Version History

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.

4.22 (03-30-2019)

• Bug Fixes:

  • Corrected a bug in ACF 3D parameter output display

  • Fixed #Photons to Read/Skip for non HDF5 files

  • Corrected a bug in the computation of quantities involving after burst rates

  • Fixed a bug where the time trace percentage of completion was incorrect when using partial read

  • Fixed bug in duration parameter interpretation in Burst Search

  • Added Verbose Error Mode and Interactive Error Mode to Settings

  • Fixed bug preventing from saving Settings & Controls

  • Minor cosmetic and bug fixes

• New Features:

  • Option to only save a single X array in multiplot saving if all arrays are identical (a single axis is saved for multiplot Charts)

  • Changed syntax of multiplot file header to be less exotic and allow reloading plots without ambiguity.

  • Added tip strips to ACF/CCF Graphs

  • Added computation of correlation function variance by time trace "slicing"

  • Added number of end points parameter to define the asymptotic value of the correlation function used in CF SDV calculation

  • Added CF Bin Definitions to Settings (and removed them from CF panel)

  • Duplicated ACF parameters for CCF operations in Settings

  • Implemented Chunk max duration in ACF/CCF calculation

  • Added # Parallel Instances parameter (General Settings)

  • Added decoding of .spc flags and display as a message if present

  • Added option to reject flagged .spc photons

  • Added "Invert Plots Selection", "Select Plots..." and "Deselect Plots..." menu items to Graph and Charts to facilitate multiple plot selections

  • Added "Single Plot Arithmetic" and "Add Selected Plots" menu items to most graphs

  • Added "Set Axes of Selected Plots" menu item to mutli-axes graphs

  • Implemented combination of Plot Types in Burst Analysis

  • Style of most controls changed to "Next Gen"

4.19 (05-23-2018)

• Chart menus mirroring Graphs menus (made more uniform throughout)

• Histogram Statistics can be included in Monitored Variables

• Added Time Trace Histogram scripting

• Better handling of error message

• Added Color List option for Selected Plot Style menu item

• Folder-level scripts are now limited to the data file type selected on the Data File page

• Added fusion of bursts separated by zero photons during search

• Added pre- and post-burst rates to Burst Data

• Refactored General Script

• Added option to compute Time Trace Histogram of NON bursts bins or NON selected bursts bins

4.18 (04-25-2018)

• Redesigned pre-compiled scripts UI

• Implemented Diffusion + Flow ACF Fit

• Implemented Diffusion + Flow ACFs global fit (multiple ACF pairs)

• Corrected bug in plot fit axis offset

• Corrected bug in LM & TRDL fits comparison

• Added Statistics name auto-completion

• Added Burst and Selected Burst time trace histograms

• Added folder batch analysis

• Added Min Time Lag x Factor for MLE and PIH Fit “automatic” threshold determination

• Minor cosmetic changes and bug fixes

4.17 (03-26-2018)

• Implemented Set Style of Selected Plots, Save Plot, Save Selected Plots & Save All Plots functions for XY Graphs

• Added Photons to Read and Photons to Skip in % (for HDF5 files only)

• Added (ACF-1) Ratios Calculation Script to ACF Graph menu

• Corrected a bug preventing from stopping time trace playback in some cases

• Added Sum Selected Plot function to XY Graphs

• Added option to align histogram bins

4.16.1 (08-21-2017)

• Minor optimizations

• Corrected bugs slowing down hdf5 loading and failing to recognize file types

• Added warning for ACF/CCF empty stream array

• Added “Paste All Channel Name Pairs” option in Scripting Tab

4.15 (08-01-2017)

• Corrected a bug in Time Trace using "Align with us ALEX Period Offset"

• Corrected a bug which prevented General Multispot Analysis Scripts to function

• Corrected a bug preventing correlation function fits to work

• Support of Photon-HDF5 file format v0.5

• Added us-PAX calculation options

4.14.3 (07-21-2017)

