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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
---------------

.. toctree::
   :maxdepth: 1
   :caption: Getting Started

   overview
   installation
   quickstart

Core Workflow
-------------

.. toctree::
   :maxdepth: 1
   :caption: Core Workflow

   image_visualization
   segmentation
   feature_extraction

Data Analysis
-------------

.. toctree::
   :maxdepth: 1
   :caption: Data Analysis

   clustering
   llm_phenotyping
   batch_correction
   quality_control

Spatial Analysis
----------------

.. toctree::
   :maxdepth: 1
   :caption: Spatial Analysis

   simple_spatial_analysis
   advanced_spatial_analysis

Advanced Topics
---------------

.. toctree::
   :maxdepth: 1
   :caption: Advanced Topics

   pixel_correlation
   spillover_matrix
   high_resolution_experimental_design
   custom_algorithms

Reproducibility & Sharing
--------------------------

.. toctree::
   :maxdepth: 1
   :caption: Reproducibility & Sharing

   state_management

API Reference
-------------

.. toctree::
   :maxdepth: 2
   :caption: API Reference

   api_core
   api_cli