First-pass quickstart notebook

docs/examples/demos/optimize/.gitignore

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+# Downloaded data files
+*.zarr

docs/examples/demos/optimize/README.md

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+# WaveOrder Optimization Quickstart
+
+A self-contained notebook demonstrating WaveOrder's optimization capabilities for computational microscopy.
+
+## Quick Start
+
+### ⚠️ Important: Branch Dependency
+
+**Current Status:** This notebook requires the `variable-recon` branch of WaveOrder.
+
+The notebook installs directly from GitHub:
+```python
+pip install git+https://github.com/mehta-lab/waveorder.git@variable-recon
+```
+
+**When `variable-recon` merges to `main`:**
+- Update the install line to use the stable release: `"waveorder>=2.0.0"`
+- Do not delete the branch (keep as reference)
+
+### Run in Google Colab
+
+1. Upload `waveorder_quickstart.ipynb` to [Google Colab](https://colab.research.google.com/)
+2. Run all cells (~15 minutes)
+3. The notebook automatically downloads demo data from CZ Biohub's public server
+
+Or use this direct link (once pushed to GitHub):
+```
+https://colab.research.google.com/github/mehta-lab/waveorder/blob/variable-recon/docs/examples/demos/optimize/waveorder_quickstart.ipynb
+```
+
+### Run Locally
+
+```bash
+cd ~/waveorder/docs/examples/demos/optimize
+jupyter notebook waveorder_quickstart.ipynb
+```
+
+## What This Notebook Demonstrates
+
+### Physics-Informed Reconstruction
+
+WaveOrder uses differentiable forward models to reconstruct quantitative phase from label-free microscopy images.
+
+### Auto-Tuning via Optimization
+
+The notebook optimizes 5 optical parameters:
+
+1. **Defocus offset** (`z_offset`) - Focal plane alignment
+2. **Detection NA** - Effective detection cone angle
+3. **Illumination NA** - Illumination cone angle
+4. **Tilt zenith** - Angle from optical axis
+5. **Tilt azimuth** - Rotation around optical axis
+
+### Mid-Band Frequency Loss
+
+Uses mid-band frequency power as the optimization objective to maximize sharpness and focus.
+
+### Results
+
+Typical improvements:
+- 10-30% increase in mid-band power
+- Sharper features
+- Better contrast
+- Physically interpretable parameters
+
+## Notebook Contents
+
+1. **Setup** (1 cell) - Install dependencies, import libraries, define helper functions
+2. **Load & Visualize Data** (1 cell) - Extract embedded data, show z-stack
+3. **Initial Reconstruction** (2 cells) - Configure parameters, run reconstruction
+4. **Optimize Reconstruction** (3 cells) - Configure optimization, run 20 iterations, analyze convergence
+5. **Compare Results** (1 cell) - Side-by-side comparison with metrics
+6. **Summary** (markdown) - Interpretation and next steps
+
+## Using Your Own Data
+
+The notebook includes embedded demo data for immediate use. To use your own data:
+
+### Option 1: Load from Array (Simple)
+
+In the data loading cell, comment out the embedded data and load your array:
+
+```python
+# Comment out these lines:
+# demo_file = load_embedded_demo_data()
+# zyx_data, z_scale, y_scale, x_scale = load_demo_data(demo_file)
+
+# Load your own data:
+zyx_data = your_data_array  # Shape: (Z, Y, X)
+z_scale, y_scale, x_scale = 0.5, 0.108, 0.108  # Your pixel sizes in µm
+```
+
+### Option 2: Load from File
+
+```python
+import numpy as np
+
+# Load from .npz
+data = np.load('your_data.npz')
+zyx_data = data['zyx']
+z_scale, y_scale, x_scale = 0.5, 0.108, 0.108
+
+# Or load from .npy
+zyx_data = np.load('your_data.npy')
+z_scale, y_scale, x_scale = 0.5, 0.108, 0.108
+```
+
+### Data Requirements
+
+- **Format**: NumPy array, shape (Z, Y, X)
+- **Z-slices**: 10-30 planes recommended
+- **FOV**: 128-512 pixels per side
+- **Data type**: Float32 or Float64
+- **Scale**: Pixel sizes in micrometers
+
+## Key Features
+
+✅ **Self-contained** - Demo data downloads automatically from public server
+✅ **Proper Jupytext format** - Clean cell structure with `# %% [markdown]`
+✅ **Prints loss every iteration** - Full optimization transparency
