AlliGator Version History

Note: version numbers followed by an asterisk have not been released.

0.86 (2024-04-11)

• Bug Fixes

  • Fixed empty phasor added to Phasor Graph (when an invalid decay was generated)

  • Fixed occasional slow ROI Decay Analysis

  • Fixed default folder in “Save Phasor Ratio Reference(s)” dialog

  • Fixed Default Max Percentile in Fit Options to 0

• New Features

  • Refreshed icon

  • Added “Set Reference n to User-entered Lifetime” menu items to Phasor Graph & Phasor Plot

  • Added Delete ROIs based on Statistics option in the Source Image ROIs menu

  • Fixed and updated Image Auto-Contrast option

  • Added Lower and Upper Percentile Targets in the Image Histogram Panel

  • Changed default name of Multiple ROIs file to include the name of the dataset

0.85.1 (2024-04-04)

• Bug Fix

  • Fixed slow single-pixel ROI to Decay extraction, speeding up related pixel-based analyses

0.85 (2024-03-31)

• Bug Fixes

  • Fixed bug in Image Histogram busy icon

  • Fixed non-functional Intensity Time Trace computation when processing a Series

  • Fixed unresponsive “Use File Time Stamp” checkbox in Intensity Time Trace panel

  • Fixed bug that would not load a common background correction in a Series Sum calculation (only the first dataset in the series would be corrected)

  • Fixed bug that required the user to select the gate channel of all SS3 datasets in a series

  • Minor cosmetic fixes

• New Features

  • Added (Rotated) Rectangle Image Profile (aka “thick” line image profile)

0.84 (2024-03-08)

• Bug Fixes

  • Fixed behavior of “Use File Timestamp” in Intensity Time Trace panel and Settings

  • Fixed bug in transcription of date/time information for PI Imaging dataset in the Dataset

  • Fixed broken loading of .phplot files in Phasor Graph

0.83 (2024-02-27)

• Bug Fixes

  • Fixed broken Phasor Ratio Map Palette selection menu

  • Fixed bug that prevented highlighting phasor ROI in Source Image

  • Fixed broken loading of Image Folder without metadata (which would erase stored settings)

  • Fixed parsing of version history

  • Fixed bug in Gate Image Folder loading which would fail to load non-PI Imaging datasets

• New Features

  • Speed up of Source Image zoom responsiveness when an image overlay is applied

  • Added options to blend overlay color to background image in Source Image and Phasor Plot Settings panels

  • Added label style options to the Phasor Plot Settings tab

0.82.1 (2024-02-14)

• Bug Fix

  • Fixed bug in Gate Image Folder loading which would fail to load non-PI Imaging datasets

0.82 (2024-02-07)

• Bug Fixes

  • Fixed a bug with Mouse Move events in Image Display & Phasor Plot introduced in v0.81 which broke a number of UI functionalities

  • Fixed a bug that could set the wrong frequency for subsequent calculation when manually exporting a plot to the Phasor Graph

  • Improved responsivity to Image Histogram Cursor Move events

• New Features

  • Added “Shot Noise Influence on Average Lifetime” to the Analysis>>Tools menu

  • Deprecated “Simple Search” algorithm when using the Phasor Calibration Map option

  • Added Dialog allowing to use the frequency of the calibration phasor (or phasor map/phasor series) if it is different from the current phasor frequency

0.81 (2024-02-03)

• Bug Fixes

  • Fixed missing “Slope” metric plot and data in IRF extraction

  • Improved Mouse Move event handling in UI

• New Features

  • Added “Draw Reference Segment” checkbox in Settings>>Phasor Plot

  • Added “Dataset Scaling Factor” to Settings>>Data Information

  • Added workaround to the bit padding implemented in SPAD512 software

  • Skipping “Gate Steps” parameter in PI Imaging PNG metadata, as it is erroneous in version 1.43 and prior

0.80 (2024-01-16)

• Bug Fixes

  • Fixed bug whereby when opening a child window, clicking into the Image panel would result in a black background

  • Fixed unresponsive “Check for update” menu item

  • Fixed plot transposition when computing Parameter 2 vs Parameter 1 in Phasor Graph

  • Fixed bug in Sum All FLI Datasets in Series preventing some sums to be computed

  • Fixed Notebook reopening with the default Notebook name even when saved (and sometimes with empty content)

• New Features

  • upgraded to v 2.15.0.149 of h5labview2 library (which should in principle dispense from having to install the HDF5 library separately)

  • AlliGator user event handling refactoring to reduce lag following Mouse Move events

  • Added Load .bin FLI Dataset & Dataset Series (Piccolo) to File menu

  • Renaming of File loading menu item for clarification

  • Changed menu location of Multi-ROI Single-Pixel scripts, now located in the Analysis menu

  • Added ROI description in Time Series Analysis Notebook output if the ROI is not one of the stored ones

  • Added progress bar when file loading

0.79.2 (2024-01-05)

• Bug Fixes

  • Fixed “forgotten” calibration when refreshing the Phasor Plot

  • Fixed mix-up between two SDV options in Multiple ROI Phasor Analysis (fast, non-interactive)

  • Fixed a bug that would return an error when using 1/D as the phasor frequency to use when exporting a decay’s phasor to the Phasor Graph

  • Fixed “Export JSON string to Clipboard” in Settings>> Phasor Frequency controls.

0.79.1 (2024-01-04)

• Bug Fixes

  • Fixed bug in calculation of calibrated phasor when SDV calculation option is checked [Analysis>>FLI Dataset>>Multiple ROIs>>Phasor Analysis (fast,non-interactive)]

  • Fixed bug in calculation of calibrated phasor when Use Estimated Average Phasor option is checked [Analysis>>FLI Dataset>>Multiple ROIs>>Phasor Analysis (fast,non-interactive)]

0.79 (2024-01-04)

• Bug Fixes

  • Fixed downloading and installing of new version

  • Fixed truncation of Folder Name when dealing with Gate Image folder

  • Fixed bogus message when loading a new file with the same background subtraction parameters as the previous one

  • Fixed sluggish Phasor Plot Reference user-controlled motion

  • Fixed long “Highlight Image ROI in Phasor Plot” step when loading new dataset and a full-frame ROI is drawn

  • Phasor Ratio Color Scale is now updated according to “Color Map Type”

  • Fixed erroneous display of Average Lifetime range in Settings>>Phasor Plot

  • Fixed Phasor Ratio/Average Lifetime overlay responsiveness

  • Fixed missing internal update of Phasor Ratio/Average Lifetime Display Range parameter

  • Fixed long-standing bug in Phasor Graph where the internal state wasn’t updated properly when one or more plots were deleted from the graph (clearing the graph was behaving as expected)

• New Features

  • Added “Transpose Plot”, “Merge Selected Plots”, “Plot Histogram” to Decay Graph

  • Added support for “Date taken” and “Time taken” of SPAD512^2 files

  • Added support for Background Series

  • Added dialog to remind the user that references are needed to compute a phasor ratio or average lifetime overlay

  • Added “Close” sub-menu to the File menu (e.g. Closing a Dataset Series before switching to an individual dataset is recommended to avoid future data confusion)

0.78 (2023-12-22)

• Bug Fixes

  • Fixed typos in GUI

  • Fixed bug in Fit Parameters Options which ignored the “Numerically Estimated” option unless the array of Guess Parameters was empty

  • Fixed bug in pixel-to-pixel phasor map calibration

  • Fixed bug preventing loading old phasor calibrations and phasor calbration maps

  • Fixed bug that would prevent reloading of dataset when the background dataset type is different from that of the dataset type (e.g. HDF5 vs Gate Folder)

• New Features

  • Added “Move Flattened Series to Folder Series” menu item in File>>Load>>FLI Dataset Series menu (to deal with SPAD512 flattened output)

  • Moved Analysis>>FLI Dataset>>Multiple ROI Analysis>>Multi-ROI Single-Pixel NLSF and Phasor Analysis to Scripts menu

  • Removed “Pixel-to-Pixel” calibration option (now automatically applied when a full image calibration map is stored)

0.77 (2023-12-16)

• Bug Fixes

  • Fixed online version check (no message if installed version is the same as latest release)

