• 1. Introduction
  • 1.1. Welcome
  • 1.2. What’s New
    • 1.2.1. SMDExplorer 1.0.5 (‘New Rules’)
    • 1.2.2. SMDExplorer 1.0.4 (‘Hallucinate’)
    • 1.2.3. SMDExplorer 1.0.3 (‘Levitating’)
    • 1.2.4. SMDExplorer 1.0.2 (‘True Blue’)
    • 1.2.5. SMDExplorer 1.0.1 (‘Lucky Star’)
• 2. Guided Tour
  • 2.1. Exploratory Data Analysis
  • 2.2. Automated Image Formation
  • 2.3. Ratiometric Imaging
  • 2.4. Peak Deconvolution
• 3. General Usage
  • 3.1. File Input / Output
    • 3.1.1. Input
    • 3.1.2. Output
  • 3.2. Acquisition Parameters
  • 3.3. Graphing
  • 3.4. Analysis of Individual Spectra
  • 3.5. Analysis of Spectral Mappings
  • 3.6. Preferences
    • 3.6.1. General Preferences
    • 3.6.2. Fitting Preferences
• 4. Preprocessing
  • 4.1. Introduction
    • 4.1.1. Remarks on Processing Datasets
    • 4.1.2. Remarks on Processing Single Spectra
  • 4.2. Background Subtraction
  • 4.3. Calibration
    • 4.3.1. Global Calibration
    • 4.3.2. Per Spectrum Calibration
  • 4.4. Range Selection
  • 4.5. Cropping
  • 4.6. Cosmic Ray Removal (Despiking)
    • 4.6.1. Outline of the Algorithm
  • 4.7. Simple Baseline Removal (Bring to Zero)
  • 4.8. Non-linear Baseline Removal
  • 4.9. Smoothing
  • 4.10. Averaging / Binning / Denoising
    • 4.10.1. Denoising by Downsampling
    • 4.10.2. Denoising by Averaging
    • 4.10.3. Statistical Denoising
  • 4.11. Normalization
  • 4.12. Differentiation
  • 4.13. Masking
• 5. Intensity Profiles / Image Formation
  • 5.1. Intensity Profile Options
  • 5.2. Comparing Spectra
  • 5.3. Comparing Intensity Profiles / Images
  • 5.4. Line Profiles
  • 5.5. Waterfall Plots
  • 5.6. Spectrograms (2D Spectral Stacks)
  • 5.7. Spectral Surface Plot
  • 5.8. Surface Plots
  • 5.9. 3D Plots
    • 5.9.1. Isosurfaces
    • 5.9.2. Volumetric Rendering
    • 5.9.3. Animation Export
    • 5.9.4. Slice Overlay
• 6. Automated Image Formation
  • 6.1. General Introduction
  • 6.2. Non-negative Matrix Factorization
  • 6.3. Principal Component Analysis
  • 6.4. Multivariate Curve Resolution
  • 6.5. K-Means Clustering
  • 6.6. Automated Image Formation - A How-to
    • 6.6.1. Whitening
  • 6.7. Display Options
• 7. Peak Deconvolution
  • 7.1. Line Shapes
    • 7.1.1. Gaussian
    • 7.1.2. Lorentzian
    • 7.1.3. Pseudo-Voigt
    • 7.1.4. Damped Harmonic Oscillator (DHO)
    • 7.1.5. Which Line Shape Should I Chose?
  • 7.2. The Peak Deconvolution Algorithm
    • 7.2.1. Initial Guesses
    • 7.2.2. Constraints
    • 7.2.3. Masking
    • 7.2.4. GPU-accelerated Fits
  • 7.3. The Fitting Window
    • 7.3.1. The Settings Pane
    • 7.3.2. The Fit Coefficients Pane
    • 7.3.3. The Fit Result Pane
  • 7.4. Peak Deconvolution - A How-to
  • 7.5. Analyzing and Visualizing Peak Deconvolution Results
• 8. Particle Analysis
  • 8.1. The Particle Analysis Window
    • 8.1.1. The Parameter Toolbar
    • 8.1.2. The Image Pane
    • 8.1.3. The Particle Detail View
    • 8.1.4. The Results Table
  • 8.2. Parameter Distributions
  • 8.3. Image Statistics
  • 8.4. Practical Considerations
• 9. Appendices
  • 9.1. HDF5 Format Specification
    • 9.1.1. HDF5 Spectral Mappings
    • 9.1.2. HDF5 Multi-Spectrum Files
    • 9.1.3. HDF5 Peak Fitting Results
    • 9.1.4. Igor Pro HDF5 export