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docs/AI_DOCUMENTATION_INDEX.md

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+# Documentation Index
+
+> **Note**: This documentation was generated with AI assistance (Claude, Anthropic)
+
+---
+
+## Overview
+
+Complete documentation for the linumpy microscopy processing library. The library provides tools for processing Serial Optical Coherence Tomography (S-OCT) data into reconstructed 3D volumes.
+
+---
+
+## Pipeline Documentation
+
+### Workflow Guides
+
+1. **[PIPELINE_OVERVIEW.md](PIPELINE_OVERVIEW.md)** - Complete overview of preprocessing and 3D reconstruction pipelines
+2. **[NEXTFLOW_WORKFLOWS.md](NEXTFLOW_WORKFLOWS.md)** - Nextflow workflow configuration and execution guide
+
+### Data Formats
+
+3. **[MOSAIC_GRID_FORMAT.md](MOSAIC_GRID_FORMAT.md)** - OME-Zarr mosaic grid format specification
+4. **[SHIFTS_FILE_FORMAT.md](SHIFTS_FILE_FORMAT.md)** - XY shifts CSV file format and usage
+
+---
+
+## Feature Documentation
+
+5. **[SLICE_CONFIG_FEATURE.md](SLICE_CONFIG_FEATURE.md)** - Slice selection and filtering system
+6. **[SLICE_INTERPOLATION_FEATURE.md](SLICE_INTERPOLATION_FEATURE.md)** - Missing slice reconstruction using registration-based morphing
+7. **[GPU_ACCELERATION.md](GPU_ACCELERATION.md)** - GPU acceleration using NVIDIA CUDA/CuPy
+
+---
+
+## Reference
+
+8. **[SCRIPTS_REFERENCE.md](SCRIPTS_REFERENCE.md)** - Command-line scripts reference guide
+9. **[LIBRARY_MODULES.md](LIBRARY_MODULES.md)** - Python library module documentation
+
+---
+
+## Contributing
+
+10. **[CONTRIBUTING.md](CONTRIBUTING.md)** - Contribution guidelines
+
+---
+
+## Source Code Structure
+
+```
+linumpy/
+├── _thread_config.py      # CPU thread management (NumPy/SciPy/Dask/JAX/ITK)
+├── io/                    # Input/output modules
+│   ├── allen.py          # Allen Brain Atlas integration
+│   ├── npz.py            # NPZ file handling
+│   ├── test_data.py      # Test dataset access
+│   ├── thorlabs.py       # Thorlabs microscope support
+│   └── zarr.py           # OME-Zarr I/O
+├── gpu/                   # GPU acceleration
+│   ├── __init__.py       # GPU detection & utilities
+│   ├── array_ops.py      # Per-pixel operations
+│   ├── corrections.py    # Galvo detection
+│   ├── cuda_env.py       # CUDA environment utilities
+│   ├── fft_ops.py        # FFT & phase correlation
+│   ├── image_quality.py  # GPU image quality assessment
+│   ├── interpolation.py  # Resampling & transforms
+│   ├── morphology.py     # Binary operations & filtering
+│   └── registration.py   # Hybrid GPU/CPU registration
+├── microscope/           # Microscope-specific modules
+│   └── oct.py            # OCT tile reading
+├── preproc/              # Preprocessing modules
+│   ├── icorr.py          # Illumination correction
+│   ├── normalization.py  # Intensity normalization
+│   ├── resampling.py     # Mosaic grid resampling utilities
+│   └── xyzcorr.py        # XYZ correction & galvo shift detection
+├── psf/                  # Point spread function
+│   └── psf_estimator.py  # PSF estimation
+├── stitching/            # Image stitching
+│   ├── FileUtils.py      # File handling utilities
+│   ├── interpolation.py  # Missing-slice interpolation
+│   ├── manual_registration.py  # GUI-based manual registration
+│   ├── motor.py          # Motor-position-based tile placement
+│   ├── registration.py   # Image registration
+│   ├── stacking.py       # 3D slice stacking utilities
+│   ├── stitch_utils.py   # Stitching utilities
+│   └── topology.py       # Mosaic topology
+├── utils/                # Utility modules
+│   ├── data_io.py        # Data I/O helpers
+│   ├── image_quality.py  # Image quality assessment (SSIM, edge, variance)
+│   ├── io.py             # CLI argument helpers
+│   ├── metrics.py        # Quality metrics collection
+│   ├── mosaic_grid.py    # Mosaic grid utilities
+│   ├── orientation.py    # Volume orientation codes & RAS transforms
+│   ├── shifts.py         # XY shift loading & outlier filtering
+│   └── visualization.py  # Orthogonal view screenshots
+├── reconstruction.py     # Core reconstruction
+├── segmentation.py       # Segmentation tools
+└── utils_images.py       # Image utilities
+```
+
+---
+
+## Workflow Files
+
+```
+workflows/
+├── preproc/
+│   ├── nextflow.config       # Preprocessing config
+│   └── preproc_rawtiles.nf   # Raw tiles → mosaic grids
+├── reconst_3d/
+│   ├── nextflow.config       # 3D reconstruction config
+│   └── soct_3d_reconst.nf    # Mosaic grids → 3D volume
+└── reconst_2.5d/
+    ├── soct_2.5d_reconst.nf              # 2.5D reconstruction workflow
+    ├── soct_2.5d_reconst_beluga.config   # Beluga HPC cluster config
+    └── soct_2.5d_reconst_docker.config   # Docker container config
+```