  • Fixed bug where deactivating Phasor Calibration Map did not result in a Phasor Plot update

  • Fixed missing shortcut menu items in Source Image ROI Manager

  • Fixed Complementary ROI calculation

• New Features

  • Added “Use Estimated Average Phasor” checkbox as part of the phasor standard deviation option in Settings:Phasor Graph

  • Added “Pixel-to-Pixel” Phasor Map Calibration for significant speed up in cases where the Calibration Map is computed for all pixels in the dataset

  • Implementation of parameter SDVs in “Export Phasor Plot Add’l Data” in Phasor Graph

  • Added support for greyscale RGB images

  • Changed ROI connectivity to 4 in ROI Mask to ROI conversion

  • Support for amplitude- or intensity-averaged lifetime output in FLI Dataset Series>>Series Phasor Analysis

  • Support for Phasor Ratio and Averaged Lifetime SDV in FLI Dataset Series>>Series Phasor Analysis

  • Consolidated “All ROIs NLSF Analysis>>Non-Interactive (Fast, Common IRF)” and “… (Fast, Individual IRF)” menu items, the option being set by the “Settings>>Fluorescence Decay>>Fit Options>>Use Local IRF” parameter

0.76 (2023-12-03)

• Bug Fixes

  • Change to Phasor Calibration Options, Gate Name, Gate Arithmetic, etc. now flags Phasor Plot for update

  • Fixed Harmonic Frequency context menu in Settings:SEPL panel

  • Fixed bug in Amplitude Phasor Ratio SDV calculation

  • Set # processors used during initialization

• New Features

  • Local Decay Graph window now displays decay for any kind of ROI (not just single-pixel ROI)

  • Deprecated Source Image:Average Dataset Sum, Source Image:Use Phasor Plot Binning settings

  • Shortened list of information sent to the Notebook in verbose mode when a new Phasor Plot is calculated

  • Added “Parameter 2 vs Parameter 1 Scatter Plot” in Phasor Graph

  • Removed “Phase Lifetime Trajectory” as being superseded by “Parameter 2 vs Parameter 1 Scatter Plot”

  • Removed “Phase Lifetime vs Parameter” scatter plot sub-menu as being superseded by “Parameter 2 vs Parameter 1 Scatter Plot”

  • Added “Use Estimated Average Phasor” checkbox as part of the phasor standard deviation option in Settings:Phasor Graph

0.75.2 (2023-11-26)

• Bug Fixes

  • Fixed update of Fit Options:Laser Period when loading a new file and Use Data Information Laser Period = TRUE

  • Fixed last version detection

0.75.1 (2023-11-22)

• Bug Fixes

  • Fixed “Use Data Information Laser Period” not updating the laser period used for fitting

• New Features

  • Changed approach to compute offset error estimation: now computed at “optimal” Chi^2 obtained by parabolic estimation, while the actual returned offset parameter is that of the best fit.

0.75 (2023-11-19)

• Bug Fixes

  • Amplitude- or Intensity-averaged lifetime shown on Phasor Graph now matches that displayed in the Notebook (when the phasor SDV option is not selected, it is the value computed from the actual decay, while when that option is selected, it is the average of all replicas)

  • Fixed a bug in “All ROIs NLSF Analysis>>Non-Interactive (Fast, Individual IRF)” that resulted in incorrect fit results

• New Features

  • Output of both amplitude- & intensity-averaged lifetime and phasor ratio in average phasor calculation (Phasor Graph right-click menu)

  • Support for “Polygon” ROI Image Profile (the ROIs created via “Create ROIs with Intensity above Min” are Polygons)

  • Deprecation of “second pass” attempt to improve fit in “All ROIs NLSF Analysis>>Non-Interactive (Fast, Individual IRF)”

0.74 (2023-11-12)

• Bug Fixes

  • Fixed “Load/Save Reference(s)” menu item in Phasor Plot

  • Locked panel splitters

  • Fixed new version check

  • Fixed SEPL parameter updates in Settings

  • Fixed missing gate exposure, duration and integration time information in saved HDF5 FLI dataset

  • Fixed missing Settings>>Data Information>>Gate Separation update

  • Removed “Interpolate Plot” (not functional)

• New Features

  • Added Option in Decay Graph to Export a plot’s phasor using the natural frequency 1/D

  • Added option to ignore differences in phasor frequencies in Phasor Graph >> Phasor Multiplication

  • Changed Phasor Plot calculation message to optional (only visible when “Verbose Mode” is on)

  • Set new Default Cursor Style to a more contrasted one

  • Added “Pair Selected Plots” menu item in Lifetime & Other Parameters graph to combine the Y axes of two plots into a single Y2 vs Y1 plot

  • Added option to enforce that the laser period used in fitting is identical to that of the Data Information

  • Added IRF Deconvolution option to use the IRF tail slope as selection criterion

  • Replaced outliers by zero in deconvolved IRFs

  • Simplified Image Histogram Options (default: 256 bins)

  • Added “Process Single Plot/Selected Plots/All Plots” option in Decay Graph

  • Implemented Multiple Plot processing for: 1-normalization, [0-1]-normalization, rebin, cumulative function, denoise, extrapolate, fold, shift, smoothen, smoothen tail, straighten

  • Rearranged/renamed Decay Graph shortcut menu

  • Implemented calculation of Phasor SDV, Phase & Modulus Lifetime SDV, Phasor Ratio SDV, Amplitude- & Intensity-Averaged Lifetime SDV

  • Added indicators for the derived quantities in the Phasor Graph panel

  • Added “Convert (All) ROI(s) to Mask Image” menu item to Source Image

  • Added support for PI Imaging PNG Metadata information

0.73 (2023-09-18)

• Bug Fixes

  • Fixed a bug in High Count Image Pixel Rejection which would reject all pixels when the “Reject High Count Puxels” option was selected

  • Updates Decay Fit Parameters Map when fit is completed

  • Fixed Dataset Image update when loading new file

  • Fixed bug using different source for Laser Period parameter in NLSF fit and fit display

• New Features

  • Added dialog during background subtraction, to allow using files datasets with different properties (e.g. laser period)

  • Now loading SSX Detector Information from HDF5 and adding it to the metadata

  • Added Compute & Plot All ROIs Statistic

  • Implemented plot of Decay Fit Parameter vs Intensity

  • Changed Settings>>Fluorescence Decay>>Fit Parameters>>Guess Parameter Options to drop-down list instead of series of checkboxes

  • Added Min of All Gates displayed image option

  • Added Decay Preprocessing Options & Reference Decay in the data saved with a Fit Parameter Map file

  • Implemented “Merge Selected Plots” and “Sliced Mean & SDV Plots” in Lifetime & Other Parameters Graph

  • Deprecated Fit Status Window (for performance improvements)

  • Added shortcut menu “Use Data Information >> Laser Period” in Fit Options

0.72 (2023-08-10)

• Bug Fixes

  • Fixed bug in histogram option preventing IRF square gate fits to work

  • Fixed bugs in ROI Statistics which would fail when encountering Inf or NaN or Negative values

  • Fixed bug in faster Hot Pixel Removal code

  • Fixed Hot Pixel Removal options Notebook message

  • Fixed truncated accumulated file name when the folder name contained a period

  • Prevented multiline input in Settings>>Plugins>>Python Version

• New Features

  • Added “Save Image as Hot Pixel Mask” to Source Image context menu

  • Added “Use Hot Pixel Mask” and “Hot Pixel Mask Image” to Settings>Source Image Hot Pixel Removal Options

  • Processing of border of images when removing hot pixels

  • Reordered FLI Dataset Series actions

  • Changed “# Bins” Image Histogram single option to full-fledged “Image Histogram Options”

  • Changed “INT-normalized” Channel Arithmetic to G2/INT*<INT>

  • Removed useless Channel Arithmetic Combinations and added (1-G2/INT)*<INT>

  • Added Auto-Adjust Contrast to saved Settings

  • Minor updates to Decay Graph context menu

  • Added “Mask Image” menu item to File>>Save menu

  • Changed menu items from “Open” to “Load”

0.71 (2023-06-26)

