified session-state capture](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/11_screenshots.md.txt)
- [Reference: session files (format 4)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/12_reference.md.txt)
- [Share links, badges and embeds](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/l_sessions_sharing/13_share_links_badges_and_embeds.md.txt)
- [State and History](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/m_state_history/index.md.txt)
- [The history](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/m_state_history/01_the_history.md.txt)
- [Branches, trackers and comparing](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/m_state_history/02_branches_trackers_and_comparing.md.txt)
- [Saved states and autosave](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/m_state_history/03_saved_states_and_autosave.md.txt)
- [Tour, pseudocode, methods and report](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/m_state_history/04_tour_methods_and_report.md.txt)
- [Recording, groups, notes and cleanup](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/m_state_history/05_recording_groups_notes_and_cleanup.md.txt)
- [Sharing, loading and replaying](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/m_state_history/06_sharing_and_replay.md.txt)
- [Benchmarking and Performance](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/n_benchmarking_performance/index.md.txt)
- [Performance mental model](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/n_benchmarking_performance/01_performance_mental_model.md.txt)
- [Performance considerations (what gets slow and why)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/n_benchmarking_performance/02_performance_considerations_what_gets_slow_and_why.md.txt)
- [Large dataset best practices](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/n_benchmarking_performance/03_large_dataset_best_practices.md.txt)
- [Benchmarking methodology and metrics](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/n_benchmarking_performance/04_benchmarking_methodology_and_metrics.md.txt)
- [Benchmark tools](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/n_benchmarking_performance/05_benchmark_tools.md.txt)
- [Edge cases (performance)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/n_benchmarking_performance/06_edge_cases_performance.md.txt)
- [Troubleshooting (performance)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/n_benchmarking_performance/07_troubleshooting_performance.md.txt)
- [Verified performance captures](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/n_benchmarking_performance/08_screenshots.md.txt)
- [Reporting performance bugs](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/n_benchmarking_performance/09_reporting_performance_bugs.md.txt)
- [Accessibility, Privacy, and Security](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/o_accessibility_privacy_security/index.md.txt)
- [Accessibility](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/o_accessibility_privacy_security/01_accessibility.md.txt)
- [Privacy model](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/o_accessibility_privacy_security/02_privacy_model.md.txt)
- [Developer Documentation (Web App Architecture)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/index.md.txt)
- [How to use this section](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/00_how_to_use_this_section.md.txt)
- [Codebase map and entry points](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/01_codebase_map_and_entry_points.md.txt)
- [Local development setup](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/02_local_development_setup.md.txt)
- [Build, run, and deployment](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/03_build_run_and_deployment.md.txt)
- [Configuration, environment variables, and feature flags](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/04_configuration_env_vars_and_feature_flags.md.txt)
- [App architecture overview](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/05_app_architecture_overview.md.txt)
- [State (DataState) and events](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/06_state_datastate_and_events.md.txt)
- [Rendering pipeline (WebGL) and performance notes](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/07_rendering_pipeline_webgl_and_performance_notes.md.txt)
- [UI modules map](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/08_ui_modules_map.md.txt)
- [Data loading pipeline and caching](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/09_data_loading_pipeline_and_caching.md.txt)
- [Sessions: persistence and serialization](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/10_sessions_persistence_and_serialization.md.txt)
- [Analysis architecture](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/11_analysis_architecture.md.txt)
- [Figure export architecture](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/12_figure_export_architecture.md.txt)
- [Debugging playbook](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/13_debugging_playbook.md.txt)
- [Testing, CI, and release process](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/14_testing_ci_and_release_process.md.txt)
- [Extension points overview](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/15_extension_points_overview.md.txt)
- [Extension point: add a UI module](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/16_extension_point_add_ui_module.md.txt)
- [Extension point: add an analysis mode](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/17_extension_point_add_analysis_mode.md.txt)
- [Extension point: add an export renderer](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/18_extension_point_add_export_renderer.md.txt)
- [Subsampling specification](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/19_subsampling_specification.md.txt)
