Contents

• List of Figures
• Introduction
• stack_analyze
  • stack_analyze quickstart
  • Acquiring a stack
  • Stack file types
  • stack_analyze: the main screen
  • Building stack lists
  • Stack alignment
  • Noise filtering
  • Reading $I_{0}$ files
  • Dose estimation
  • Movies of stacks
  • stack_plot_spectrum
  • Related software to install
  
  
• The program pca_gui
  • The pca_gui main menu
  • The File menu: loading data into the program
  • Preprocess: data preprocessing
  • Components: the principal component calculation
  • Clusters: cluster analysis
  • Target spectra and maps
  
  
• Dose estimation numerical factor
• The format of .stk files
• Bibliography