• Bug Fixes

  • Removed duplicate vertices in Freehand Tool ROIs

  • Fixed cosmetic glitch in Phasor Plot display of local phasor information

  • Fixed Histogram update when changing Gate Slider position

  • Fixed bug in Histogram calculation when the first array element is NaN or Inf

  • Fixed glitch in Gate Selection Dialog which sometimes opened with a “-1” selection

  • Fixed bug improperly applying pile-up correction to Background Dataset

  • Fixed bug that would overwrite Gate Selection when using background correction

  • Skip Gate Selection Dialog when a single gate type is available

• New Features

  • Added Average Lifetime Profile to Image Profile Window Plots (when the Average Lifetime is selected as Overlay Type in the Settings>>Phasor Plot panel)

  • Added “ROI Description Max Characters” to Settings>>Miscellaneous

  • Added support of Drag & Drop loading of Phasor Ratio References

  • Added “Auto-Adjust Contrast” option in Image Histogram panel

  • Optimized noise level in Extrapolate Decay (only applies to decays that are not normalized)

  • Added “Overlay Analyzed ROI Center” option in Settings->Source Image (Default: False)

  • Changed Phasor Plot Destination (in Phasor Algebra tools) to enum (from 3-radio buttons control)

  • Added Save dual-channel FLI Dataset to HDF5

  • Added support for Dataset Channel switch without Dataset Reloading (when Channel Arithmetic = None)

0.70 (2023-05-30)

• Bug Fixes

  • Support for Multi-ROIs Single-Pixel NLSF Fits with common IRF (handles parameters map properly although it only contains one IRF)

  • Added working option to specify a User-Defined separator inLoad Plot(s) Dialog

  • Fixed bug in Load Plot(s) dialog which would not show the abscissa options on first call

  • Fixed bug in Settings which used stale values of Decay Shift Parameters

  • Fixed round-off error preventing a zero offset to be reached when letting the offset parameter float

  • Fixed NaN parameter uncertainty when one of the parameter gradients equals 0

  • Fixed Local Decay Window not quitting properly when AlliGator closes

• New Features

  • Added Decay Graph “Plot Convolution” menu item

  • Clean-up and refactoring of convolution code (using FFT)

  • Minor edits to Phasor Math Dialog Window

  • Modified Sequence of actions in Decay Fit (important change!)

  • Implemented Fixed Parameters Multi-Exponential Decay Fit (vs “constrained in 0-size interval”)

  • Implemental Analytical Computation of Partial Derivatives for NLSF Fit

  • Added optional “Use Legacy Fitting Approach” in Settings>>Decay Analysis>>Fit Options

  • Switched to fitting the square root of lifetimes to enforce positivity

  • Implemented new fitted offset approach (parallelized and uncertainty estimate)

  • Changed criterion for selection of “Best of All” Fits to max R^2 instead of min Chi^2 (since the Chi^2 is computed without weights for an unweighted fit)

  • Added parallelism in some multiROI scripts

  • Changed Default Fit Options Parameters to lower values to improve convergence and fit speed

  • Reverted GUI Layout to v0.67

0.69 (2023-04-17)

• Bug Fixes

  • Corrected bug in 1D Histogram that affected Image Histogram (among other things)

  • Fixed AlliGator sluggishness

  • Fixed a bug that prevented loaded Plots from being fitted unless a script had been run

  • Fixed a bug in Multiplot loading when each plot is comprised of two axes (no common axis)

  • Fixed a bug making submenu items inactive in Decay Fit Parameters Map

  • Fixed a bug preventing Gate Image Series Analysis (Fitting & Phasor)

  • Fixed Drag & Drop of Plots into the Lifetime & Other Parameters Graph

  • Fixed mangled Notebook output for IRF Deconvolution

  • Associate correct axes to Parameter Plots in Lifetime & Other Parameters Graph

• New Features

  • Improved Phasor Plot decorations (ticks, labels and references ROI)

  • Added busy icon for additional tasks

  • Added Source Image Overlays as option to the Erase button in Phasor Plot

  • Modifications to support SwissSPAD Live File version 0.7

  • Added support for Mask Images comprised of 0 and 255 only

  • Added Multiplot Math item in the Plot Math submenu of the Decay Graph

  • Added Background Correction & Gate Arithmetic to Dataset Series Sum

  • Using a transparent color for Phasor ROI/Image ROI highlight erases the corresponding highlight

  • Added IRF Deconvolution Metrics option in Settings

  • Restored Series Phasor Analysis menu item

  • Added Notebook message when single image is processed (Mask or White Light)

  • Added optional White Light Image background subtraction

  • Check that a ROI is selected before starting a Series analysis

  • Grayed out Global Fit of Selected Plots in Decay Graph

  • Added display of phasor information when moving reference in Phasor Plot

0.68.1

• Bug Fixes

  • Loading ROIs(s) by drag & drop now returns a Notebook message

  • Fixed Send All Settings to Notebook

• New Features

  • Added warning message in Multiple ROIs Multi-Pixel script dialog to remind the user to define Settings for the Dataset (and/or IRF)

  • Speed up of Phasor Plot calibration by Phasor Calibration Map in the Phasor Graph

0.68 (2023-03-05)

• Bug Fixes

  • Fixed error returned if an image folder is missing a metadata file: no returns a warning only

  • Fixed missing progress bar in Multiple ROIs Analysis>>All ROIs Decay Fit Non-Interactive (Fast)

  • Fixed erroneous update of internal variables when a decay is invalid

  • Fixed generation of empty plot, bogus phasor, etc. when a decay is invalid (i.e. empty)

  • Corrected typos in Notebook messages

  • Fixed bug erasing gate parameters when loading Gate Folder without metadata file

  • Fixed bug in Image Histogram that would slow down calculation for large images

  • Fixed a bug in ROI to individual pixel ROI conversion (skipped when the ROI is not a closed shape)

  • Fixed a bug preventing output of Settings to the Notebook

  • Fixed a bug in Phasor Calibration that would compute abs(g) instead of g

  • Fixed a bug that would erase all overlays each time the Source Image was updated

• New Features

  • Added Phasor Graph output message

  • Added Bin Number option in Histogram options (Settings>>Miscellaneous)

  • Moved ‘Compute Optimal Calibration from Phasor References’ Phasor Graph menu item

  • Changed Phasor Calibration Type ‘No’ to ‘None’

  • Implemented Phasor Graph Algebra GUI

  • Simplified internal computation of calibration

  • Minor improvements to calibration map handling

  • AlliGator Calibration menu checkmark validation at startup

  • Added option to display Phasor Calibration Map ROI Centers on Source Image (Calibration>>Show Phasor Calibration Map ROI Centers)

  • Faster Phasor Plot calibration

  • Added Phasor Plot Calibration Algorithm option: “Simple Search” or “Min Distance”

  • Better support of “Backup Calibration Option” to enable combining “Simple Search” Map Calibration for the calibrated ROI(s) and “Single Calibration” for the remainder of the image

  • Cosmetic changes to AlliGator main window

  • Improved Notebook message when loading calibration and after Phasor Plot calculation

  • Added option to not store the Phasor Harmonics computed for each Phasor Plot

0.67 (2023-01-23)

• Bug Fixes

  • Fixed Phasor Plot error thrown when no Phasor Ratio References are defined

  • Fixed unresponsive “FLI Dataset Series” menu items

  • Fixed bug preventing from deleting a Phasor Plot in the Phasor Graph

  • Fixed a bug preventing highlighting Image Source ROIs in the Phasor Plot

• New Features

  • Removed requirement of providing a dummy plot in Decay Graph Python Plugin if no plot is output

  • Correspondingly, removed the requirement of an input parameters and/or output parameters section, if no such parameters is passed (for instance if the function’s output is simply a string output to the Notebook, or a file, etc.)

  • Supports sending plots to other graphs than the Decay Graph (except the Phasor Graph)

  • Changed example Python Plugins script file names to XXX_Example.py to make it clear they are only examples

  • Added option to precede a Python Plugin idem menu by a separator, by starting the function’s name with an underscore

  • Better error reporting for Python Plugins

  • Added “Process Multiple Plots” submenu to Decay Graph as a Python Script. First function: Linear Combination (Selected Plots).

