Example Scripts

iPA provides a comprehensive set of example scripts to demonstrate its capabilities across different imaging modalities. All scripts are located in the examples/ directory.

Cryo-Electron Tomography (Cryo-ET)

  • Filament Prediction: examples/examples_et/demo_cryoET_filament_predict.py * Demonstrates filament skeletonization and prediction on denoised subvolumes.

  • Morphology Analysis: examples/examples_et/demo_ET_morphology.py * Calculates tubular length and filament statistics.

  • Spatial Arrangement: examples/examples_et/demo_ET_arrangement.py * Analyzes the angular distribution of anchored filaments.

  • Interaction Analysis: examples/examples_et/demo_ET_interaction.py * Studies interactions between actin, vesicles, mitochondria, and ER.

Soft X-ray Tomography (SXT)

  • Composite Mask Generation: examples/examples_sxt/demo_SXT_composite_mask.py * Combines cell, nucleus, mito, and ISG masks into a multi-class label map.

  • Spatial Partitioning: examples/examples_sxt/demo_SXT_partitioning.py * Divides cytoplasm into concentric shells based on NE and PM boundaries.

  • Spatial Arrangement (RDF): examples/examples_sxt/demo_SXT_spatial_arrangement.py * Computes Radial Distribution Functions for organelles.

  • Interaction Analysis: examples/examples_sxt/demo_SXT_interaction.py * Analyzes ISG-Mitochondria contacts and distances.

  • Morphology Analysis: examples/examples_sxt/demo_SXT_morphology.py * Extracts volume distributions for individual ISGs and Mitochondria.

  • Denoising (N2N/N2V): examples/examples_sxt/demo_SXT_n2n_predict.py, demo_SXT_n2v_predict.py * Applies Noise2Noise and Noise2Void for tomogram enhancement.

Structured Illumination Microscopy (SIM) & Widefield (WFM)

  • ISG Segmentation: examples/examples_sim_wfm/demo_SIM_isg_segmentation.py * Threshold-based segmentation for insulin granules.

  • ER Prediction: examples/examples_sim_wfm/demo_SIM_ER_predict.py * Uses the ERNet transformer model for ER segmentation.

  • RDF Analysis: examples/examples_sim_wfm/demo_SIM_rdf_analysis.py * Calculates organelle distribution relative to cell boundaries.

  • Partitioning: examples/examples_sim_wfm/demo_SIM_partitioning.py, demo_WFM_partitioning.py * Spatial partitioning for SIM and WFM datasets.

  • Dynamics Analysis: examples/examples_sim_wfm/demo_WFM_dynamics.py * Analyzes 3D and radial velocities from tracking data.

  • Interaction: examples/examples_sim_wfm/demo_SIM_WFM_interaction.py * Cross-organelle distance analysis in fluorescence data.

Cross-Modal Comparison

  • SIM vs SXT: examples/examples_cross_modal/demo_SIM_SXT_comparison.py * Compares organelle distribution patterns across different imaging techniques using Pearson correlation.

Running Examples

All examples can be run directly from the command line:

# Navigate to examples directory
cd examples/examples_sxt

# Run a demo script
python demo_SXT_partitioning.py

Each example includes detailed comments and generates output in the results/ directory with corresponding log files in logs/.