Embedded Files
Note: version numbers not followed by an asterisk have been released. All other versions are internal only and features described might not be available in subsequent released versions.
0.31 (2021-01-29)
Bug Fixes
Corrected a few bugs/cosmetic issues in HDF5 file loading
Corrected a bug in Time Series loading that prevented proper extraction of file name root in some special cases
Fixed "Phasor Plot Update Needed" flag erased by Settings Window
New Features
Support for HDF5 FLI dataset v 0.3
Handling of incomplete image gate series in HDF5 file
New experimental IRF deconvolution (undocumented in this version)
0.30 (2020-08-12)
New Features
Implemented compression of HDF5 FLI dataset
0.29 (2020-08-11)
New Features
Added Phasor Ratio Display Range slider to afford better control of the phasor ratio color map
Implemented Use UC/Axis of Inertia Intersections as References in the Phasor Plot
Added support for PicoQuant .bin files
0.28 (2020-08-03)
Bug Fixes
Support for rootless file name series (eg. 1.hdf5, 2.hdf5, etc.)
Phase Lifetime vs Intensity Scatterplot now rejecting pixels with NaN phase lifetime values
Minor bug fixes
Some code refactoring
New Features
Introduction of an Image Profile tool to visualize Intensity/Phase Lifetime and Phasor Ratio
Introduction of Phasor Harmonic Manager to handle harmonic data (currently only supporting 2-component Weber analysis)
Output of Calibration information to the Notebook (including X & Y Resolution) when computing a Phasor Plot
Display of Phasor Ratio/Amplitude at the mouse location in the Source Image/Phasor Plot
Update of Phasor Ratio References when the phasor harmonic is changed
Minor cosmetic changes
0.27 (2020-07-06)
Bug Fixes
Fixed bug preventing Histogram calculation in Graphs
Fixed a bug where the Phasor Plot analysis functions did not take into account the conditions used to compute the Phasor Plot (e.g. min intensity)
Fixed a bug of invisible Lifetime Graph tipstrip introduced in a recent release
Minor bug fixes
New Features
Added Phasor Plot ROI resizing with Shift-Click
Added Phasor Ratio color map display in Settings when interpolation is used
Added constant baseline subtraction method
Added Pixel-Normalize Decay option
Modified Histogram Fit to use weighted fits and better estimates of the SDV of multi-Gaussians models
Minor cosmetic changes
0.26 (2020-06-28)
Bug Fixes
Fixed bug preventing pixel intensity conditions from being used for Phasor Plot calculation
Cosmetic and minor bug fixes
New Features
Improves .set and RecSettings.txt decoding (LaVIsion dataset)
Added display of Phasor at Source Image pixel (in the Phasor Plot tab)
Support of stored ROI resizing/moving for the Phasor Plot (shift-click)
Added Phase Lifetime/Phasor Ratio Histogram and Phase Lifetime vs Pixel Intensity calculations in the Phasor Plot
Settings>>Phasor Plot now shows the color scale used when interpolation between the two references colors is used.