• Upgraded to LabVIEW 2017

• Improved ALEX modulation and afterpulsing corrections in ACF/CCF

• Support for multispot single-channel TCSPC photon-hdf5 files

• Corrected a bug which prevented reading multispot photon-hdf5 DCR files

4.13.1: (10-25-2016)

• Changed graph style

• Fixed a dependency preventing SNA to work

4.13: (10-20-2016)

• Added tipstrip for most relevant graph legends

• Fixed a couple of bugs in the computation of FSBC, the stoichiometry and brightness compensated burst size

• Corrected a bug in ALEX analysis where background corrections were applied only when ALEX corrections were

• Modified SNA to allow turning off background corrections

• Added Beta Distribution of E model in SNA

• Better behavior of skippable warning dialogs

• Cancelling a script load does not reset settings to default anymore

4.12: (09-29-2016)

• Upgraded to LabVIEW 2016

• Added Notebook access from SNA window

• E or S Histogram bin change keeps SNA results (and recomputes MSE)

• Normalized Residuals options in SNA does not need recomputation

• Parameter conversion/p(E) plot in SNA was extended to the truncated Gaussian p(E) model

• Corrected a bug when reading ht3 files converted to photon-hdf5

• Cosmetic modifications

4.11: (07-31-2016)

• Cosmetic Changes

• Added "historical" interpretation of burst search criterion

• Added “FRETBursts” option in Settings>>Background Rates for MLE estimation of Background Rates

• Corrected a bug in ACF afterpulsing correction for CW data

• Fixed problems with loading of afterpulsing correction files

• Refactoring of Fit Models and addition of error bars, RMSE and R^2

• Fixed bug in Time Trace exploration of bursts with Burst Inspector

• Improved responsiveness of Burst Inspector to mouse click close to bursts

• Added number of bursts in time bin indicator

• Significant Burst Search speed up

• Added a Burst Search option whereby a Min Burst Separation Time < 0 results in no burst fusion after search, even if bursts overlap (to emulate a default mode of FRETBursts)

• Migrated to a Rich Text Box for Notebook, supporting different font/style/color and graph export

• Save/Load Multispot Script buttons for reproducing complex analyses

• Shot Noise Analysis: Added Rod+Linkers Parameter Conversion to E and corresponding FRET Distribution plot

4.10: (05-09-2016)

• Photon-HDF5 v0.4 support

• Cosmetic changes to the Multispot Scripting tab

• Improvements to Settings window behavior

• Save/Load/Reset ALiX Controls & Settings values (Edit Menu) 

4.9.4 (*):

• Refactoring to implement Photon-HDF5 support

• File loading requires specifying Measurement Type

• Background Analysis & Advanced Background Analysis buttons added

• Minor cosmetic changes

4.9.3: (04-11-2016)

• Cosmetic fixes to Nanotime Display and Analysis

• Corrected a bug in multiple periods definition in Nanotime Display

• Added a “beta” button to About ALiX to unlock scripting tabs 

4.9.2: (04-07-2016)

• Fixed a bug occurring when unchecking the Select Bursts in ROI checkbox

• Now sets Use ALEX-Selected Bursts Only (Burst Statistics Definitions) to False after a Burst Search

• Fixed a bug preventing the update of the time trace legend

• Fixed a bug preventing the update of the time trace window size while computing the time trace

• Fixed a bug preventing the time trace window size from being used when pressing the play button

• Now supports switching from Paused Time Trace Playback to Manual Stepping

• Changed time-trace dependent background analysis algorithm to use percentile

• Corrected correlation function bin definitions for Multitau-10 and Logarithmic

• Fixed a newly introduced bug in constrained- or ALEX selected burst correlation functions

4.9.1: (03-31-2016)

• Fixed Table of Content Hide/Show behavior

• Fixed multiple Statistics vs Duration plots legend bug

• Various cosmetic fixes

4.9: (03-28-2016)