- [Read path architecture](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/20_read_path_architecture.md.txt)
- [Decision record: decoders and codecs](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/21_decisions_decoders_and_codecs.md.txt)
- [Decision record: link model and request planning](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/22_decisions_link_model_and_request_planning.md.txt)
- [Decision record: partial reading](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/23_decisions_partial_reading.md.txt)
- [Decision record: graph edges at scale](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/24_decisions_graph_edges_at_scale.md.txt)
- [Decision record: cell exports](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/25_decisions_exports.md.txt)
- [Decision record: served stores and notebook widgets](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/26_decisions_served_store_and_widgets.md.txt)
- [Decision record: memory model](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/27_decisions_memory_model.md.txt)
- [Decision record: rendering layers, the gene-sample look and levels of detail](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/28_decisions_rendering_layers.md.txt)
- [Action layer, state domains and history](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/29_action_layer_domains_and_history.md.txt)
- [Action reference](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/30_action_reference.md.txt)
- [Local agent connection (cellucid mcp)](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/31_local_agent_connection.md.txt)
- [Agents in the tab: chat bar, permissions, data guard and relay](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/p_developer_docs/32_agents_in_the_tab.md.txt)
- [Troubleshooting (Web App): Start Here](https://docs.cellucid.com/en/latest/_sources/user_guide/web_app/q_troubleshooting_index/index.md.txt)
- [Python Package Guide](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/index.md.txt)
- [Installation](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/installation.md.txt)
- [What is cellucid-python?](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/a_landing_pages/01_what_is_cellucid_python.md.txt)
- [Compatibility matrix](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/a_landing_pages/03_compatibility_matrix_must_be_explicit.md.txt)
- [Quick start (3 levels)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/a_landing_pages/04_quick_start_3_levels.md.txt)
- [Landing Pages](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/a_landing_pages/index.md.txt)
- [What is a “viewer” object?](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/b_concepts_mental_models/01_what_is_a_viewer_object.md.txt)
- [Data flows](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/b_concepts_mental_models/02_data_flows.md.txt)
- [State, persistence, and scope](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/b_concepts_mental_models/03_state_persistence_and_scope.md.txt)
- [Dataset identity and reproducibility](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/b_concepts_mental_models/04_dataset_identity_and_reproducibility.md.txt)
- [Sessions → AnnData (No-Download Bridge)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/b_concepts_mental_models/05_sessions_to_anndata_bridge.md.txt)
- [Sessions → AnnData (Design notes)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/b_concepts_mental_models/05_sessions_to_anndata_design.md.txt)
- [Privacy, security, and network requirements](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/b_concepts_mental_models/06_privacy_security_and_offline_vs_online.md.txt)
- [Performance mental model and scaling](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/b_concepts_mental_models/07_performance_mental_model_and_scaling.md.txt)
- [Debugging mental model (where to look first)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/b_concepts_mental_models/08_debugging_mental_model_where_to_look.md.txt)
- [Concepts and Mental Models (Python-side)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/b_concepts_mental_models/index.md.txt)
- [prepare() overview](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/01_prepare_overview.md.txt)
- [Input requirements (global)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/02_input_requirements_global.md.txt)
- [Embeddings and coordinates](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/03_embeddings_and_coordinates.md.txt)
- [obs (cell metadata)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/04_obs_cell_metadata.md.txt)
- [var (gene metadata) and gene names](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/05_var_gene_metadata.md.txt)
- [Gene expression matrix](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/06_gene_expression_matrix.md.txt)
- [Connectivities (neighbour graph)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/07_connectivities_knn_graph.md.txt)
- [Vector fields (velocity / displacement)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/08_vector_fields_velocity_displacement.md.txt)
- [Cellucid-ready AnnData specification](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/09_cellucid_ready_anndata_specification.md.txt)
- [Performance and storage](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/10_performance_and_storage.md.txt)
- [Troubleshooting prepare()](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/11_troubleshooting_prepare.md.txt)
- [Prepare an AnnData or a MuData whole (data=)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/12_prepare_from_anndata_or_mudata.md.txt)
- [Preparing an AnnData for Cellucid](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/c_data_preparation_api/index.md.txt)
- [Viewing methods overview](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/01_viewing_methods_overview.md.txt)