Minor cosmetic changes, including new layout of main menus
0.25 (2020-06-22)
Bug Fixes
Fixed non-functioning Playback and Loop scripts
Corrected a bug preventing decoding of LaVision .set metadata files
Minor bug fixes
New Features
Support for PicoQuant .ptu FLI datasets
Added a # Gates parameter in Settings>>Fluorescence Decays to define the number of bins to use for .ptu files
Added Right-Click menu for the Phasor Frequency controls to allow setting it to 1/T or n/T, where T is the laser period
Added Save Image Data as TIFF right-click option for Source and Phasor Images
Added Save Dataset as TIFF Series File menu item
Minor cosmetic (notably File menu) changes
0.24 (2020-06-12)
Bug Fixes
Fixed a bug preventing proper loading of Gate Image Folder
Fixed sticky Phasor Plot Reference in Phasor Plot
New Features
Added Phasor Plot ROI Manager Window mirroring the functionality of the Source Image ROI Manager Window
Added output of Phasor References to Notebook when choosing "Use Segment Extremities as References"
Added "Use UC/Segment Intersections as References" to Phasor Plot menu
Added "Show UC Ticks" in Phasor Plot and Phasor Graph Settings
Added UC tau ticks & labels to Phasor Plot and Phasor Graph
Minor cosmetic changes
0.23.1 (2020-05-19)
New Features
Added support for compressed B&H sdt files
Better formatting of complex data output in the Notebook
0.22 (2020-05-17)
Bug Fixes
Diverse inconsistencies in LED indicators have been fixed
Fixed Reset Settings to Default in Settings
Fixed Phasor Color Map Picker Save/Load menuÂ
New Features
Image Binning can now be used to bin a dataset when loading it
Phasor Frequency control added to the Phasor Plot tabs of AlliGator and Settings
0.21.1 (2020-05-11)
Bug Fixes
Fixed a bug preventing from exporting the Complex Phasor Data to file
0.21 (2020-05-10)
Bug Fixes
Avoid discontinuities in square-gated IRF fits
Corrected a bug resulting in gate image order scrambling and/or image mask creation failure
Plot Editor improvement
File: Fixed Open Folder not remembering the last opened folder
New Features
Paste ROI Description from Notebook (or elsewhere) to create a ROI
Decay Graph: IEEE square pulse analysis
Script: Square Pulse Characteristics Map
Import: SS1 Loading modified to account for older formats
Phasor Plot: now includes Full Decay Preprocessing
Phasor Plot: Parallelization to speed up processing
Phasor Plot: Added Phasor Ratio Reference mouse control
Phasor Plot: Added (m, phi), tau_phi and tau_m display
File/Phasor Plot: Export Complex Phasor Data menu item to export complex phasor matrix to csv file
Phasor Graph: extended right-click menu features for phasor ratio reference manipulation
File: Added support for uncompressed B&H .sdt FLIM datasets (and dataset series)
Cosmetic items
Changed calibration & reference status indicator
Removed Reload Dataset button to prevent confusion
Phasor Map Color Picker cosmetic fixes and improvements
0.20.4 (2019-11-26)
Bug Fixes
Corrected a bug in File Background Correction (leading to failure to correct background Max Image)
New Features:
Added Simple & Complex Plot Formula in Decay Graph
Added Background Scaling Factor parameter to adjust amount of background file to subtract
0.20.3 (2019-11-21)
Bug Fixes:
Fixed a second bug where the decay pre-processing order wasn't saved properly
Fixed a bug where the total intensity of a decay was not saved if no background subtraction operation was used
Corrected a bug in the Phasor Plot calculation in the absence of background correction
Skip Square Gated Background Correction if one of the parameters is invalid (extrema positions, gate duration, laser period)
Fixed new version download/installation
New Features:
Added Settings menu/modified menu layout
Implemented Tilted Square Gated IRF Fit (and corresponding Map script)
Changed Open Image Folder dialog behavior to show folder content and remember last open folder
Improved error handling when loading datasets
Added output to the Notebook of # Gates loaded
Improved ROI Grid creation speed
Additional information added to Dataset Information Window
SS1 File importing now out of beta
Made SS1 Laser Frequency dialog skippable
0.20.2 (2019-11-04)
Bug Fixes:
Fixed a bug where the decay pre-processing order wasn't saved properly
Fixed a bug where the total intensity of a decay was not saved if no background subtraction operation was used
0.20.1 (2019-10-23)
Bug Fixes:
Fixed output format of Square-Gated IRF Characteristics Map Script
Fixed AlliGator not closing upon quitting
0.20 (2019-10-05)
Bug Fixes:
Corrected the definition of the "Fixed High Background Threshold" (Settings>>Source Image) to refer to the Intensity Histogram mode instead of the maximum intensity value
Corrected formula for square-gated exponential decay amplitude in Background Correction
New Features:
Added "Phase Lifetime vs Fitted Lifetime", "Phase Lifetime vs Amplitude" menu items in Phasor Graph
Added Square-Gated IRF Fit model in Fluorescence Decay Graph
Added Plot Histogram to Phasor Ratio Graph (to study phasor ratio distributions when analyzing ROI series)
Added "Skip this Dialog" in the Create Phasor Plot Dialog Window
Added "Reset" button in Settings>>Miscellaneous to restore skipped dialog windows
Implemented Phasor Calibration Map in Phasor Plot
Added Color Scale indicator in Settings>>Phasor Plot to display the user-selected custom Phasor Ratio color scale
Minor cosmetic changes
0.19 (2019-09-15)
Bug Fixes:
If a HDF5 Dataset has already been pile-up corrected, it will not be corrected again even if the option has been checked in the Settings.