  • Added Abort button and Progress Bar during FLI Dataset saving

  • Improved Notebook message after FLI Dataset saving

  • Made AlliGator window resizeable to allow larger Source Image display

  • Added New Decay plot message

  • Drag & Drop of files (or folder of images) still works but the target is now the Source Image (not any random location in the main AlliGator window). This works for both FLI Datasets (or Dataset Series) and plots, ROIs, phasor plots, calibration, etc. All should be dragged and dropped in the Source Image. AlliGator will figure out what type of file they are and dump them in the appropriate object.

0.66 (2022-12-31)

• Bug Fixes

  • Fixed a bug in Python Plugins.zipped archive preventing from updating outdated Plugins

• New Features

  • Added Compute Average Lifetime to Decay Graph>>Process Plot menu

  • Added Average Lifetime Options to Settings>>Fluorescence Decay>>Advanced Decay Analysis

  • Added Positive constraint on extracted IRF, by replacing negative values Y by a normally distributed values in N(0,abs(Y)/3)

  • Added option to use a smoothed metrics for Optimal IRF Extraction

  • Added corresponding Savitzky-Golay parameters in Settings (Number of Side Points, Polynomial Order)

  • Added “Create Complementary ROI” function in the Source Image>>ROIs context menu

  • Added “[0-1]-Normalize Decay” option in Settings>>Fluorescence Decay>>Decay Pre-Processing and as a function in Decay Graph>>Process Plot context menu

  • Added “All ROIs Average Lifetimes” to FLI Dataset menu

0.65 (2022-12-15)

• Bug Fixes

  • Syntax error in Python Plugin doesn’t crash Python session anymore (a LabVIEW bug)

• New Features

  • Improved Error and Warning reporting for Python Plugins

  • The demo Python Plugins coming with a new version are not reinstalled after the first run, allowing the user to remove them

0.64 (2022-12-04)

• Bug Fixes

  • Unknown error in Python is now followed by an automatic reset of the Python session

  • Fixed issues with passing String or Path parameter to Python Plugin

• New Features

  • Support for Python Plugin in Analysis>>Decay Graph and Analysis>>Source Image menus

  • Support for Python plugin user-input parameter description

  • New installation does not overwrite Python Plugin files if they are newer than the version provided with the installer (kept in the data folder as a zip archive)

0.63 (2022-11-26)

• Bug Fixes

  • Fixed bug in ROI Manager which showed a warning when the selected ROI ID > 10,000 (should only occur if ‘Show All ROIs’ is selected)

  • Check the Clipboard content before trying to paste it in the Plot Editor

• New Features (Python Plugins API)

  • A script’s target is defined in the script itself, not by the location of the script in a folder hierarchy (the latter is now ignored to give more freedom to users).

  • Implemented modified version of Python plugin interface using named tuples to pass core data in and out of Decay Graph plugins

  • Implemented additional returned dictionary to pass additional information back to AlliGator (including updates of AlliGator parameters)

  • Added “Python Plugins” button in Settings>>Plugins to open the Plugins folder

  • Changed installation directory to C:UsersUserNameAppDataLocal in order to not require Administrator rights to install AlliGator or to modify files in the Python Plugins folders

  • Added support for insertion of plugins in window menus and object menus, with one insertion point max per location

  • Added alligator.py type definition file

  • Changed Python plugin syntax to use ### for all lines intended for AlliGator decoding

  • Modified Output section to be similar to the Input section

• Other New Features

  • Removed Ctrl+V shortcut to paste the Clipboard in Plot Editor

  • Added 256 characters limit to ROI description output to Notebook (inactive in verbose mode)

  • Removed separate shortcut Ctrl+Shift+R for “Reload FLI Dataset Series” and used it instead to open the Image ROI Manager

0.62.2 (2022-11-08)

• Minor Improvement

  • Improved Background Subtraction File compatibility and better warning dialog

0.62.1 (2022-11-04)

• New Features

  • Reverted to Toeplitz Matrix inversion method for deconvolution

  • Added IRF Optimization parameters to Notebook output

  • Changed IRF Optimization range parameter to ns instead of fraction of range center

0.62 (2022-11-02)

• Bug Fixes

  • Fixed bug in Extrapolate Decay (failed when large vertical offset was present)

  • Fixed bug where Plot Extrapolation failed for a normalized decay

  • Fixed display glitch in Settings >> Gates to Keep

• New Features:

  • Added Export Plot and Data options in IRF Extraction parameters

  • Improved Optimal IRF extraction criteria

  • Changed display of Python plugin scripts and functions in menus by replacing all underscore characters by spaces

  • Changed the way a plot is passed to a Python plugin: instead of two 1D-arrays, a single 2 x N array is used

  • Added support for Python plugins acting on FLI Dataset (Analysis>>FLI Dataset menu)

0.61 (2022-10-23)

• Bug Fixes

  • Fixed a bug that added a carriage return in the name of extrapolated decay plots (which prevented saved plots to be properly loaded)

  • No Notebook message is output if plot rebinning cancelled

  • Fixed a few Notebook output formatting issues

  • Fixed error returned when a series of HDF5 dataset missing individual timestamps was selected

  • Fixed Files->Load menu bugs (menu items were not active)

  • Removed a number of error messages returned when the user cancels a file selection

  • Fixed a glitch in the dialog for Multi-ROI single Pixle analysis scripts

• New Features

  • Source Image Settings: Added option to remove hot pixels when loading SSx datasets

  • Decay Graph: Edited menus (Decay -> Plot)

  • Decay Graph: Better plot names and support for imported files without abscissa column

  • Decay Graph: Added “Rebin Plot” menu item

  • Decay Graph: Modified algorithm to extract IRF from decay with known lifetime, and added automatic smoothing and removal of outliers at the beginning of the IRF

  • Fluorescence Decay Settings>>Advanced Analysis: Added new IRF extraction options

  • Added average lifetime information for 2-Exp fit in Notebook output

0.60.4 (2022-08-18)

• Bug Fixes

  • Fixed “Save All/Selected Phasor Plots” Phasor Graph menu items

  • Fixed bug preventing Single Phasor Calibration Load/Save/Clear menu items to work

  • Fixed bug preventing from loading Single Phasor Calibration or Phasor Calibration Series if the frequency was identical to the current one (should be the opposite. Worked fine for Calibration Map)

  • Fixed issue with Series Phasor Analysis missing corresponding metadata

0.60.3 (2022-08-15)

• Bug Fixes

  • Restored “Export Add’l Phasor Plots Data (ASCII)” menu of Phasor Graph

• New Features

  • Grouped basic phasor plot save functions under “Save Plots (ASCII)” sub-menu

  • Grouped phasor plot save functions under “Save Phasor Plots (.phplot)” sub-menu

0.60.2 (2022-08-13)

• Bug Fixes

  • Fixed display glitches in Multi-ROIs Single-Pixel Analysis dialog window

  • Speed up of Phasor Information Display in Phasor Plot when shift-hovering over the Source Image with the mouse

• New Features

  • Replaced “Phasor Ratio Calculation” checkbox by “Phasor Ratio Type” radio buttons: Intensity-weighted or Amplitude-weighted

0.60.1 (2022-08-04)

• Bug Fixes

  • Fixed bug that would not display the newly added file in the Batch Export Window

0.60 (2022-08-03)

• Bug Fixes

  • Fixed bug in Image Python Plugin handling of output image

  • Fixed error generated when loading single TIFF Images of different size in succession

  • Fixed bug in Image Type selection (which would allow selecting a non-existing image)

  • Removed the (bogus) ability to drop an ASCII plot in the Phasor Graph. Only phplot files (Phasor Plot Data) can be imported in the Phasor Graph

  • Removed bogus Lifetime plot created when performing Data Series Phasor Analysis

  • Fixed bug that would erase the last Phase Lifetime plot when performing a new Data Series Phasor analysis

• New Features

  • Modified Mask Image to ROIs to allow handling binary images (as was the case up to now) as well as “labeled” mask images

  • Removed “Export Phasor Graph Data” menu items (they were equivalent to “Save Phasor Plot” items, now renamed “Save Phasor Plot Data”) to disambiguate them from the standard ASCII plot menu items (“Save Plot(s)”).

