Alligator User Guide

The following pages introduce the user to different topics and functions of AlliGator. A first time user may benefit from reading them in the order they are listed below. Alternatively, tutorial videos found on the AlliGator Tutorials page can be consulted as either a complement or an introduction to these topics.

• Loading & Saving FLI Datasets
  • Introduction
  • single HDF5 FLI Dataset
  • Folder of Gate Images
  • Becker & Hickl .sdt FLI Dataset
  • PicoQuant .ptu Dataset
  • PicoQuant .bin Dataset
  • Reloading a Dataset
• Loading & Saving FLI Dataset Series
  • Folder of HDF5, .sdt or .ptu Datasets
  • Folder of Folders of Gate Images
  • Notes
• Regions of Interest
  • Drawing a ROI
  • Managing ROIs
    • Source ROI Manager
    • ROI Navigation
    • ROI Display
  • ROI Storage
    • ROI Storage
    • Saving and Loading ROIs
    • Importing ROI description
  • ROI Definition
    • Defining ROI(s) by a decay peak threshold
    • Defining ROI(s) by a image intensity threshold
    • ROI Grid
    • Convert ROI to Individual Pixel ROIs
  • ROI Information
    • ROI Statistics
    • Export ROI Description to Notebook
  • Using a ROI Mask Image
• Decay Pre-processing
• Fluorescence Decay Fitting
  • Single decay fit
    • Overview
    • Fit Options
    • Fit Parameter Constraints
    • Fit Results
  • Time-series decay fit