New Features:
Added user-defined decay pre-processing operations order
Background subtraction added to the pre-procesing operations list (allows performing it after other operations)
Unified SS2 HDF5 and AlliGator HDF5 dataset loading (no need to "import" SS2 datafiles)
0.18.2 (2019-09-13)
Bug Fixes
Corrected a bug which prevented plotting phasor graph series when one of the ROIs was invalid
Handled cases of duplicated ROIs when computing a phasor calibration map: duplicates are now removed before computing the map and do not result in an error.
New Features
Added "Rotate" option flag for decay shift
Added default shift decay option controlled by "shift" parameter (no longer equivalent to no shift)
Added Phasor Ratio Color Map option
Added option to remove out-of-bound values in the Plot Editor (to clean up data points before histogramming)
Decay pre-processing order changed from: Revert/Normalize/Smooth/Shit-Rotate/Extrapolate/Straighten to: Revert/Smooth/Straighten/Shift-Rotate/Extrapolate/Normalize
0.18.1 (2019-08-05)
Bug fix: invalid phasor calculation when no background correction was applied
0.18 (2019-06-19)
Bug Fixes:
Fixed Load Phasor Plot Data bug preventing from loading older file versions
Check for phasor plot adequation to be used as phasor calibration map
Does not automatically apply calibration anymore to the last plot when calibration (or type) is changed interactively
Fixed various Phasor Plot Overlay and Phasor Calibration issues
0.18 beta* (2019-06-03)
Bug Fixes
Corrected bug preventing cumulative phasor plot computation
Fixed a bug resulting in scrambled gate images after a few files with different number of gates are loaded
New Features
Handling of decays with min preceding max (for square gate background correction)
Messages added for decay processing
Added partial Settings export to Notebook
Added Background-subtracted Intensity to decay metadata (this is what is now returned instead of the amplitude, when using Phase Lifetime vs Bkgd-subtracted Intensity plot)
Added automatic style choice for histograms and fits
Added option to select 8-bit frames when importing SS2 dataset
Invert Plots Selection added to Lifetime Graph
Added right-click menus to Update Phasor Plot & Erase Overlay button to allow selecting which items are updated (and avoid unnecessary recomputation of the phasor plot)
Updated implementation of Image Brightness use for Phasor Overlay: the histogram cursor positions are now used, not the image min and max
Implemented it for Phasor Ratio and Phasor Color Map
Optimized Binned Phasor Plot calculation
Added Phasor Calibration Map Definition/Loading/Saving in Phasor Graph
Added Update/Clear Selected Plots Calibrations
Removed "Save Phasor Plot as..." and made it the default function of "Save Phasor Plot" on Phasor Graph (dialog always shows up)
Implemented Mouse Wheel and Alt-Rectangle Zoom on Source & Phasor Images
Implemented Phasor Calibration Maps (# Gates Series) Script
Implemented Calibrated Phasor Map Series Script
0.17.5 (2019-05-03)
Bug Fixes:
Handling of corner cases where a gate image contains a NaN
Corrected message output when saving single plot
Fixed exported color bar size glitch
Fixed Notebook close and open (keeps track of saved status and file path)
Various fixes in child windows (Histogram & Plot Editor)
New Features:
Minor changes to SS2 file import
Added "Show/Hide Tool Panel" Graph shortcut menu item
Added Phase lifetime vs Background Plot
