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
  • System Requirements
  • Download the installer(s)
    • AlliGator Installer
    • LabVIEW and Vision Development Module RTE
    • Installation Instructions
    • AlliGator and LabVIEW Versions
    • HDF5 library installation
• AlliGator Version History
  • 0.86 (2024-04-11)
  • 0.85.1 (2024-04-04)
  • 0.85 (2024-03-31)
  • 0.84 (2024-03-08)
  • 0.83 (2024-02-27)
  • 0.82.1 (2024-02-14)
  • 0.82 (2024-02-07)
  • 0.81 (2024-02-03)
  • 0.80 (2024-01-16)
  • 0.79.2 (2024-01-05)
  • 0.79.1 (2024-01-04)
  • 0.79 (2024-01-04)
  • 0.78 (2023-12-22)
  • 0.77 (2023-12-16)
  • 0.76 (2023-12-03)
  • 0.75.2 (2023-11-26)
  • 0.75.1 (2023-11-22)
  • 0.75 (2023-11-19)
  • 0.74 (2023-11-12)
  • 0.73 (2023-09-18)
  • 0.72 (2023-08-10)
  • 0.71 (2023-06-26)
  • 0.70 (2023-05-30)
  • 0.69 (2023-04-17)
  • 0.68.1
  • 0.68 (2023-03-05)
  • 0.67 (2023-01-23)
  • 0.66 (2022-12-31)
  • 0.65 (2022-12-15)
  • 0.64 (2022-12-04)
  • 0.63 (2022-11-26)
  • 0.62.2 (2022-11-08)
  • 0.62.1 (2022-11-04)
  • 0.62 (2022-11-02)
  • 0.61 (2022-10-23)
  • 0.60.4 (2022-08-18)
  • 0.60.3 (2022-08-15)
  • 0.60.2 (2022-08-13)
  • 0.60.1 (2022-08-04)
  • 0.60 (2022-08-03)
  • 0.59 (2022-08-01)
  • 0.58 (2022-07-28)
  • 0.57 (2022-07-21)
  • 0.56.4 (2022-07-17)
  • 0.56.3 (2022-06-30)
  • 0.56.2 (2022-06-29)
  • 0.56.1 (2022-06-27)
  • 0.56 (2022-06-26)
  • 0.55 (2022-05-13)
  • 0.54 (2022-05-12)
  • 0.53.1 (2022-05-10)
  • 0.53 (2022-05-07)
  • 0.52 (2022-05-05)
  • 0.51 (2022-03-07)
  • 0.50 (2022-01-31)
  • 0.49 (2022-01-30)
  • 0.48.4 (2022-01-14)
  • 0.48.3 (2022-01-14)
  • 0.48.2 (2022-01-11)
  • 0.48.1 (2022-01-08)
  • 0.48 (2022-01-07)
  • 0.47 (2021-12-18)
  • 0.46 (2021-12-11)
  • 0.45.2 (2021-12-03)
  • 0.45.1 (2021-12-01)
  • 0.45 (2021-11-30)
  • 0.44.3 (2021-11-12)
  • 0.44.2 (2021-11-11)
  • 0.44.1 (2021-11-07)
  • 0.44 (2021-11-06)
  • 0.43 (2021-11-03)
  • 0.42.3 (2021-10-29)
  • 0.42.2 (2021-10-27)
  • 0.42.1 (2021-10-21)
  • 0.42 (2021-10-158)
  • 0.41 (2021-10-10)
  • 0.40.1 (2021-10-08)
  • 0.40 (2021-10-07)
  • 0.39.4 (2021-10-06)
  • 0.39.3 (2021-09-30)
  • 0.39.2 (2021-09-29)
  • 0.39.1 (2021-09-28)
  • 0.39 (2021-09-27)
  • 0.38.1 (2021-09-14)
  • 0.38 (2021-09-13)
  • 0.37 (2021-08-16)
  • 0.36 (2021-08-05)
  • 0.35 (2021-07-26)
  • 0.34.4 (2021-07-23)
  • 0.34.3 (2021-07-22)
  • 0.34.2 (2021-07-22)
  • 0.34.1 (2021-07-01)
  • 0.34 (2021-06-28)
  • 0.33.7 (2021-06-27)
  • 0.33.6 (2021-06-27)
  • 0.33.5 (2021-06-26)
  • 0.33.3 (2021-06-24)
  • 0.33.2 (2021-06-24)
  • 0.33 (2021-06-22)
  • 0.32 (2021-04-01)
  • 0.31 (2021-01-29)
  • 0.30 (2020-08-12)
  • 0.29 (2020-08-11)
  • 0.28 (2020-08-03)
  • 0.27 (2020-07-06)
  • 0.26 (2020-06-28)
  • 0.25 (2020-06-22)
  • 0.24 (2020-06-12)
  • 0.23.1 (2020-05-19)
  • 0.22 (2020-05-17)
  • 0.21.1 (2020-05-11)
  • 0.21 (2020-05-10)
  • 0.20.4 (2019-11-26)
  • 0.20.3 (2019-11-21)
  • 0.20.2 (2019-11-04)
  • 0.20.1 (2019-10-23)
  • 0.20 (2019-10-05)
  • 0.19 (2019-09-15)
  • 0.18.2 (2019-09-13)
  • 0.18.1 (2019-08-05)
  • 0.18 (2019-06-19)
  • 0.18 beta* (2019-06-03)
  • 0.17.5 (2019-05-03)
  • 0.17.4 (2019-04-04)
  • 0.17.3 (2019-03-22)
  • 0.17.2 (2019-03-12)
  • 0.17.1 (2019-03-12)
  • 0.17 (2019-03-10)
  • 0.16.2 (2019-03-01)
  • 0.16.1 (2019-02-28)
  • 0.15.2 (2019-02-19)
  • 0.15.1 (2019-02-17)
  • 0.15 (2019-02-09)
  • 0.13 (2018-09-18)
  • 0.12 (2018-03-29)
  • 0.10.11 (2018-03-13)
  • 0.10.10 (2018-03-11)
  • 0.10.9 (2018-02-21)
  • 0.10.8 (2018-02-10)
  • 0.9.13 (not released)
  • 0.9.12 (2017-09-08)
  • 0.9.11 (2017-08-22)
  • 0.9.10 (2017-05-17)
  • 0.9.9 (2017-03-26)
  • 0.9.8 (2017-01-22)
  • 0.9.7 (2017-01-13)
  • 0.9.6 (2017-01-03)
  • 0.9.5 (2016-12-14)
  • 0.9.4 (2016-12-01, updated 2016-12-08)
  • 0.9.3 (2016-10-29)
• Bibliography
• Acknowledgments
• AlliGator Support
  • How to report an issue

• Search Page