- [Every loading route](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/02_loading_routes.md.txt)
- [Choose your workflow (decision tree)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/03_choose_your_workflow_decision_tree.md.txt)
- [CLI: cellucid serve quickstart](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/04_cli_cellucid_serve_quickstart.md.txt)
- [Python: serve_anndata() quickstart](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/05_python_serve_anndata_quickstart.md.txt)
- [Jupyter: show_anndata() quickstart](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/06_jupyter_show_anndata_quickstart.md.txt)
- [How the viewer reads AnnData (show_anndata() / serve_anndata())](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/08_anndata_mode_show_anndata_and_serve_anndata.md.txt)
- [Server mode (advanced)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/09_server_mode_advanced.md.txt)
- [Notebook / widget mode (advanced)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/10_notebook_widget_mode_advanced.md.txt)
- [Viewer lifecycle, cleanup, ports, and multiple viewers](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/11_viewer_lifecycle_cleanup_ports_and_multiple_viewers.md.txt)
- [Remote servers, SSH tunneling, and cloud](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/12_remote_servers_ssh_tunneling_and_cloud.md.txt)
- [Security, privacy, CORS, and networking](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/13_security_privacy_cors_and_networking.md.txt)
- [Performance, scaling, and lazy loading](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/14_performance_scaling_and_lazy_loading.md.txt)
- [Troubleshooting (viewing)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/15_troubleshooting_viewing.md.txt)
- [FAQ (viewing)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/16_faq_viewing.md.txt)
- [HPC clusters: Slurm, compute nodes, and --host 0.0.0.0](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/17_hpc_slurm_and_compute_node_serving.md.txt)
- [Local agents (MCP): Claude Code, Claude Desktop, Cursor](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/18_local_agents_mcp.md.txt)
- [Viewing APIs (cellucid serve / serve_anndata / show_anndata + loading options)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/d_viewing_apis/index.md.txt)
- [Overview: bidirectional communication (Python ↔ viewer)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/01_overview_bidirectional_communication.md.txt)
- [Quickstart: minimal round-trip (select → highlight)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/02_quickstart_minimal_roundtrip.md.txt)
- [Supported environments matrix](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/03_supported_environments_matrix.md.txt)
- [Glossary and mental model](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/04_glossary_and_mental_model.md.txt)
- [Architecture: the viewer channel](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/05_architecture_viewer_channel.md.txt)
- [Python → frontend actions](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/06_python_to_frontend_commands.md.txt)
- [Frontend → Python events](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/07_frontend_to_python_events.md.txt)
- [Writing robust callbacks](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/08_writing_robust_callbacks.md.txt)
- [Viewer state and wait_for_event](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/09_viewer_state_and_wait_for_event.md.txt)
- [Sessions: capture from the browser (request_session)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/10_session_bundles_request_session_bundle.md.txt)
- [Sessions: apply to AnnData (apply_session_to_anndata)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/11_session_bundles_apply_session_to_anndata.md.txt)
- [Security model](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/12_security_model.md.txt)
- [Security: CORS, origins, and mixed content](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/13_security_cors_origins_and_mixed_content.md.txt)
- [Troubleshooting (hooks)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/14_troubleshooting_hooks.md.txt)
- [Reference (hooks, commands, schemas, endpoints)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/16_reference.md.txt)
- [Jupyter Hooks System (Python ↔ Frontend)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/e_jupyter_hooks/index.md.txt)
- [Start here (how to use these tutorials)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/00_start_here.md.txt)
- [Beginner notebooks (wet lab friendly)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/01_beginner_notebooks_wet_lab_friendly.md.txt)
- [Open a dataset and color by clusters](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/11_open_a_dataset_and_color_by_clusters.md.txt)
- [Find marker genes and export a figure](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/12_find_marker_genes_and_export_a_figure.md.txt)
- [Intermediate notebooks (computational workflows)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/02_intermediate_notebooks_computational_workflows.md.txt)
- [Prepare a Cellucid-ready AnnData](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/21_prepare_a_cellucid_ready_anndata.md.txt)
- [Large dataset: server mode + lazy gene expression](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/22_large_dataset_server_mode_and_lazy_gene_expression.md.txt)
- [Advanced notebooks (expert / developer)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/03_advanced_notebooks_expert_developer.md.txt)
- [Exact message schemas and diagnostics](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/31_exact_message_schemas_and_diagnostics.md.txt)
- [Real-world dataset recipe](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/04_real_world_dataset_recipes_gallery.md.txt)