Added Transpose Plot in Lifetime Graph
Added Delete/Insert Element in Plot Editor
0.17.4 (2019-04-04)
Bug Fixes:
Minor fixes
New Features:
Style changed to LabVIEW "Next Generation"
Added Low and High Percentile rejection criteria in Image Source Settings
Implemented faster (non-interactive) All ROI Analysis
0.17.3 (2019-03-22)
Bug Fixes:
Better graph legend clean-up
New Features:
"Straighten Decay" now accounts for background
Added "Straighten Decay" as a decay processing option in Settings
0.17.2 (2019-03-12)
Bug Fixes:
Fixed Histogram right-click menu
Fixed delayed histogram bin input
0.17.1 (2019-03-12)
New Features:
Added a Hide/Show Grid menu item for Graphs
Bug Fixes:
Restored missing right-click menus in a couple of Graphs
0.17 (2019-03-10)
New Features:
Plot Histogram function added to Intensity Time Trace and Lifetime Graph
Added support for HDF5 Dataset Series
Support for Playback of all types of Dataset Series
Graph Style change
Changed file format for phasor plots and ROIs to JSON (from XML) for speed up and size reduction
Added support for background HDF5 Dataset subtraction
Bug fixes:
Restored compatibility with v1 of Raw Phasor Plot Data file (XML)
Added ROI validity check before analysis
Corrected a bug resulting in a dialog when reloading HDF5 dataset
Corrected a bug preventing reloading of image folders
Fixed memory leak problem most noticeable when dealing with dataset series
0.16.2 (2019-03-01)
Fixed a bug preventing reloading a folder of images
Added busy animated icon for Phasor Plot calculation and ROI Highlighting
0.16.1 (2019-02-28)
Added support for SwissSPAD 2 Dataset Series
Added Verbose Error Mode option in Settings>>Miscellaneous for support and debugging purposes
Converted the "Recycle" button of the Image Source to "Reload Dataset"
Changed the icon of the "Clear Overlay" buttons on both Source Image and Phasor Plot (the latter operation now skips Phasor Plot recalculation, which is done using the other "Refresh Phasor Plot"Â button
Added Sum All Datasets in Series function (with an "Average Dataset Sum" option in Settings>>Source Image)
Open/Save HDF5Â Dataset functions added
Bug fixes and cosmetic changes
0.15.2 (2019-02-19)
Corrected a bug introduced in the Phasor Plot
Fixed a bug to render Notebook persistent
0.15.1 (2019-02-17)
Parallelism in Phasor Plot calculation
Added "Reload" menu item for all file formats (to apply gate specification changes)
Renamed "Decay Points to Skip" to "Gates to Skip"
Renamed "Revert Gates" to "Reverse Gates"
Added File Path to AlliGator Window Title for all files
Minor cosmetic changes and bug fixes
0.15 (2019-02-09)
Bug fixes and cosmetic changes
Added option to represent phase lifetime vs total intensity or background-subtracted intensity (Phasor Graph)
Settings: Moved "Laser Period" parameter to Fluorescence Decay tab and "Pseudo Phasor Add'l Parameters" to Phasor Graph tab
Removed Ctrl+C and Ctrl+Shift+C shortcuts to avoid conflict with the standard usage
Added Amplitude/Background/Lifetime parameter display in the Fluorescence Decay panel (from background subtraction, when relevant)
Added "Square Gated Single-Exponential" background subtraction method
Renamed "Compute Phase Lifetime Plot" into "Phase Lifetime Trajectory"
Added "Phase Lifetime vs Intensity Scatter Plot" menu item to Phasor Graph menu
Added Timing Information to Notebook for image folder
Added Active Graph/Plot flag to Settings
Added support for SS2 HDF5 File
