flow-panel-designer

# Flow Panel Designer

Fluorophore selection optimizer.

## Use Cases
- Multicolor panel design (10+ colors)
- Compensation planning
- Marker-fluorophore matching
- Spectral flow setup

## Parameters

| Parameter | Type | Default | Required | Description |
|-----------|------|---------|----------|-------------|
| `--markers` | string | - | Yes | Comma-separated target antigens |
| `--instrument` | string | - | No | Cytometer model |
| `--n-colors` | int | 8 | No | Number of fluorophores |
| `--output`, `-o` | string | stdout | No | Output file path |

## Returns
- Optimal fluorophore assignments
- Spillover predictions
- Compensation control list
- Panel validation checks

## Example
T-cell panel: CD3-BV421, CD4-FITC, CD8-PE...

## Risk Assessment

| Risk Indicator | Assessment | Level |
|----------------|------------|-------|
| Code Execution | Python/R scripts executed locally | Medium |
| Network Access | No external API calls | Low |
| File System Access | Read input files, write output files | Medium |
| Instruction Tampering | Standard prompt guidelines | Low |
| Data Exposure | Output files saved to workspace | Low |

## Security Checklist

- [ ] No hardcoded credentials or API keys
- [ ] No unauthorized file system access (../)
- [ ] Output does not expose sensitive information
- [ ] Prompt injection protections in place
- [ ] Input file paths validated (no ../ traversal)
- [ ] Output directory restricted to workspace
- [ ] Script execution in sandboxed environment
- [ ] Error messages sanitized (no stack traces exposed)
- [ ] Dependencies audited
## Prerequisites

No additional Python packages required.

## Evaluation Criteria

### Success Metrics
- [ ] Successfully executes main functionality
- [ ] Output meets quality standards
- [ ] Handles edge cases gracefully
- [ ] Performance is acceptable

### Test Cases
1. **Basic Functionality**: Standard input → Expected output
2. **Edge Case**: Invalid input → Graceful error handling
3. **Performance**: Large dataset → Acceptable processing time

## Lifecycle Status

- **Current Stage**: Draft
- **Next Review Date**: 2026-03-06
- **Known Issues**: None
- **Planned Improvements**: 
  - Performance optimization
  - Additional feature support