AlliGator Manual

Contents

• How to use this manual
  • Notations
• AlliGator Overview
• AlliGator Windows
  • Main windows
  • Accessory windows
• AlliGator Panels
  • Source Image Panel
    • Gate Image Slide
    • Time Point Slide
    • Displayed Image Selector
    • Image Color Ramp
    • Image & Phasor Overlay Tools
    • Use ROI as Search Area
    • Image Tool Palette
    • Save Image
    • Context Menu
  • Image Histogram Panel
    • Histogram Min & Max Cursors
    • Lower & Higher Percentiles
    • Intensity Thresholds
  • Fluorescence Decay Panel
    • Decay Graph Custom Menu
  • Fluorescence Decay Statistics Panel
  • Intensity Time Trace Panel
  • Phasor Plot Panel
  • Phasor Graph Panel
  • Lifetime & Other Parameters Analysis Panel
  • Phasor Ratio Analysis Panel
  • Decay Fit Parameter Map Panel
• AlliGator Menus
  • File Menu
  • Windows Menu
  • Scripts Menu
  • Analysis Menu
  • Calibration Menu
  • Settings Menu
  • Help Menu
• Alligator User Guide
  • 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
    • ROI Storage
    • ROI Definition
    • ROI Information
    • Using a ROI Mask Image
  • Decay Pre-processing
  • Fluorescence Decay Fitting
    • Single decay fit
    • Time-series decay fit
• Alligator Reference
  • AlliGator HDF5 File Format
    • v 0.7 (2023-09-02)
    • v 0.6.1 (2022-07-27)
    • v 0.6 (2022-04-13)
    • v 0.5 (2021-04-27)
    • v 0.4 (2021-02-27)
    • v 0.3 (2021-01-29)
    • v 0.2
    • v 0.1
    • Notes
  • Python Plugins
    • Design Principle
    • Plugins Folder
    • Plugin Files
    • Plugin Function Names
    • Plugin Functions Special Syntax
    • Decay Graph example
  • AlliGator Python Plugins API v 0.1
    • parameter types
  • Graph Object
    • Graph Object Anatomy
    • Plot Area
    • Plot Legend
    • Plot Menu
    • Custom Graph Menu
    • Graph Scales
    • Scale Legend
    • Graph Palette
    • Cursor Legend
  • Image Color Palette
  • Selected Plot Style Window
• AlliGator Tutorials
• AlliGator Shortcuts
• AlliGator Installation
• AlliGator Version History
• Bibliography
• Acknowledgments
• AlliGator Support
  • How to report an issue

• Search Page