Added option to save/load AlliGator Settings to file
Added Laser Period & Decay Offset to Settings>>Fluorescence Decay>>Basic Settings
Option to plot Pseudo UC in the Phasor Graph and Phasor Plot (beta feature)
Whole image phasor scatter plot activated
0.13 (2018-09-18)
Added Image subtraction as one of the background correction modes
Added Whole Image Phasor Scatter Plot Calculation
Added optional guess fit parameters for decay fitting
Added "Integration" mode for decay fitting of data obtained with large gates, in addition to the previous "Convolution" mode
Bug fixes and cosmetic changes
0.12 (2018-03-29)
Added pile-up correction option for Swiss SPAD data
Added ROI Grid tool
Added ROI to pixel ROIs tool
0.10.11 (2018-03-13)
Corrected a bug in Fluorescence Decay Statistics
Improved performance of Fluorescence Decay Statistics
0.10.10 (2018-03-11)
Color scale min and max color (Source Image and Phasor Plot Image) are updated upon clicking the color scale
PDF version of the manual (on the AlliGator Manual page)
Added "Revert Gates" option to handle SwissSPAD 2 data (beta)
Periodic Boundaries option (beta)
Beta version option in About window
Swiss SPAD data support (beta)
Minor bug and cosmetic fixes
0.10.9 (2018-02-21)
Color scale min and max color (Source Image and Phasor Plot Image) are updated upon clicking the color scale
Added "Revert Gates" option to handle Swiss SPAD 2 data (beta)
Added "Max Lifetime" parameter to be used in determining how far to compute the model decay (beta)
Implementation of periodic boundary convolution 1-Exp fit (beta)
Swiss SPAD 1 support (beta)
Added beta version option in About... window
minor bug and cosmetic fixes
0.10.8 (2018-02-10)
Added Plot Decay Shifts as an shortcut menu of Lifetimes Graph
Added support for PNG file type for gate images
Added option to not compute fit parameter uncertainties (for memory saving)
Added separate histogram for white light image contrast
Added ability to show overlay on white light image (and save the image)
Added Thresholded IRF function
Added export dataset information to Notebook right-click menu
Added Verbose Settings Mode option
Added Wavelet Analysis Options to Settings & Decay context menu
Added Decay Extrapolation to Settings & Decay context menu
Added IRF denoising to Decay Graph
Added Selected Plots Locking to either phasor ratio references
Added Optimal IRF Computation
Cosmetic changes
Added Use Cursor n as Reference n menu item
Implemented Optimal Calibration from Reference Pair
Implemented ROI modification
Added Plot Editor
Added keyboard shortcut option to New Plot dialog
Added All ROIs Analysis script
Allowed rearranging ROIs in ROI manager
Added choice of individual Fit Algorithm (or Best of All)
Output of Global Fit parameters to Lifetime Graph if requested (Displayed parameter list)
Added AlliGator Global Fit Status Window
Minor bug fixes and cosmetic improvements
0.9.13 (not released)
Minor bug fixes (including one which would not take into account the image threshold settings)
Phasor Ratio/Lifetime Plot now take the name of the source Phasor Plot
Added option to only show the last decay plot
Decay plot/fit/residuals colors can be set in Settings>>Fluorescence Decay>>Styles
Added plots of user selected decay fit parameters during Time Series Decay Fit Analysis
Handling of truncated decays (min amd max percentile approach)
Further improvements on lifetime fitting: added weighted fit option, parameter fit bounds, etc.
