Initial commit: organized project structure for student handoff

Reorganized flat 41-file directory into structured layout with:
- scripts/ for Python analysis code with shared config.py
- notebooks/ for Jupyter analysis notebooks
- data/ split into raw/, metadata/, processed/
- docs/ with analysis summary, experimental design, and bimodal hypothesis tutorial
- tasks/ with todo checklist and lessons learned
- Comprehensive README, PLANNING.md, and .gitignore

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

tasks/lessons.md

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+# Lessons Learned
+
+## Pseudoreplication Pitfall
+
+**The most important lesson in this project.**
+
+The raw data has ~230K data points per group, but the true independent samples are ROIs (N=18 per group). Each ROI contributes thousands of correlated time points. Running t-tests on all data points inflates significance massively (p < 1e-200) while the actual effect size is negligible (Cohen's d = 0.09).
+
+**Rule**: Always compute per-ROI summary statistics first, then compare groups at the ROI level.
+
+## Significance vs Effect Size
+
+A tiny p-value does NOT mean a meaningful difference. With N=230K, even a Cohen's d of 0.09 (96% overlap between distributions) gives p < 1e-200. Always report and interpret effect sizes alongside p-values.
+
+## Data Type Mismatches
+
+Machine names are stored as integers in metadata (76, 145, 268) but as strings in some contexts. The barrier_opening.csv uses "076" format. Always convert to string with `.astype(str)` before matching.
+
+## Time Unit Mismatches
+
+- SQLite databases: time `t` is in **milliseconds**
+- `2025_07_15_barrier_opening.csv`: `opening_time` is in **seconds**
+- Must multiply barrier opening times by 1000 before aligning
+
+## Missing Data
+
+Machine 139 has 6 ROIs in the metadata (3 trained, 3 untrained) but:
+- No tracking database file exists
+- No entry in barrier_opening.csv
+- This reduces the effective N from 18 to 15 per group
+
+## Single-Fly Detection Handling
+
+When only one fly is detected (instead of two), the tracker reports a single bounding box. If the area of that box is large (>1.5x median two-fly area), it likely means the flies are overlapping (distance ~0). If the area is small, one fly is probably out of frame (distance = NaN, excluded from analysis).
+
+## Path Management
+
+All scripts use `from config import DATA_PROCESSED, FIGURES, ...` for consistent paths. Notebooks use `Path("..")` relative to the `notebooks/` directory. Never use hardcoded absolute paths.