  • Added option to use the current phasor calibration/IRF(s) for Multi-ROI Single-Pixel Phasor or NLSF Analysis script

0.59 (2022-08-01)

• Bug Fixes

  • Fixed bug generated when loading single TIFF Images of different size in succession

  • Fixed Sticky Help Ballon in Batch Export Window

• New Features

  • Added support for 16-bit Mask Image

  • Modified Mask Image to ROIs to allow handling binary images (as up to now) as well as labeled mask images

  • Added “Paste Plot(s) from Clipboard” in Decay Graph and other Graphs

0.58 (2022-07-28)

• Bug Fixes

  • Added missing “SYNC Period” in exported HDF5 files

• New Features

  • Added (optional) Help Balloon in Batch Export Window

  • Implementation of Multiframe loading and batch exporting (ptu files)

  • Added “Dataset Timestamp” field in AlliGator HDF5 File format v0.6.1

  • Added warning dialog when requesting to “Show All ROIs” when N > 10,000

  • Optimization of ROI to Pixel ROIs action

0.57 (2022-07-21)

• Bug Fixes

  • Fixed bug in Phasor Graph->Export Phasor Plot(s) Data, which would not output the full header line

  • Fixed initialization of “Gates to Use” parameter in Settings->Data Information

  • Fixed “jumping” scrollbar in Notebook

  • Fixed disappearing selection when using context menu in Notebook

• New Features

  • Code refactoring for loading/closing speed up

  • Added font size options in Notebook

0.56.4 (2022-07-17)

• Bug Fixes

  • Fixed display of calibrated L_N[W] SEPL

  • Fixed bug in loading “Gate Separation” for Becker & Hickl .std files

  • Fixed a bug in “Skip Gate” file loading options, which was swapping “start” and “end” values

0.56.3 (2022-06-30)

• Bug Fixes

  • Deprecated “Whole Image Phasor Scatter Plot” in Analysis->Phasor Graph, as it is now done by selecting a ROI encompassing the whole image and converting it to single-pixel ROIs, followed by Analysis->Dataset->Multiple ROIs Analysis->All ROIs Phasor Analysis->Non-Interactive (Fast) [Ctrl+Shift+A]

0.56.2 (2022-06-29)

• Bug Fixes

  • Fixed a bug preventing updating the SEPL harmonic frequency

• New Features

  • Added context menu item to SEPL:Harmonic Frequency to set it to the Dataset Phasor Frequency

  • Default IRF period is now 12.5 ns (used to be 0, resulting in no SEPL being plotted for anything but the UC option)

0.56.1 (2022-06-27)

• Bug Fixes

  • Fixed a bug which would not properly update the Reference Lifetime Indicators in the Phasor Graph panel

• New Features

  • Updated “# Gates” parameter description to explain that it is ignored in most cases

0.56 (2022-06-26)

• Bug Fixes

  • Fixed bug in Sum of Datasets

  • Fixed bug related to gate arithmetic in case of single gate datasets

  • Fixed bug in Gate Name storage after user selection dialog

  • Fixed bogus first Intensity Time Trace point in Phasor Series Analysis

  • Fixed unneeded ROI output to Notebook when Decay Graph & Phasor Graph are inactive

  • Fixed “sticky” Series Slide when loading an indiviual dataset

  • Fixed “busy” icon and UI sluggishness when adjusting Image Histogram cursors

  • Fixed Image Contrast Image Type

  • Fixed incorrect SEPL plot name in Phasor Graph

  • Fixed a bug in “ROI to single pixel ROIs” which would not remove the original ROI unless it was the first in the list

  • Fixed bug preventing loading FLI dataset files of different type during a single AlliGator session

  • Fixed released .ini file

  • Removes -Inf, Inf and NaN values from the Image Histogram

  • Removes -Inf & +Inf Sum of All Gates pixel values from ROI Decay calculation

  • Does not create empty decay plots (when no valid pixels)

  • Fixed UI update issues (busy icon, status message, file path controls, SS3 gate selection, etc.)

• New Features

  • Added Splash Screen on launch and shutdown

  • ms precision for date/time stamps in Notebook messages

  • Added dialog when loading single image (Mask or White Light)

  • Reorganized AlliGator menu bar

  • Removed “Average Dataset Sum” checkbox in Settings->Source Image (replaced by two menu items in Analysis->Dataset Series

  • Added option to save a “Phase Lifetime vs X” scatter plot during “Multi-ROI Single Pixel Phasor Analysis”, where X is in {None, Total Intensity, Background-subtracted Intensity, Amplitude, Background, Fitted Lifetime (Bkgd Subtraction)}

  • AlliGator file loading refactoring to support dual-channel dataset

  • Removed Import I/m/phi dataset from File menu

  • Renamed Other Files->Open White Light Image and Open Mask Image to Other Files->8- or 16-bit White Light Image and 8-bit Mask Image

  • Added Python plugin support for Source Image & Decay Graph

  • Added Settings->Plugins panel

  • Added “Export JSON String to Clipboard” right-click menu item to Settings controls (this string being used to pass each parameter to Python plugins).

  • Added “Send” AlliGator Parameters JSON Strings to Clipboard button in the Settings->Plugins tab

  • Implemented support for internal AlliGator parameter passing to Python Plugins in addition to user-specified parameters

  • Added support for python doc string and sending them to the Notebook when using the ‘H’ key pressed while selecting a plugin menu item

0.55 (2022-05-13)

• Bug Fixes

  • Fixed Image Histogram failure when NaN pixel values were encountered

  • Fixed bug in “Define Shortest Lifetime as” Settings which would always set it to Reference 1

• New Features

  • Added G2/INT*max(INT) gate arithmetic option

0.54 (2022-05-12)

• New Features

  • Added “Define Shortest Lifetime as” (Reference 1, Reference 2) radio button to Settings->Phasor Graph window to tell how to define which reference is 1 or 2 when using UC/Fit intersection or Minor/Major Axis/UC Intersection in either Phasor Plot or Phasor Graph

0.53.1 (2022-05-10)

• Bug Fixes

  • Fixed erroneous saving of Phasor Plot image with overlay irrespective of the selected option

  • Fixed erroneous Decay Name when using File Background correction (was set to the background file name)

  • Fixed erroneous Dataset Information when using File Background correction (showed background file information: now shows both)

0.53 (2022-05-07)

• Bug Fixes

  • Removed Graph Index Display because of conflict with plot identification

• New Features

  • Implemented 1-Normalize, Shift and Fold decay in the Decay Graph context menu

0.52 (2022-05-05)

• Bug Fixes

  • Fixed a bug in 2-Exp Fit which converted it into a 1-Exp fit

  • Fixed a bug in the Drag & Drop behavior of the ROI Managers

  • Fixed a bug in Settings>>Fluorescence Decay>>Decay Pre-Processing, which did not preserve either the Pile-up Correction flag or the Max Value.

