AlliGator Manual

Contents

• How to use this manual
  • Notations
• AlliGator Overview
• AlliGator Windows
  • Main windows
    • AlliGator Window
      • AlliGator Panels
      • Analysis Status Indicator LEDs
      • Other buttons and indicators
    • Notebook Window
      • Saving & Loading the Notebook
      • Tip
    • Settings Window
      • Source Image
      • Data Information
      • Fluorescence Decay
      • Fluorescence Decay Statistics
      • Intensity Time Trace
      • Phasor Plot
      • Phasor Graph
      • Single-Exponential Phasor Locus (SEPL)
      • Phasor Calibration
      • Lifetime Analysis
      • Plugins
      • Miscellaneous
  • Accessory windows
    • About AlliGator Window
    • Context Help
    • Dataset Information Window
    • Source Image ROI Manager Window
    • Phasor Plot ROI Manager Window
    • Phasor Harmonic Manager Window
    • Image Profile
      • Averaged Profile
      • Average Intensity Profile
      • Split Profile
      • Current ROI Definition
    • Local Decay Graph Window
    • Histogram Window
    • Plot Editor Window
      • Warning
  • Analysis Tools windows
    • Intensity Corrections Definition
    • Fit Method Benchmark
      • Simulations panel
      • Decay, Fit & Residuals Plots Panel
      • Settings Panel
    • Shot Noise Influence on Average Lifetime
• AlliGator Panels
  • Source Image Panel
    • Gate Image Slide
    • Time Series 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
      • Process Plot(s)
      • Nonlinear Least Square Fit
      • IRF/Reference Plot
      • Export Decay to Phasor Graph
      • Python Plugins
  • Fluorescence Decay Statistics Panel
  • Intensity Time Trace Panel
  • Phasor Plot Panel
    • Phasor Plot Image Size, Aspect Ratio and Binning
    • Phasor Plot Settings and Controls
    • Phasor Indicator
    • Highlighting Phasor ROIs in the Source Image
    • Phasor Plot Context Menu
      • Saving the Phasor Plot Image
      • Export Complex Phasor Map
      • Export Phasor Ratio Map
      • Export Average Lifetime Map
      • Defining Phasor Ratio References in the Phasor Plot
    • Representing Phasor Ratio/Average Lifetime/User-defined Quantities as a Color Map in the Source Image
      • Color Map Style Options
      • Alias Definitions Window
    • Color-coding Phasors with a user-defined Color Map
      • Phasor Color Map Picker window
  • Phasor Graph Panel
    • Introduction
    • Managing plots in the Phasor Graph
    • Loading and Saving Phasor Plots
    • Phasor Calibration
      • 1. Introduction
      • 2. Defining a new single calibration phasor
      • 3. Defining a phasor calibration series
      • 4. Defining a phasor calibration map
    • Phasor Ratio References
      • 1. Introduction
      • 2. Loading/Saving Phasor Ratio References
      • 3. User-picked Reference
      • 4. Current Phasor as Reference
      • 5. Cursor Location as Reference
      • 6. Cursor-Defined Line/UC Intersection
      • 7. Selected Plots Fitted Line/UC Intersection
      • 8. Selected Plots Major or Minor Axis/UC Intersection
      • 9. Clearing References
    • Phasor Ratio Line
    • Shot Noise-limited Standard Deviations
    • Exporting Additional Phasor Quantities
    • Phasor Math
      • 1. Average Phasor
      • 2. Phasor Multiplication
    • Computing a phasor ratio and its associated average lifetime
    • Parameter 2 vs Parameter 1 Scatterplot
    • Compute Multiple Average Phasors & Derived Quantities
    • Note on the Phase Lifetime vs Total Intensity/Background-Subtracted Intensity/Background/Fitted Lifetime/Amplitude functions
  • Phasor Ratio Panel
    • Introduction
    • Phasor Ratio Graph
      • Computation of a single phasor ratio
      • Computation of a series of phasor ratios
      • Computing the average phasor ratio of a phasor plot
    • Fitting a phasor ratio series to a line
  • Lifetime & Other Parameters Panel
    • Introduction
      • Average lifetime
      • Decay fit parameters
    • Lifetime & Other Parameters graph context menu
  • Decay Fit Parameters Map Panel
    • Decay Fit Parameter Map Menu
• AlliGator Menus
  • File Menu
  • Windows Menu
  • Analysis Menu
  • Scripts Menu
  • Calibration Menu
  • Settings Menu
  • Help Menu
• Alligator User Guide
  • 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 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
    • 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
      • 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
• 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
      • Destination
      • Plugin Flag
      • Input Parameters Definition
      • Output Value Type & Destination
    • Decay Graph example
  • AlliGator Python Plugins API v 0.1
    • 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
    • parameter types
  • Graph Object
    • Graph Object Anatomy
    • Plot Area
    • Plot Legend
    • Standard 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
  • System Requirements
  • Download the installer(s)
    • AlliGator Installer
    • LabVIEW and Vision Development Module RTE
    • Installation Instructions
    • AlliGator and LabVIEW Versions
    • HDF5 library installation
• Bibliography
• Acknowledgments
• AlliGator Support
  • How to report an issue

• Search Page