• Added new threshold type in burst search: fixed rate above background

• Unconventional parameter values are contrast inverted for better spotting

4.8.1 (*):

• Fixed folder name bug in export of Shot Noise Analysis data to Origin

• Improved performance of Shot Noise Analysis performance for Rod+Linker model in the case s = 0

• Fixed a bug in constrained- or ALEX selected burst correlation functions

• Fixed a bug in burst search that prevented from setting F (threshold in background unit) directly

• Various cosmetic changes and bug fixes

4.8: (02-19-2016)

• Added basic Burst Search combination capabilities

• Added basic Advanced Plotting Toolkit support

• Corrected a bug in Normalization of ALEX Correlation Function introduced in a past version

• Corrected a bug in afterpulsing correction of ALEX ACF to account for the fraction of the alternation period covered by the photon stream under consideration

• Corrected a bug in background correction of CCF where the Fitted Background Rates were used instead of the Uncorrelated Background Rates 

4.7 (*):

• Fixed bugs in Matrix export to Origin in Shot Noise Analysis (large matrices were not exported, matrices were not transposed)

• Fixed Burst Separation & Duration Statistics inversion in Notebook output

• Added General Multispot Script Capability

• Added Mean and SDV of Burst Statistics Histograms to Monitored Variables

• Added Show/Hide All Plots shortcut to multiplot graphs

• Added option to keep F1 vs F2 scatter plots from analysis run to analysis run

4.6: (12-07-2015)

• Implemented Shot Noise Analysis

• Replaced page tabs by ALiX Table of Content

• Corrected a bug in Burst Search whereby Time-Dependent Background Arrays were never used

4.5.2 (*):

• Corrected a bug in the PIH of All Photons which would give bogus values in cases where the timestamps of different channels were not ordered chronologically

• Corrected a bug in PIH Fit where the Bin Location was assumed to be left rather than that defined by the corresponding user-defined parameter

• Added a Background Rate MLE button on the Background Analysis page, in order to bypass the need to compute PIHs

• Export Burst Data button moved to Burst Analysis page

• Added Baseline Subtraction option to Nanotime Histograms

• Added Time Axis Boundaries for Goodness of Fit calculation in Nanotime Histogram Fitting

• Added Burst Index Offset option in F2 vs F1 Scatter Plot

• Added Afterpulsing Probability Estimate Script for Multispot Data

• Extended scripting capabilities for Multispot ACF and CCF Analysis

• Added basic statistics Notebook output for E & S Histograms

4.5.1: (10-9-2015)

• Added E and H Histogram Fit capabilities to the Sliding Window Analysis Script

• Fixed a bug which prevented the Settings window inputs to be taken into account

• Fixed a bug which prevented some buttons to be used in Sliding Window Analysis

• Few Cosmetic changes

4.5: (10-2-2015)

• Added Sliding Window Analysis Script Tab (.sm files only)

• CCF Graph now supports multiple plots

• Busy cursor replaced by a busy icon

4.4.16 (*):

• Upgraded to LabVIEW 2015

• Added Phasor Analysis Tab

• Replaced export of script report from HTML to Microsoft Word

• Corrected a bug in ACF/CCF whereby the CF was offset if the first timestamp was not zero (noticeable when using file slices)

4.4.15 (*):

• Added a script to Analyze TCSPC SPAD array data files (burst analysis of fluorescence decay

• Added export of report to HTML

4.4.14: (8-20-2015)

• Added raw (photon) time stamps file format to load SMS simulation results

• ACF correction now supports gamma-distribution prefactor of exponential component (relevant mostly for SPAD arrays, but outdating previous correction files)

• Burst Data export now doesn’t include the unit string of time parameters

• Support for Polimi TCSPC SPAD arrays data including the following

• New Settings: TAC bin size array and TAC offset array

• Corrected a rarely occurring bug in Time Trace display

4.4.13: (7-7-2015)

