Quickstart Guide

This guide will walk you through your first analysis with SCOPE-XR using the provided example images.

Prerequisites

Make sure you have SCOPE-XR installed. If not, see Installation.

Your First Focal Spot Analysis

SCOPE-XR includes sample images in the examples/ folder to help you get started.

Step 1: Locate Example Files

After installation, download the example files from the repository:

examples/fs_args.yaml - Focal spot configuration
examples/Image_FS2_Double_Asym_Clean.tif - Sample focal spot image

Step 2: Run the GUI

The easiest way to start is with the graphical interface:

scopexr-gui

What happens next:

The GUI opens with two tabs: “Focal Spot (FS)” and “PSF”
Click the Focal Spot (FS) tab
Click “Browse” to select Image_FS2_Double_Asym_Clean.tif
The image preview appears in the GUI (PNG, TIFF, and DICOM images show previews)
Click “Run Analysis”
Watch the output in the console window
Results are saved to the output directory (default: output_fs/)

Step 3: Interpret Results

After analysis completes, check the output folder. You’ll find:

Generated Files:

reconstructed_fs.png - 2D visualization of the focal spot
sinogram.png - Derivative profiles used for reconstruction
profiles.png - Extracted radial profiles
results.txt - Numerical measurements (FWHM, dimensions)

Key Metrics to Check:

Focal Spot FWHM (horizontal): 0.598 mm
Focal Spot FWHM (vertical): 0.546 mm
Magnification: 5.85

Your First PSF Analysis

Step 1: Switch to PSF Mode

In the GUI:

Click the PSF tab
Click “Browse” to select Image_PSF_Asym_1.5px_Clean.tif
Review the automatically loaded parameters from psf_args.yaml

Step 2: Run PSF Analysis

# Or use CLI:
scopexr-psf --f "examples/Image_PSF_Asym_1.5px_Clean.tif"

Step 3: Interpret PSF Results

The output folder (output_psf/) contains:

reconstructed_psf.png - 2D detector response function
sinogram.png - Processed edge profiles
mtf_plot.png - Modulation Transfer Function curve
results.txt - PSF dimensions and MTF values

Typical PSF Output:

PSF FWHM (horizontal): 1.542 pixels
PSF FWHM (vertical): 2.005 pixels
MTF at 10% (horizontal): 1.54 cycles/pixel
MTF at 10% (vertical): 2.01 cycles/pixel

CLI Quick Reference

For automated workflows, use the command-line interface:

Focal Spot:

# Basic usage
scopexr-fs --f "path/to/image.tif"

# Override pixel size
scopexr-fs --f "image.tif" --p 0.15

# Specify output directory
scopexr-fs --f "image.tif" --o "my_results/"

PSF:

# Basic usage
scopexr-psf --f "path/to/image.tif"

# With sub-pixel oversampling
scopexr-psf --f "image.tif" --oversample --dtheta 2 --resample2 3 --gaussian_sigma 0.5

Common First-Time Issues

Issue: “No circular object detected”

Solution: Your image may have low contrast. Try adjusting Hough transform parameters in the YAML file or via the GUI, or skip circle detection entirely (if the circle is centered):
```
hough_params:
  minRadius: 50
  maxRadius: 500
```

Issue: “Magnification estimation failed”

Solution: Provide magnification manually:
```
scopexr-fs --f "image.tif" --m 1.5
```

Issue: Results look noisy

Solution: Enable sinogram symmetrization:
```
scopexr-fs --f "image.tif" --sym
```

Next Steps

Read the full Usage guide for all available parameters
Understand the Physical Methodology behind the measurements
Review the Processing Pipeline for quality control
See Troubleshooting for common issues

For batch processing, create custom YAML configuration files and use the CLI in scripts:

#!/bin/bash
for img in data/*.tif; do
    scopexr-fs --f "$img" --config my_config.yaml
done