Addition of messages for a few more script actions
Added information output to Notebook (ROI used)
Added Save Phasor Graph Image Option
Added Cumulative Function extraction
Added Source Image ROI Manager
New Decay Plot's name is set to "Dataset Name: ROI Name"
Delete Selected Plots function added to all Graphs
Added Visible Items menu to all Graphs
Implemented Global Fit of Selected Decays
Option to export tabulated global fit results to file
Added Selected Plot Style Dialog
Abort option for Global Fits
Added Average of Selected Plots
Added Show Reference Decay/IRF
Decay Plot Saving/Loading
Added IRF Fit by a Gaussian-Exponential
Support of new LaVision file format
0.9.12 (2017-09-08)
Added Set/Copy Phasor Graph Cursor to/from Current Phasor
Added ROI Statistics menu to Source Image
Added Compute Average Plot Phasor
Added Baseline Subtraction Method
Implemented 1- or 2-Exp + IRF Convolution Fit (and Time-Series script)
Added option to turn off Image Histogram/Contrast and Phasor Plot to speed up analysis
Added Phasor (m, phi) control next to (g, s) version
Output of Phase Lifetime each time these values are updated
Allowed "transparent" color for ROI overlay on image or phasor plot
Cosmetic fixes to Settings window behavior
0.9.11 (2017-08-22)
Switched to LabVIEW 2017
Added High and Low Color for Source Image and Phasor Plot
Changed the way Image Source ROIs are stored and saved
Introduced some optimization
Set different file extensions for different types of XML files
Corrected a bug reporting wrong number of files in gate folders
0.9.10 (2017-05-17)
Corrected bug in Export Settings to Notebook
0.9.9 (2017-03-26)
Added option to compute amplitude ratio instead of phasor ratio (Phasor Graph)
Introduced Phasor Color Map Picker (Phasor Plot) and Phasor Color Map option (Source Image)
Introduced Intensity Time Trace Correction option (Intensity Time Trace)
Introduced Intensity Correction definition UI (Analysis menu)
Added Computation of Phase Lifetime Plot option (Settings>>Phasor Graph)
0.9.8 (2017-01-22)
Fixed a bug in decay background correction (min and max gate were not taken into account)
Search ROI now returns the barycenter of all the maxima as center
Corrected bug in Phasor Ratio plot linear fit
Added Reject High Decay Peak Pixel options
Minor bug fixes and cosmetic changes
0.9.7 (2017-01-13)
Decay Smoothing and Shifting
Recalibration of multiple phasor plots
Saving and Loading of phasor plots
Minor bug fixes and cosmetic changes
0.9.6 (2017-01-03)
Improved Threshold Analysis of decays
Improved Zero-Crossing Analysis of decays
Analysis of decays does not require to go through IRF extraction
Added Dataset Information Window
Added Normalize Decay option
Implemented cross-correlation decays shift analysis
corrected bug with hiding tipstrip
Optimized gate file loading
Show File Time Stamp below image (in time series)
Added fading Phasor Ratio Map option
File numbering doesn’t need to be justify-formatted anymore
Phasor Ratio Reference can be defined in the Phasor Plot and using a line ROI
0.9.5 (2016-12-14)
Added Source Image ROI handling options
Added option to save the Overlay as an 8-bit image
Introduced a Phasor Ratio Map Representation
Various bug fixes and cosmetic changes
0.9.4 (2016-12-01, updated 2016-12-08):
Introduced a separate Settings window, as well as saving of settings from one session to the next
Added Multiplot capabilities in most graphs to allow comparison between different samples, etc.
Added the ability to load a White Light Image and a ROI Mask Image
ROI selection and handling improvements
Added Tip strips for Plot Legends
Various bug fixes and cosmetic changed
0.9.3 (2016-10-29):
Added Slider in Phasor Graph panel to replay time series one step at a time
Phasor Calibration and Phasor Calibration Curve can now be saved an reloaded
ROIs can be saved and reloaded in both Source image and Phasor Plot image
Actual ROI center is displayed as an overlay on the Source image
Added option to display cumulative Phasor Plot
Changed location of Phasor Calibration menu items
Distinction between applying a single calibration or a curve calibration
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