  • Corrected Example String in single variable and 2-variables formula input dialogs

  • Fixed update bug in Plot Editor “Fill Array with Ramp” dialog

  • Fixed a bug in Export Phasor (multiple) Plot Data to ASCII where the header might be incomplete

  • Fixed longstanding bug in Phasor Plot computation when decay pre-processing is selected

• New Features

  • Added Gate Arithmetic Enum to combine SS3 gates: None, INT-G2, (<INT>+INT)/2-G2, G2+(<INT>-INT)/2

  • Moved Background File Subtraction parameters from Decay pre-processing to Data Information

  • Added Plot Legend Index Display to Graphs to complement scrollbar

  • Fixed missing Notebook message when saving images with overlay

  • Fixed ambiguity when saving SGL image to 16-bit TIFF

0.51 (2022-03-07)

• Bug Fixes

  • Fixed Error in reduced Chi2 expression (Chi2/DOF, was Chi2/N)

  • Fixed NLSF Fit

  • Fixed Notebook backup issues with new logic and added message bar at the bottom to inform on most recent backup

• New Features

  • Upgraded to LabVIEW 2021 SP1

  • Changed Fit Weight option from boolean to enum (unweighted, 1/Variance, Best of Both)

  • Uses normalized decay fit internally but returns scaled parameters

  • Now outputs correct reduced Chi2 in Notebook (was RMSE)

  • Outputs Guess Parameters even if fit fails

  • Added Gate Names ring control to Settings (for multigate FLI datasets such as encountered in SS3)

  • Added export of intensity and amplitude-phasor ratio and average lifetiem in export tool

  • Implemented Batch Conversion to HDF5 and TIFF series

0.50 (2022-01-31)

• New Features

  • Added ProcessID to Notebook backup file name to distinguish between processes

  • Added “Live” Highlight of Source Image pixels in Phasor ROI (H key pressed while moving selected ROI in Phasor Plot)

0.49 (2022-01-30)

• New Features

  • Replaced Image Sum readout in nested loops by Array indexing (Image Sum array created upon creation)

  • Implemented # Logical Processors Used in Settings, in order to control CPU usage for resource-demanding functions such as NLSF

  • Compares unweighted & weighted fit results when weighted fit is requested, returning the best of both

0.48.4 (2022-01-14)

• Bug Fixes

  • Fixed bug in Clear Graph in Histogram Windows

• New Features

  • Added LED indicator when IRF options have been defined in Multi-ROI Single-Pixel Scripts

  • Added Set Options button (and LED) for dataset (for consistency)

  • Added message to Notebook after saving it (if it fails, a warning is printed)

  • Updates Parameter Range when changing selected parameter in Decay Fit Parameter Map

0.48.3 (2022-01-14)

• Bug Fixes

  • Fixed transition from Accumulated to Single File and back

  • Fixed bug that prevent intensity time trace from being computed when no decay pre-processing options were selected

0.48.2 (2022-01-11)

• Bug Fixes

  • Fixed ROI Statistics error when at least one of the pixel value is negative (now removed from SNR statistics)

  • Fixed ROI Color update at startup

  • Fixed bug in “Export ROI Data as ASCII” and “Export All ROIs Data as ASCII” in Decay Fit Parameter Map

0.48.1 (2022-01-08)

• Bug Fixes

  • Fixed a bug in Sum All Datasets in Series that prevented it from working

  • Notebook fails to save when path is longer than 259 characters

0.48 (2022-01-07)

• Bug Fixes

  • Fixed a bug which prevented the “Save As…” menu of the Notebook to work

  • Fixed a bug in the Notebook that made it non-persistent

• New Features

  • Switched to HDF5 format for IRFs & Fit Data Map

  • Lifetime Analysis panel renamed Lifetime & Other Parameters Analysis

  • Image ROIs (stored in the ROI Manager) are now shown in the Decay Fit Parameter Map

  • Support for exporting Selected ROI(s), All ROIs or All Map Data to Lifetime & Other Parameters Analysis Graph

  • Replaced Phasor Calibration checkboxes replacement by Pull-down menu

  • Added ROI ID selection and corresponding UI

  • Implemented Multi-ROIs Single-Pixel NLSF Analysis Script & Implemented Multi-ROIs Single-Pixel Phasor Analysis Script

  • Added IRFs & Fit Data Map export

  • Implemented single ROI pixel-wise phasor calculation and phase lifetime export

  • Added “Delete All Unselected ROIs” to ROI Manager and Image context menu

  • Changing the selected ROI (in Source ROI Manager) updates the Local Decay Graph window if the ROI is a point

  • IRF number does not need to be identical to decay number in All ROIs Decay Fit (No-interactive, fast, Individual IRF)

  • Added “Fold Decay” preprocessing option (parameter: # Folds)

  • Added Analysis>>Series Analysis>>Show Dataset Series Sum menu item

  • Updated Settings parameters change triggering Phasor Plot update flag (background-correction related parameters)

  • Added Histogram Options to Settings>>Miscellaneous: used for scripts

  • Added Export All Maps Data as ASCII menu item to Decay Fit Parameter Map

  • Added “Export ROI Data as ASCII” and “Export All ROIs Data as ASCII” menu items

  • Implemented IRF Options in NLSF/Phasor Script

  • Added Color Boxes to Select ROI Color for Source Image/Phasor Plot and Decay Fit Parameter Map

  • Linked Decay Fit Parameter Map ROI to Source Image ROI

0.47 (2021-12-18)

• New Features

  • Added mode, median and SNR statistics to ROI Statistics output to Notebook

  • Added option to use a First Gate index larger than Last Gate index when using the “Gates to Keep” option. In that case, the gate images (F, F+1, …, N-1) are loa

0.46 (2021-12-11)

• New Features

  • Changed Phasor Graph menu item: Phase Lifetime Trajectory >> Phase Lifetime Series

  • Added Save Phasor Plot Add’l Data submenu: Save Single Phasor Plot Add’l Data, Export Selected Phasor Plots Add’l Data, Export

  • Added Export Single Phasor Plot Data, Export Selected/All Phasor Plots Data

0.45.2 (2021-12-03)

• New Features

  • Updated dialog window message when exporting average lifetime map from Phasor Plot

0.45.1 (2021-12-01)

• New Features

  • Tweaked amplitude fit parameters adjustment when selecting “Use Last Fitted Parameters”

  • Changed IRF normalization for convolution so that its integral is equal to 1 => fitted parameters (baseline, amplitudes) are accordingly rescaled

  • Removed a few innocuous error messages showing up in verbose error mode

0.45 (2021-11-30)

• Bug Fixes

  • Fixed update of Phasor Ratio References with Phasor Frequency (Phasor Plot & Phasor Graph)

  • Fixed a bug in Extrapolate Decay as part of Pre-Processing (Head & Tail fractions were reversed)

• New Features

  • Changed UI behavior of “Clear Source Image Overlay” and “Clear Phasor Overlay” buttons, by removing adjacent checkmarks and moving all options to right-click menu. See context help for description.

  • Added option to define the Phasor Ratio References by Phase Lifetime value (in Phasor Graph)

  • Added dashed line connecting references in Phasor Plot

  • Added support for decay pre-processing in the Local Decay Window

  • Changed style of warnings in Notebook

  • Implemented baseline and amplitude fit parameters adjustment when selecting “Use Last Fitted Parameters”

0.44.3 (2021-11-12)

• Bug Fixes

  • Fixed Calibration Map change detection, resulting in subsequent speed up of phasor plot update’

  • Fixed bug preventing loading of Calibration, Calibration Series or Calibration Map

• New Features

  • Changed the Phasor Ratio/Amplitude output from f2 to f1 (fraction of reference 1). The other derived quantities (e.g. average lifetime) were computed correctly and therefore remain unchanged. This definition is now made clear in Notebook outputs or indicator captions.

  • Changed some default Fit Options Termination Criteria (1E+/-6 -> 1E+/-9) to improve convergence

0.44.2 (2021-11-11)

• Bug Fixes

  • Fixed fit parameters map file loading error

  • Fixed error when drag & dropping plot when the visible Graph does not support drag & dropping

  • Fixed bug in 2-Exp NLSF introduced in v0.42

• New Features

  • Minor menu edits

  • Added Fit Options & Parameters to IRFs & Fit Data Map output

0.44.1 (2021-11-07)

• Bug Fixes

  • Fixed missing Pixel-Normalize Decay step in Phasor Array Calculation

  • Fixed problem with computing Phasor Plot when a large number of ROIs is defined

0.44 (2021-11-06)

• Bug Fixes

  • Minor fixes to handling of Fit Parameter Constraints/Guess Parameters and Displayed Fit Parameters arrays in Settings>>Fluorescence Decay>>Fit Parameters

  • Fixed cases where no ROI exists

• New Features

  • Opens the Notebook on startup

  • Added Major/Minor Axis option in UC Intersection in Phasor Plot and Phasor Graph

  • Added Linear Fit - UC Intersection in Phasor Pot

  • Changed Phasor Plot Reference manipulation approach: now uses keyboard key 1 and 2 to select reference 1 and 2, the buttons being highlighted when used

  • Added “Selected Phasor Plot ROI(s)” and “All Phasor Plot ROIs” option to analyze the Phasor Plot (e.g. Reference calculation)

