Slide Scanner v3 - Final Package

Quick Start

One-Command Complete Workflow

python3 run_slide_scan_complete.py

This will:

1. Check prerequisites
2. Scan calibration region
3. Scan slide region
4. Create simple grid composite
5. Generate session summary

File Structure

final/
├── README.md                    # This file
├── QUICK_START_GUIDE.md        # Detailed usage guide
├── run_slide_scan_complete.py  # Main workflow script
├── sweep_and_stitch.py         # Imaging script
├── simple_grid_stitch.py       # Stitching script
├── slide_scanner.py            # Legacy slide scanner
├── scan_both_regions.py        # Calibration and slide scanning
├── calibration/                # Calibration scripts
│   ├── slide_position_calibration.py  # Interactive slide positioning
│   ├── focus_calibration.py           # Auto-focus calibration
│   ├── coverage_planning.py           # Scan pattern planning
│   ├── select_slide_corners.py        # Slide corner selection
│   └── select_calibration_corners.py  # Calibration corner selection
├── utils/                      # Hardware interfaces
│   ├── camera_interface.py     # Camera control
│   └── printer_interface.py    # 3D printer control
└── config/                     # Configuration files (create these)
    ├── slide_corners.json      # Slide corner positions
    └── calibration_corners.json # Calibration region corners

Prerequisites

1. Hardware Setup

• 3D printer connected and configured
• Camera connected and working
• Slide properly positioned

2. Initial Setup (First Time Only)

For first-time setup, run the calibration sequence:

# 1. Interactive slide positioning
python3 calibration/slide_position_calibration.py

# 2. Auto-focus calibration
python3 calibration/focus_calibration.py

# 3. Coverage planning
python3 calibration/coverage_planning.py

# 4. Select slide corners
python3 calibration/select_slide_corners.py

# 5. Select calibration corners
python3 calibration/select_calibration_corners.py

This will create the necessary configuration files in config/.

3. Configuration Files

After calibration, these files will be created in config/:

config/slide_corners.json:

{
  "bottom_left": {"X": 0.0, "Y": 0.0, "Z": 2.2},
  "bottom_right": {"X": 25.0, "Y": 0.0, "Z": 2.2},
  "top_right": {"X": 25.0, "Y": 75.0, "Z": 2.2},
  "top_left": {"X": 0.0, "Y": 75.0, "Z": 2.2}
}

config/calibration_corners.json:

{
  "bottom_left": {"X": 0.0, "Y": 0.0, "Z": 2.2},
  "bottom_right": {"X": 10.0, "Y": 0.0, "Z": 2.2},
  "top_right": {"X": 10.0, "Y": 10.0, "Z": 2.2},
  "top_left": {"X": 0.0, "Y": 10.0, "Z": 2.2}
}

Usage Options

Complete Workflow (After Calibration)

python3 run_slide_scan_complete.py

Initial Calibration (First Time Setup)

# Run complete calibration sequence
python3 scan_both_regions.py

Individual Calibration Steps

# 1. Interactive slide positioning
python3 calibration/slide_position_calibration.py

# 2. Auto-focus calibration
python3 calibration/focus_calibration.py

# 3. Coverage planning
python3 calibration/coverage_planning.py

# 4. Select slide corners
python3 calibration/select_slide_corners.py

# 5. Select calibration corners
python3 calibration/select_calibration_corners.py

Individual Scanning Steps

# 1. Scan calibration region
python3 sweep_and_stitch.py --corners config/calibration_corners.json --output calibration_images/

# 2. Scan slide region
python3 sweep_and_stitch.py --corners config/slide_corners.json --output slide_images/

# 3. Create composite
python3 simple_grid_stitch.py --capture_dir slide_images/

Stitch Only (Use Existing Images)

python3 run_slide_scan_complete.py --stitch-only

Output Structure

After running the complete workflow:

scan_session_YYYYMMDD_HHMMSS/
├── calibration/           # Calibration images
│   ├── img_x0_y0.png
│   ├── img_x0_y1.png
│   └── ...
├── slide/                # Slide images + final composite
│   ├── img_x0_y0.png
│   ├── img_x0_y1.png
│   ├── ...
│   └── simple_grid_slide.png  # Final stitched output
└── session_summary.json  # Session metadata

Troubleshooting

Missing Configuration Files

If you get "Missing required files" error:

1. Create the config/ directory
2. Add the corner position JSON files
3. Adjust coordinates for your specific setup

Hardware Connection Issues

• Check 3D printer connection
• Verify camera is working
• Ensure slide is properly positioned

Image Quality Issues

• Clean camera lens and slide
• Check lighting conditions
• Verify focus settings

Performance Notes

• Typical scan time: 5-15 minutes
• Image count: 20-100 images
• Output size: 10-50 MB
• Memory usage: ~1-2 GB

Calibration Features

Interactive Slide Positioning

• File: calibration/slide_position_calibration.py
• Purpose: Find exact slide center and test corner positions
• Controls: WASD keys for movement, R/F for Z-axis, C to capture position

Auto-Focus Calibration

• File: calibration/focus_calibration.py
• Purpose: Automatically find optimal focus using sharpness analysis
• Features: Z-axis sweep with Laplacian variance measurement

Coverage Planning

• File: calibration/coverage_planning.py
• Purpose: Calculate optimal scan patterns with minimal overlap
• Features: Field of view measurement and grid optimization

Corner Selection

• Files: calibration/select_slide_corners.py, calibration/select_calibration_corners.py
• Purpose: Interactive corner selection for slide and calibration regions
• Features: Visual feedback and position validation

Customization

Adjust Grid Density

Modify in sweep_and_stitch.py:

GRID_STEP_X = 1.0  # mm between images
GRID_STEP_Y = 1.0  # mm between images

Change Image Quality

Modify in sweep_and_stitch.py:

frame = camera.capture_and_save(filename, quality=95)  # JPEG quality

Adjust Focus Settings

Modify in sweep_and_stitch.py:

SHARPNESS_THRESHOLD = 30.0  # Laplacian variance threshold
LOCAL_SWEEP_RANGE = 1.0     # mm autofocus range

Additional Resources

• See QUICK_START_GUIDE.md for detailed instructions
• Check session summary files for statistics
• Review captured images for quality assessment

Success Indicators

• Complete workflow: Session directory created with images
• Good quality: Sharp, well-lit images in composite
• Proper alignment: Grid pattern visible in stitched output
• Full coverage: No missing regions in final composite