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
  • Data Information
    • Gate Characteristics
    • Define Gates to Skip or Keep
    • Channel Selection
    • Laser & SYNC periods
    • Data Pile-up Correction (*)
    • Scaling Factor
    • Background File Subtraction (*)
  • 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 an 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
  • Background Subtraction
    • 1. Mean or Min Baseline
    • 2. Square Gated Single-Exponential method
    • 3. Constant Background
  • Decay Normalization
  • Decay Straightening
  • Decay Folding
  • Gate Reversing
  • Decay Smoothing
  • Decay Shifting
  • Decay Extrapolation
• Fluorescence Decay Fitting
  • Instrument Response Function (IRF)
  • Single decay fit
    • Overview
    • Fit Options Details
    • Fit Parameters
    • Fit Results
  • Multiple ROIs decay fit
  • Series decay fit
• All ROIs Single-Pixel Analysis
  • NLSF Analysis
  • Phasor Analysis
• AlliGator Exposed Internal Parameters
  • AlliGator exposed internal parameters JSON strings with default values
  • AlliGator exposed internal variables JSON strings with values
  • AlliGator exposed internal data JSON strings with values