  • Added Selected Phasor Plot ROI(s)” and “All Phasor Plot ROIs” option for Linear Fit/UC intersections

  • Added support for Phasor Plot ROI file Drag & Drop

0.43 (2021-11-03)

• New Features

  • Added “Selected Image ROI(s)” and “All Image ROIs” option to compute the Phasor Plot

  • Simplified phasor plot computation

  • Implemented faster smoothing algorithm (at the expense of less accurate pixel rejection)

  • Added option for smoothing algorithm

  • Added “Phasor Ratio Color-Coded Quantity” parameter in Phasor Plot Settings, to select between Phasor Ratio and Average Lifetime when overlaying the phasor plot results onto the Source Image

  • Export of Phasor Ratio Map and Average Lifetime Map added to Phasor Plot contextual menu

0.42.3 (2021-10-29)

• Bug Fixes

  • Fixed bug in Gates to skip/Gates to keep calculation

0.42.2 (2021-10-27)

• Bug Fixes

  • Corrected bug in amplitude weighted average phase lifetime calculation (Phasor Graph)

  • Fixed non-functioning “Save Phasor Plot Image with Overlay” menu item (Phasor Plot)

0.42.1 (2021-10-21)

• Bug Fixes

  • .ptu loading files touch-up (inlining, code separated from VI, shift register initialization) to improve performance

  • Fixed default filename when exporting HDF5 dataset

0.42 (2021-10-158)

• Bug Fixes

  • Fixed a bug in Fit Function weight calculations

• New Features

  • Added “Define Gates to Keep” option (in addition to Gates to Skip)

  • Removed Error in NL Fit if the Hessian cannot be inverted

  • Fit Options are now used throughout AlliGator (e.g. Histogram)

0.41 (2021-10-10)

• Bug Fixes

  • Fixed Drag & Drop of folder of folder of gate images

• New Features

  • Removed White Light Image Histogram (fusioned with Fluorescence Image Histogram)

  • Support for Drag & Drop of Mask, White Light Image

  • Support for Drag & Drop of individual Phasor Plot (phplot) in Phasor Graph

  • Support for Drag & Drop of calibration, calibration series & calibration map

  • Support for Drag & Drop of IRFs & Fit Data files

0.40.1 (2021-10-08)

• Bug Fixes

  • Fixed a bug in Compute Average Phasor (Selected Plots) that would remove the first selected plot if the UC was not selected

• New Features

  • Modified zero-weight replacement to use interpolated values whenever possible (instead of 1)

  • Added Average Lifetime to Phasor Plot & Phasor Graph display and Notebook output when references are defined

0.40 (2021-10-07)

• New Features

  • Added transparent option for Phasor Plot References and Boundary

  • Added Phase Lifetime SDV output for Average Phasor (as well as Modulus and SDV)

  • Added Compute Average Phasor (Selected Plots) to Phasor Graph

  • Added Phasor Ratio (or Amplitude Ratio if selected) as Notebook output for the previous operations

0.39.4 (2021-10-06)

• Bug Fixes

  • Fixed context menu for phasor frequency and initialization in SEPL Settings

• New Features

  • Update Phasor Frequency at startup

  • Added Reference Point Radius parameter for Phasor Plot

0.39.3 (2021-09-30)

• Bug Fixes

  • Corrected a bug in Multiple ROI Analysis that could result in some ROIs’ data to not be processed

0.39.2 (2021-09-29)

• Bug Fixes

  • Corrected bug in Export Decay to Phasor Graph menu item added to Decay Graph

0.39.1 (2021-09-28)

• New Features

  • Added Create ROI(s) from Pixel with Intensity over Min

0.39 (2021-09-27)

• New Features

  • Modified description of fit parameter map parameters

  • Added Export Bounding Cursors Definition to Notebook menu item to Decay Graph

  • Bounding cursors follow multiple/all plots

  • Added separate Pile-up Correction option for Background File

  • Does not show the Create Phasor Plot Dialog if Phasor Graph is inactive

  • Added Export Decay to Phasor Graph menu item added to Decay Graph

  • Moved some items in Decay Graph menu

  • Output Decay Fit results even in case of convergence or other failure (with error message)

  • Added verbose message for ROI manipulation

  • Added more colors to Notebook

  • Force file dialog when saving IRFs & Fit Data

0.38.1 (2021-09-14)

• Bug Fixes

  • Fixed bug in standard File menu based data loading

0.38 (2021-09-13)

• Bug Fixes

  • Fixed a but preventing from aborting Playback

  • Fixed a bug in loading ptu files

  • Fixed a bug in Playback Script where the dataset index was not incremented

  • Fixed Natural Frequency calculation to take into account the “User Decay Pre-Processing” flag

  • Fixed progress bar display for parallel loops

  • Corrected bug in Notebook output of Phasor Plot calculation (was returning number of valid phasors instead of invalid phasors)

  • Corrected a bug in Phasor Plot calculation (phasor calibration map case) and simplified code

  • Fix bug where a background constant subtraction was not applied when computing the Phasor Plot

  • Corrected a bug in Phasor Amplitude Ratio calculation

  • Cancel in Phasor Ratio abscissa input is now handled properly

  • Fixed OpenG bug resulting in erroneous interpretation of .ptu files

• New Features

  • Implemented drag & drop file/folder to open a file or a series

  • Added Drag & Drop of ROI definitions

  • Added support for Drag & Drop of plots

  • Added option to create new Phasor Ratio plot in input dialog window

  • Output of phasor frequency in multipoint Phasor Plot calculation

  • Improved display precision for several numeric indicators

  • Save Image or Phasor with Overlay now does not require computing any overlay

  • Made error message when no Reference Decay/IRF is found clearer (it could be due to the “Use Local IRF” checkbox being checked

  • Changed menu item from Compute Phasor Plot’s Phasor Ratio to Compute Phasor Plot’s Average Phasor Ratio

  • Added Phasor Plot name(s) used to compute references in Phasor Graph

  • Improved Decay Extrapolation by increasjing weight of head part in case of periodicity

  • Added overwrite warning in Notebook Save As…

  • Improved extrapolated decay (fixed NL Fit Options, head weights, shotnoise)

  • Phasor Explorer-related updates (using identical Settings Parameters for SEPL definition)

  • Added “Store Cursor-defined Head & Tail Fractions” in Decay Graph context menu (to use in automated analyses)

  • Restored Algebraic IRF deconvolution

  • Added verbose Notebook message for Phasor Ratio reference updates

  • Added “Phasor Graph Active” checkbox

0.37 (2021-08-16)

• Bug Fixes

  • Corrected bug in Use Single Plot Fitted Line/UC Intersections

  • Corrected bug in Multiple Plots Fitted Line/UC intersections which include UC in the calculation

  • Update Phasor Graph line if reference is updated

  • Fixed bug in Load Plot(s) which was missing partially empty columns

  • Modified Linear Fit in Phasor Ratio Graph to encompass min and max values

• New Features

  • Added Use Multiple Plots Fitted Line/UC Intersections to Phasor Graph contextual menu

  • Added Single Phasot Plot Phasor Ratio calculation

0.36 (2021-08-05)

• Bug Fixes

  • Does not reject Phasor Plot calculation if an individual phasor cannot be computed

  • Fixed Image contrast update frequency when moving mouse in the image histogram(s) by requiring the mouse to be down for this to happen

  • Fixed Preprocess Decay checkbox impact on calculations throughout AlliGator (was partially implemented)

• New Features

  • Added ability to view decay profile at location in Image Source

  • Added requirement to press the Left or Right Shift key for Phasor update at current location to actually update phasor information in the phasor plot panel (in order to avoid queueing too many events), when moving the mouse in either the Source Image or the Phasor Plot image

0.35 (2021-07-26)

• Bug Fixes

  • Fixed Clear ROI bug in Decay Fit Parameter Map Image

  • Fixed Square Gate Fit corner case issue

• New Features

  • Added Save/Load IRFs & Fit Data Maps

  • Added IRF to Local Decay Graph Window

  • Added Mouse Click requirement to update Local Decay Profile window

  • Added controls for Square Gate Fit Parameter Map

  • Improved Logistic Gate Fits

  • Implemented option to use local IRF for decay fits (manual)