• Burst Data export now offers two more options: one to export photon timestamps and another to export nanotimes

4.4.12: (7-3-2015)

• Notebook now preserves its content when closing (even without save) and reopening

• Corrected a bug in the normalization of logarithmically binned histograms (including Sigworth & Sine representation)

• Burst Data export now offers the option to export individual photon IDs in a separate ASCII file (one line per burst) 

4.4.11: (6-2-2015)

• Added tilted ALEX ROI functionality

• Quitting ALiX opens up a warning window

• Added Ctrl-Shift+O shortcut for Load + All Analyses

• Rate formula is now (m – 2)/(t_i+m-1 – t_i) which is unbiased

• Count Rate calculation now includes an option to remove alternation period gaps

• Save/Load Burst Search Parameters buttons

• Save/Load Burst Statistics Definitions buttons

• Various cosmetic changes

4.4.10: (5-15-2015)

• Fixed a bug in burst nanotime data update during burst search (introduced in 4.4.8)

• Released Count Rate Analysis page

• Added Burst Count Rate statistics

• Added option to use a fixed threshold rate for burst search

4.4.9: (5-5-2015)

• ALiX Notebook is backed-up every min (in the temp directory)

• Fixed bug in loading .std calibration data file

4.4.8: (5-1-2015)

• Various cosmetic changes and bug fixes

• Changed the way channel identities are stored and handled internally, in order to correct a bug introduced in ns-ALEX histogram display

• Corrected a bug whereby Ctrl-P (Period Definition) did not work in ns-ALEX

• Store/Recall cursor positions for period definition and nanotime calculation in Nanotime Display

• Nanotime computation now updates average nanotime values for bursts (no need to perform a burst search again)

• Burst Statistics KDE bandwidths definitions are now separate

• Link to the Manual and Downloads pages in the Help menu

4.4.7 (*): (4-23-2015)

• First implementation of simulated background addition

4.4.6 (*): (4-26-2015)

• Bootstrap analysis of Kernel Density Estimation peak position uncertainty

• Option to not compute Statistics Plot

• Option to switch to Advanced Background Analysis after standard Background Analysis

• All Analysis Steps shortcut

• Options and Control Values saved in ALiX Settings file

4.4.5: (4-14-2015)

• Added time-dependent calculation of background rate and implementation for burst search, burst analysis, ALEX calculations, burst inspector and burst data export

4.4.4:

• Added individual bin size for burst statistics histogram, as well as the ability to keep plots from job to job

4.4.3: (3-25-2015)

• Added Burst Rate Analysis Script 2 based on Savitzky-Golay filtering

• Corrected a bug in 3-Asymmetric Gaussian Fit

• Cosmetic changes

4.4.2: (3-18-2015)

• Added Burst Rate Analysis Script 2 to automatically determine max burst rate as a function of a control parameter

4.4.1: (3-12-2015)

• Added Plot clipping according to Graph boundaries in Histogram Fit

• Corrected bug in Time Trace axis scale

• Corrected bug in Burst Rate Analysis

4.4.0 (*): (3-2-2015)

• Started developing a general scripting framework

4.3.0: (2-26-2015)

• Alternation Period now allows selecting the whole period (one bin was missing)

• Scripting of Burst Rate Analysis

4.2.12:

• Allows loading ACF correction files one at a time, change their associated channel name and delete them (in Settings)

4.2.11 (*): (2-10-2015) 

• Added background rates settings, us ALEX offset option for time trace

4.2.10 (*): (2-5-2015)

• Improvements in PIH fitting

• Implementation of MLE and PIH Fit Sliding Window analysis of background in Advanced Background Analysis

4.2.9:

• Implementation of multispot SPAD Array photon-hdf5 data support

4.2.8: (12-23-2014)

• Implementation of CCFs batch computation

4.2.7 (*):

• Implementation of SPAD Array ACF correction