Add colocalization visualization notebook with explanatory figures

[Copilot]

Creates an interactive Jupyter notebook demonstrating colocalization analysis for presentation slides, using toy regionprops data for Abeta plaques and Iba1 microglia.

Implementation

Notebook: examples/notebooks/colocalization_visualization.ipynb

• Generates synthetic regionprops data (30 Abeta, 40 Iba1) with realistic spatial clustering
• Implements full colocalization pipeline matching spimquant/workflow/scripts/compute_colocalization.py
• 5 visualization types:
  • Spatial distribution (magenta Abeta, yellow Iba1 with black outline)
  • KDTree nearest neighbor search with radius visualization
  • Overlap ratio calculation across 4 scenarios
  • Colocalization map with color-coded spatial links
  • Statistical distributions (distance, overlap ratio, size relationships)

Documentation: examples/notebooks/README.md

• Catalog of all example notebooks with usage instructions

Example Usage

# Generate toy data
df_abeta = pd.DataFrame({'stain': 'Abeta', 'pos_x': ..., 'nvoxels': ...})
df_iba1 = pd.DataFrame({'stain': 'Iba1', 'pos_x': ..., 'nvoxels': ...})

# KDTree-based colocalization
tree = KDTree(coords_iba1)
indices = tree.query_ball_point(pos_abeta, r=radius * 3.0)

# Calculate overlap ratio
overlap_ratio = max(0, 1 - distance / (radius_a + radius_b))

All visualizations are presentation-ready with configurable parameters (search_radius_multiplier, overlap_threshold).

Original prompt

can you make a jupyter notebook to make some toy regionprops data, and then run colocalization analysis on it, to create some figures? looking to make some explanatory figures for some presentation slides.. something showing 2d scatter plots of objects of two diff classes (Abeta, Iba1), plotting diff colors for each (magenta Abeta, yello(with black outline) Iba1), and then demonstrating the kd-tree, and nearest neighbour search, with distance and overlap_ratio.. any other plots or visuals you think may be helpful to describe the colocalization approach

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