- [Prepare a real Pancreas dataset for Cellucid](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/prepare_pancreas.ipynb.txt)
- [Jupyter embedding, hooks, and sessions](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/05_jupyter_embedding_hooks_sessions_gallery.md.txt)
- [Explore real Pancreas data in Jupyter](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/jupyter_pancreas.ipynb.txt)
- [Cellucid in your pipeline: notebook round trip (Python and R)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/06_cellucid_in_your_pipeline_python_and_r.md.txt)
- [Show a dataset in any notebook (JupyterLab, VS Code, Colab)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/41_show_a_dataset_in_any_notebook.ipynb.txt)
- [Compare two groups and interpret results](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/13_compare_two_groups_and_interpret_results.md.txt)
- [Programmatic highlighting + selection callbacks](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/23_programmatic_highlighting_and_selection_callbacks.md.txt)
- [CITE-seq as a MuData: prepare and show](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/24_citeseq_mudata_prepare_and_show.md.txt)
- [Serve Loom, 10x and MatrixMarket files](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/25_serve_loom_10x_and_matrixmarket.md.txt)
- [Session persistence and restoring analysis artifacts](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/32_session_persistence_and_restoring_analysis_artifacts.md.txt)
- [Vector fields and velocity overlay end-to-end](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/33_vector_fields_and_velocity_overlay_end_to_end.md.txt)
- [Pull everything back: highlights, labels and scores](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/42_pull_everything_back.ipynb.txt)
- [Push clusters into the viewer, refine them there, pull them back](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/43_push_clusters_refine_and_pull.ipynb.txt)
- [The round trip without a notebook: export from the web app, read in one call](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/44_round_trip_without_a_notebook.ipynb.txt)
- [Gene sets round trip: GMT in, signature scores out](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/45_gene_sets_round_trip.ipynb.txt)
- [Export an .h5ad subset of a selection and re-analyse it](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/46_export_an_h5ad_subset_and_reanalyse.ipynb.txt)
- [Subsampled views: pull from a share of the cells, and reproduce it exactly](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/47_subsampled_views.ipynb.txt)
- [Notebooks / Tutorials (Very Detailed, Step-by-Step)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/f_notebooks_tutorials/index.md.txt)
- [Public functions and classes (coverage map)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/01_public_functions_and_classes.md.txt)
- [Error messages and exceptions](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/02_error_messages_and_exceptions_document_patterns.md.txt)
- [CLI (cellucid)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/api/cli.md.txt)
- [API Reference (cellucid-python)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/api/index.md.txt)
- [Jupyter (notebook embedding + hooks)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/api/jupyter.md.txt)
- [Server (browser tab + local HTTP server)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/api/server.md.txt)
- [Data preparation (prepare)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/api/prepare.md.txt)
- [Viewer classes (Jupyter objects you control from Python)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/api/viewers.md.txt)
- [Round trip (results back from the viewer, columns and gene sets into it)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/api/round_trip.md.txt)
- [Sessions (.cellucid-session files)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/api/sessions.md.txt)
- [Subsampling](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/api/subsample.md.txt)
- [Vector fields (velocity / drift overlays)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/api/vector_fields.md.txt)
- [Local agents (cellucid mcp)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/api/mcp.md.txt)
- [API Reference Coverage (and the canonical API reference)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/g_api_reference_coverage/index.md.txt)
- [How to use this section](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/00_how_to_use_this_section.md.txt)
- [Codebase architecture](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/01_codebase_architecture.md.txt)
- [Repo layout and entry points](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/02_repo_layout_and_entry_points.md.txt)
- [Local development setup](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/03_local_development_setup.md.txt)
- [Build, install, and packaging](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/04_build_install_and_packaging.md.txt)
- [CLI architecture and commands](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/05_cli_architecture_and_commands.md.txt)
- [Configuration, environment variables, and logging](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/06_configuration_env_vars_and_logging.md.txt)
- [prepare() writer architecture](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/07_prepare_writer_architecture.md.txt)
- [Server mode architecture, endpoints, and security](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/09_server_mode_architecture_endpoints_and_security.md.txt)
- [Jupyter embedding architecture](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/10_jupyter_embedding_architecture.md.txt)
- [Hooks/events protocol and schema](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/11_hooks_events_protocol_and_schema.md.txt)
