Analysis Module
===============

The analysis module provides comprehensive tools for quantitative analysis of cellular imaging data, extracting biologically meaningful features from segmented organelles and partitioned cytoplasmic regions.

Overview
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Based on the radial cytoplasmic partitioning framework, iPA extracts diverse organelle features across four key dimensions (as described in the manuscript):

1. **Morphology**: Volume, surface area, length, and shape descriptors of subcellular structures
2. **Spatial Arrangement**: Radial Distribution Functions (RDF), organelle pools, angle distributions, and aggregation patterns
3. **Dynamics**: 3D velocity and radial velocity from time-lapse imaging
4. **Interactions**: Distance-based and contact-based analysis between different organelle types

This multi-dimensional feature extraction enables both intra-modal analysis (within a single imaging modality) and inter-modal comparison (across WFM, SIM, SXT, and cryo-ET), providing a comprehensive view of cell structure and function.

Key Capabilities
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* **Radial Distribution Function (RDF)**: Standardized quantification of organelle localization from NE to PM
* **14 Predefined Interaction Types**: Comprehensive coverage of organelle-organelle spatial relationships
* **Multi-Organelle Support**: ISGs, F-actin, microtubules, mitochondria, ER, vesicles
* **Cross-Modal Compatibility**: Consistent analysis pipeline across all supported imaging modalities
* **Statistical Rigor**: Pearson correlation, distance statistics, contact probability calculations

Supported Analyses
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The analysis module is organized into four specialized sub-modules:

* **Morphology Analysis**: Extract structural features (volume, length, shape) from segmented masks
* **Distribution Analysis**: Calculate RDF and analyze spatial arrangement patterns
* **Interaction Analysis**: Quantify distances and contacts between different organelle types
* **Dynamics Analysis**: Analyze velocity and motion patterns from time-lapse data

Each sub-module provides both low-level functions for custom workflows and high-level analysis pipelines for standard use cases.

Sub-modules
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.. toctree::
   :maxdepth: 2

   morphology
   distribution
   interaction
   dynamics