+✅ **Convergence analysis** - Recommends next steps if not converged
+✅ **Grayscale visualizations** - Publication-ready figures
+✅ **Central crops** - Shows middle 50% for clarity
+✅ **Streamlined** - Only 8 executable cells
+
+## Version Management
+
+### Current (Pre-Merge)
+
+```python
+pip install git+https://github.com/mehta-lab/waveorder.git@variable-recon
+```
+
+### After Merge to Main
+
+Update the notebook's install command to:
+```python
+pip install "waveorder>=2.0.0"
+```
+
+Then:
+1. Test notebook with new version
+2. Update Colab links from `blob/variable-recon/` to `blob/main/`
+3. Keep the branch (don't delete it)
+
+## Troubleshooting
+
+### Optimization not converging
+
+- Increase `NUM_ITERATIONS` to 50 or 100
+- Reduce learning rates in `OPTIMIZABLE_PARAMS` (try halving them)
+- Run the optimization cell again to continue from current parameters
+
+### Out of memory
+
+- Use a smaller FOV (fewer pixels or z-slices)
+- Close other Colab notebooks
+- Restart runtime and try again
+
+### Poor reconstruction quality
+
+- Verify wavelength matches your microscope
+- Check pixel sizes are correct
+- Adjust regularization strength
+- Ensure initial parameter guesses are reasonable
+
+## For Developers
+
+### Repository Structure
+
+This directory contains:
+
+**Files to commit:**
+- `waveorder_quickstart.py` (~27 KB) - Jupytext source
+- `README.md` - Documentation
+- `.gitignore` - Excludes downloaded data
+
+**Files NOT to commit (in .gitignore):**
+- `waveorder-5x-demo.zarr` (~5 MB) - Downloaded demo dataset
+- `waveorder_quickstart.ipynb` - Generated notebook file
+
+### Developer Workflow
+
+#### Making Changes
+
+1. **Edit the source file**: `waveorder_quickstart.py` (Jupytext format)
+
+2. **Generate the notebook**:
+   ```bash
+   jupytext --to ipynb waveorder_quickstart.py
+   ```
+
+3. **Test the notebook** end-to-end:
+   ```bash
+   jupyter notebook waveorder_quickstart.ipynb
+   ```
+
+   The notebook will automatically download demo data on first run.
+
+4. **Commit only the source**:
+   ```bash
+   git add waveorder_quickstart.py README.md .gitignore
+   git commit -m "Update WaveOrder quickstart notebook"
+   ```
+
+#### What Gets Committed vs. Downloaded
+
+| File | Size | Commit? | Why? |
+|------|------|---------|------|
+| `waveorder_quickstart.py` | ~27 KB | ✅ Yes | Source code |
+| `README.md` | Small | ✅ Yes | Documentation |
+| `.gitignore` | Small | ✅ Yes | Git configuration |
+| `waveorder-5x-demo.zarr` | ~5 MB | ❌ No | Downloaded from public server |
+| `waveorder_quickstart.ipynb` | Varies | ❌ No | Generated from .py |
+
+### Demo Data
+
+The demo data is hosted on CZ Biohub's public server:
+- **URL**: https://public.czbiohub.org/comp.micro/neurips_demos/waveorder-5x-demo.zarr
+- **Size**: ~5 MB
+- **Format**: OME-Zarr
+- **Contents**: 3D label-free microscopy z-stack
+
+The notebook automatically downloads this file using `wget` if not already present.
+
+## Files
+
+## Publishing Checklist
+
+Before publishing:
+
+- [ ] Notebook runs end-to-end in Colab
+- [ ] All cells execute without errors
+- [ ] Visualizations render correctly
+- [ ] Optimization converges
+- [ ] Final comparison shows improvement
+- [ ] Embedded data extracts correctly
+- [ ] File size is reasonable (<10 MB)
+
+## References
+
+- Chandler T., Ivanov I.E., Hirata-Miyasaki E., et al. "WaveOrder: Physics-informed ML for auto-tuned multi-contrast computational microscopy from cells to organisms." [arXiv:2412.09775](https://arxiv.org/abs/2412.09775) (2025).
+
+- WaveOrder GitHub: https://github.com/mehta-lab/waveorder
+- WaveOrder Documentation: https://mehta-lab.github.io/waveorder/
+- WaveOrder PyPI: https://pypi.org/project/waveorder/
+
+## Contact
+
+For questions or issues:
+- **GitHub Issues**: https://github.com/mehta-lab/waveorder/issues
+- **Documentation**: https://mehta-lab.github.io/waveorder/
+- **Model Card**: https://virtualcellmodels.cziscience.com/model/waveorder
+
+## License
+
+BSD-3-Clause (matches WaveOrder software license)