- [Debugging playbook](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/12_debugging_playbook.md.txt)
- [Testing and CI](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/13_testing_and_ci.md.txt)
- [Release process](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/14_release_process.md.txt)
- [Docs development and style guide](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/15_docs_development_and_style_guide.md.txt)
- [Performance profiling and scaling](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/16_performance_profiling_and_scaling.md.txt)
- [Security, privacy, and networking](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/17_security_privacy_and_networking.md.txt)
- [Extension points overview](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/18_extension_points_overview.md.txt)
- [Extension point: add a new hook event or command](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/20_extension_point_add_new_hook_event_or_command.md.txt)
- [Developer Docs (Python Package)](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/h_developer_docs/index.md.txt)
- [Installation and dependency issues](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/i_troubleshooting_index/01_installation_and_dependency_issues.md.txt)
- [Data preparation issues](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/i_troubleshooting_index/02_data_preparation_issues.md.txt)
- [Viewer embedding issues](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/i_troubleshooting_index/03_viewer_embedding_issues.md.txt)
- [Server mode issues](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/i_troubleshooting_index/04_server_mode_issues.md.txt)
- [Hooks and events issues](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/i_troubleshooting_index/05_hooks_and_events_issues.md.txt)
- [Performance and memory issues](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/i_troubleshooting_index/06_performance_and_memory_issues.md.txt)
- [HPC and remote access issues](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/i_troubleshooting_index/07_hpc_and_remote_access_issues.md.txt)
- [Python troubleshooting index](https://docs.cellucid.com/en/latest/_sources/user_guide/python_package/i_troubleshooting_index/index.md.txt)
- [R Package Guide](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/index.md.txt)
- [Installation](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/installation.md.txt)
- [What is cellucid-r?](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/a_landing_pages/01_what_is_cellucid_r.md.txt)
- [Supported Inputs and Workflows](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/a_landing_pages/03_supported_inputs_and_workflows.md.txt)
- [Quick Start (3 Levels)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/a_landing_pages/04_quick_start_3_levels.md.txt)
- [Landing Pages](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/a_landing_pages/index.md.txt)
- [What is a Cellucid-ready AnnData?](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/b_concepts_mental_models/01_what_is_a_cellucid_ready_anndata.md.txt)
- [Data Flow: R → Store → Browser](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/b_concepts_mental_models/02_data_flow_r_to_browser.md.txt)
- [Dataset Identity and Reproducibility](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/b_concepts_mental_models/03_dataset_identity_and_reproducibility.md.txt)
- [Concepts & Mental Models](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/b_concepts_mental_models/index.md.txt)
- [cellucid_prepare() overview](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/c_data_preparation_api/01_cellucid_prepare_overview.md.txt)
- [Input requirements (global rules)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/c_data_preparation_api/02_input_requirements_global.md.txt)
- [Embeddings and coordinates](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/c_data_preparation_api/03_embeddings_and_coordinates.md.txt)
- [obs: cell metadata](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/c_data_preparation_api/04_obs_cell_metadata.md.txt)
- [var: gene metadata and gene names](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/c_data_preparation_api/05_var_gene_metadata.md.txt)
- [Gene expression (X)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/c_data_preparation_api/06_gene_expression_matrix.md.txt)
- [Connectivities (neighbour graph)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/c_data_preparation_api/07_connectivities_knn_graph.md.txt)
- [Vector fields (velocity / displacement)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/c_data_preparation_api/08_vector_fields_velocity_displacement.md.txt)
- [Cellucid-ready AnnData specification (R writer)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/c_data_preparation_api/09_cellucid_ready_anndata_specification.md.txt)
- [Performance and storage](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/c_data_preparation_api/10_performance_and_storage.md.txt)
- [Troubleshooting cellucid_prepare()](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/c_data_preparation_api/11_troubleshooting_prepare.md.txt)
- [Data Preparation API](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/c_data_preparation_api/index.md.txt)
- [Open a Store in the Cellucid Web App](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/d_viewing_loading/01_open_stores_in_cellucid_web_app.md.txt)
- [Host a Store for Sharing](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/d_viewing_loading/02_host_stores_for_sharing.md.txt)
- [Validate a Store & Debug Loading](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/d_viewing_loading/03_validate_stores_and_debug_loading.md.txt)
- [View an Object in RStudio or Positron](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/d_viewing_loading/04_view_in_rstudio_positron.md.txt)
