OpenIMC Documentation¶
Welcome to the OpenIMC documentation. This guide covers everything you need to know to use OpenIMC for IMC data analysis, from basic workflows to advanced spatial analysis and reproducibility features.
Quick Navigation:
Getting Started: Overview, installation, and quick start guide
Core Workflow: Image visualization, segmentation, and feature extraction
Data Analysis: Clustering, phenotyping, batch correction, and quality control
Spatial Analysis: Simple and advanced spatial analysis methods
Advanced Topics: Pixel correlation, spillover correction, high-resolution analysis, and custom algorithms
Reproducibility & Sharing: State management and analysis step export for publication
API Reference: Core API and CLI reference documentation
Getting Started¶
Getting Started
Core Workflow¶
Core Workflow
Data Analysis¶
Spatial Analysis¶
Advanced Topics¶
Reproducibility & Sharing¶
Reproducibility & Sharing
API Reference¶
API Reference
- Core pipeline API
batch_correction()build_spatial_graph()build_spatial_graph_anndata()cluster()dataframe_to_anndata()deconvolution()export_anndata()extract_features()generate_spillover_matrix()get_panel()load_mcd()parse_denoise_settings()pixel_correlation()preprocess()qc_analysis()segment()spatial_autocorrelation()spatial_cooccurrence()spatial_distance_distribution()spatial_enrichment()spatial_neighborhood_enrichment()spatial_ripley()spillover_correction()
- CLI API Reference