0.34.4 (2021-07-23)

• Bug Fixes

  • Fixed progress bar problem

  • Fixed Settings>>Data Information export to Notebook

0.34.3 (2021-07-22)

• Bug Fixes

  • Fixed 2nd-pass fit approach in Decay Fit Parameter Map

0.34.2 (2021-07-22)

• Bug Fixes

  • corrected a bug in the Decay Fit Parameter Map output for 2-Exp decays

• New Features

  • Implemented more robust clip decay for fit

  • Added NaN check in decay before fit

  • updated definition of derived fit parameters and added better description of their definition

0.34.1 (2021-07-01)

• Bug Fixes

  • Fixed bug where the periodicity option (and period) were not taken into account in “Extrapolate Decay” when extracting a decay

  • Fixed glitches in Settings>>Fluorescence Decay>>Decay Pre-Processings update of “Extrapolate Decay” options

0.34 (2021-06-28)

• New Features

  • Image Profile (Windows>>Image Profile) shows the selected parameter in the Decay Fit Parameter Map. It is plotted associated with the lifetime axis (to the right). You need to draw a line on the image for this to show anything and there are some “features” as far as the update goes, but it essentially does the job.

  • Local Decay Graph (Windows>>Local Decay Graph) shows the decay, fit and residuals at the point in the Decay Fit Parameter Map when the “Point” tool is selected (bottom of the list on the left of the map). Don’t forget to adjust the Intensity Axis to show the correct range of values.

0.33.7 (2021-06-27)

• Bug Fixes

  • Fixed a cosmetic bug with min/max decay parameters

• New Features

  • Added condition to retry fit in decay fit map: R2 < 0.95

0.33.6 (2021-06-27)

• Bug Fixes

  • Progress bar edits

  • Minor cosmetic changes to Decay Fit Parameter Map behavior

0.33.5 (2021-06-26)

• Bug Fixes

  • Fixed bug in decay fit parameter output

  • Fixed missing Guess Parameters output to Notebook in Settings>>Export Settings to Notebook

  • Fixed Fit Parameter Map color scale update

  • Fixed missing Settings string outputs

• New Features

  • Added Use Decay Pre-Processing Option

  • Turned back parallel computation on for decay fits

  • Added 2nd round of fits for decay fit parameter map, using successfull neighboring fits

0.33.3 (2021-06-24)

• Bug Fixes

  • Fixed some newly introduced Settings memory bug

  • Fixed HDF5 Dataset Parameter saving

0.33.2 (2021-06-24)

• Bug Fixes

  • Added dlls needed for h5labview in build

0.33 (2021-06-22)

• Bug Fixes

  • Fixed an inactive menu item in Settings

  • Fixed error when ROI pixel is outside image

  • Fixed a bug in Fit Decay parameter passing for fitted decay calculation

  • Fixed bug where 1-Normalize Decay was ignored

  • Corrected bug in Save Plot dialog

  • Fixed bug in reading HDF5 files version 0.4 (introduced with file version 0.5)

  • Fixed Pile-up Correction update bug in Settings

  • Corrected a bug in Accumulate/Average Datasets where the number of gates was used instead of the number of datasets

  • Corrected UI bug which would remember Background Dataset as last used files

  • Fixed bugs in Histogram Window

  • Corrected typo in Define ROI(s) above Min Peak menu item

  • Fixed bugs in Phasor Image calculation

  • Fixed high CPU usage in Source Image local Phasor display

  • Fixed missing menu items in Phasor Graph

  • Fixed missing Operation Order parameter in Settings

  • Fixed Phasor Frequency synchronization (removed Phasor Calibration Frequency in Settings)

• New Features

  • Modified IRF & Decay Parameter name in SEPL tab: “IRF Period”

  • Added IRF Period to Fluorescence Decay >> Basic Analysis and Fluorescence Decay >> Fitting

  • Right-click menu allows setting IRF Period in Fitting and SEPL to the same value as in Basic Analysis

  • Right-click menu allows Setting IRF Period in Basic Analysis to Laser Period

  • Implemented PSED + IRF convolution fit

  • Implemented 2-Exp periodic convolution fit

  • Added “Use Last Fitted Parameters” to Guess Parameters Tab in Fluorescence Decay Tab & associated logic

  • Added plot clipping information in Decay Fit output

  • Added Guess Fit Parameters in Decay Fit output

  • Added repetition of fit to improve convergence

  • Added All ROIs Decay Fit scripts (interactive and fast)

  • Added optional export of tabulated fit results in non-interactive mode

  • Renamed Settings>>Decay Analysis>>Fitting to Fit Options, and moved some controls to >>Fit Parameters

  • Added Max Fit Iterations and Tolerance as part of the Fit Options

  • Added Oval and Point ROI Grid definition

  • Added all Termination Conditions to Fit Options

  • Added Support for version 0.5 of HDF5 File Format

  • Added automatic switch to unweighted fit when performing offset fit, followed by weighted fit pass if this is the user choice

  • Added check to avoid mistakenly overwriting plot files.

  • Modifed Decay Extrapolation to support periodic decays

  • Added “Use Periodicity” checkbox in Settings>>Fluorescence Decay>>Basic Analysis under “Extrapolate Decay”

  • Added “Period” parameter to Extrapolate Decay (in case of periodicity)

  • Using tail and head part of the decay for periodic decay extrapolation

  • Added cursors option to define head and tail fraction for extrapolation (only interactively)

  • Added Head Fraction as a Settings parameter

  • Outputs fit range when using min/max percentile

  • Suggested HDF5 FLI Dataset File Name now returns current dataset and folder

  • Added output of number of averaged/accumulated datasets in Notebook

  • Updated Save FLI Dataset as HDF5 to follow the new HDF5 File format (and to implement compression more efficiently)

  • Added All IRF Analysis (fast & slow) scripts

  • Implemented All ROIs Decay Fit Non-Interactive (Fast + Individual IRF)

  • Added Progress Bar to main window (supported in All ROIs Decay Fit Non-Interactive (Fast + Individual IRF))

  • Added Status Indicators for Reference/IRF and Individual IRFs Defined

  • Added Decay Fit Parameter Map

  • Implemented contextual menu for Decay Fit Parameter Map

  • Implemented Use Image Brightness in Decay Fit Parameter Map

  • Added Merge All ROIs in Source & Phasor Plot Image ROI Manager

  • Added Invert Binary Mask Option in Settings>>Source Image

  • Added busy icon display for potentially lengthy tasks

  • Implemented Export Phasor Ratio Map to ASCII in Source Image

  • Added support for binning of white light image and ROI mask

  • Added Send Map Data to Lifetime Graph shortcut menu

  • Added support for binning of white light image and ROI mask

  • Added Send Map Data to Lifetime Graph shortcut menu

0.32 (2021-04-01)

• Bug Fixes

  • Handling of incomplete image gate series in HDF5

  • Corrected a bug in partial loading of HDF5 Datasets

  • Corrected a bug in the computation of natural frequency in Settings

  • Fixed popping-up dialog when some mondane error was encountered

  • Fixed default settings bug in Histogram Fit

  • Fixed bug in v0.3.1 support

  • Fixed a LV bug with IMAQ Read Image.vi which misreads U16 TIFF images

  • Fixed a bug with Time Gate Slider

  • Updated dependencies after Phasor Explorer project update

• New Features

  • Added support for FLI HDF5 file version 0.3.1 adding Image Information (cropping)

  • Added support for FLI HDF5 v0.4

  • Moved Calibrations settings to a separate panel in Settings

  • Added SEPL in Phasor Graph & Phasor Plot and SEPL Parameters panel in Settings

  • Removed “Show Ticks” for SEPL (common option with UC)

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 menu

• 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 Fixes: 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” button

• Added Sum All Datasets in Series function (with an “Average Dataset Sum” option in Settings>>Source Image)

• Open/Save HDF5 Dataset functions added

• Minor 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 bug fixes and cosmetic changes

0.15 (2019-02-09)

• Minor 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

• Minor 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