- [Serve from a Cluster or over SSH](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/d_viewing_loading/05_serve_from_hpc_and_ssh.md.txt)
- [Hooks, Selections and Sessions](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/d_viewing_loading/06_hooks_selection_and_sessions.md.txt)
- [Multimodal Assays (RNA + ADT, RNA + ATAC)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/d_viewing_loading/07_multimodal_assays.md.txt)
- [View an Object in a Jupyter Notebook (R kernel)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/d_viewing_loading/08_view_in_jupyter_notebooks.md.txt)
- [Local Agents (MCP): Claude Code, Claude Desktop, Cursor](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/d_viewing_loading/09_local_agents_mcp.md.txt)
- [Viewing and Loading](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/d_viewing_loading/index.md.txt)
- [Seurat Recipe](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/e_integrations_recipes/01_seurat_recipe.md.txt)
- [SingleCellExperiment Recipe](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/e_integrations_recipes/02_singlecellexperiment_recipe.md.txt)
- [Raw Matrices + Data Frames](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/e_integrations_recipes/03_raw_matrices_and_data_frames_recipe.md.txt)
- [Integrations & Recipes](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/e_integrations_recipes/index.md.txt)
- [Beginner Tutorial (Wet Lab Friendly)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/01_beginner_notebooks_wet_lab_friendly.md.txt)
- [Intermediate Tutorial (Computational Workflows)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/02_intermediate_notebooks_computational_workflows.md.txt)
- [Advanced Tutorial (Expert / Developer)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/03_advanced_notebooks_expert_developer.md.txt)
- [Explore a Seurat Object from R](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/04_explore_a_seurat_object_from_r.md.txt)
- [Share a SingleCellExperiment on GitHub](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/05_share_a_singlecellexperiment_on_github.md.txt)
- [CITE-seq: a Seurat Object with RNA and ADT](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/06_citeseq_seurat_to_mudata.md.txt)
- [View an object in a notebook (Jupyter, Colab, RStudio)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/07_view_in_a_notebook.ipynb.txt)
- [Pull everything back: highlights, labels and scores (Seurat, SingleCellExperiment)](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/08_pull_everything_back.ipynb.txt)
- [Push clusters into the viewer, refine them there, pull them back](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/09_push_clusters_refine_and_pull.ipynb.txt)
- [The round trip without a notebook: export from the web app, read in one call](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/10_round_trip_without_a_notebook.ipynb.txt)
- [Gene sets round trip: GMT in, signature scores out](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/11_gene_sets_round_trip.ipynb.txt)
- [Take a selection into a fresh analysis](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/12_subset_and_reanalyse.ipynb.txt)
- [Subsampled views: pull from a share of the cells, and reproduce it exactly](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/13_subsampled_views.ipynb.txt)
- [Notebook Tutorials](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/f_notebooks_tutorials/index.md.txt)
- [Public Functions](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/g_api_reference_coverage/01_public_functions_and_classes.md.txt)
- [Error Messages](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/g_api_reference_coverage/02_error_messages_and_exceptions_document_patterns.md.txt)
- [API Reference Coverage](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/g_api_reference_coverage/index.md.txt)
- [Codebase Architecture](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/h_developer_docs/01_codebase_architecture.md.txt)
- [Testing and CI](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/h_developer_docs/02_testing_and_ci.md.txt)
- [Release Process](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/h_developer_docs/03_release_process.md.txt)
- [Developer Docs](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/h_developer_docs/index.md.txt)
- [Installation and Dependency Issues](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/i_troubleshooting_index/01_installation_and_dependency_issues.md.txt)
- [Data Preparation Issues](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/i_troubleshooting_index/02_data_preparation_issues.md.txt)
- [Store Format and Validation Issues](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/i_troubleshooting_index/03_store_format_and_validation_issues.md.txt)
- [Web App Loading Issues](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/i_troubleshooting_index/04_web_app_loading_issues.md.txt)
- [Performance and Disk Usage Issues](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/i_troubleshooting_index/05_performance_and_disk_usage_issues.md.txt)
- [Troubleshooting Index](https://docs.cellucid.com/en/latest/_sources/user_guide/r_package/i_troubleshooting_index/index.md.txt)
- [Contributing](https://docs.cellucid.com/en/latest/_sources/contributing.md.txt)
- [Contributing to Cellucid (Web App)](https://docs.cellucid.com/en/latest/_sources/contributing/web_app.md.txt)
- [Contributing to Cellucid (Python)](https://docs.cellucid.com/en/latest/_sources/contributing/python.md.txt)
- [Contributing to Cellucid (R package)](https://docs.cellucid.com/en/latest/_sources/contributing/r.md.txt)
- [Releasing Cellucid](https://docs.cellucid.com/en/latest/_sources/contributing/releasing.md.txt)
- [Changelog](https://docs.cellucid.com/en/latest/_sources/changelog.md.txt)
- [Citing Cellucid](https://docs.cellucid.com/en/latest/_sources/citing.md.txt)