**2015-10-29 (GIT: 4464)****QuickFit**- on MacOS X: We don't use any Sheets/Drawers any more, but true dialog windows (as on windows)
- bugfix: improved preset window styles (were set strangely, when the settings dialog was opened the first time)
- on MacOS X: added configuration option to choose whether menus in sub-dialogs (e.g. RRD/Eval editor) are used as application menus
- added configuration option to choose whether many of the number edits use the mouse-wheel (or not) for changing the edit-value (this can be useful for the mighty-mouse on MacOS X, as it is hard to prevent mouse-wheel operations there)
- added sub-menu to the View-menu that contains links to raise any of the currently open QuickFit windows
- added context-submenu to table widgets that allow to directly create table RDRs from the selected cells

**tcspcimporter**- bugfix: Save Multi-Eval to Project did not work correctly (table columns were scrambled) [thanks to K. Toth]
- added background correction to TCSPC correlator

**FCS/FCCS**- bugfix: Groups were not set correctly for PicoQuant *.cor-files
- added background correction to TCSPC correlator

**2015-10-26 (GIT: 4444)****new code repository:****new plugins:****fit_nlopt**: makes the global optimizaton algorithms from the NLopt library available in QuickFit as (least-squares) fit algorithms**curve**: simple x/y (+errors) curves in the project. The source code of this plugin is also described online under https://github.com/jkriege2/QuickFit3/wiki/Write-an-RDR-plugin.**curve_fit**: simple least-squares fit for graphs/curves in curve- and table-RDRs.**qfe_alexeval**: added old evaluation code for ALEX-spFRET measurements from Sebastian Isbaner as plugin (registered in the extensions.menu of the main window!).**qfe_alexcontrol**: added old hardwrae control code for ALEX-spFRET measurements from Sebastian Isbaner as plugin (registered in the extensions.menu of the main window!).**qfqtimageimporter**: provides image series readers for BMP-, GIF-, PNG-, JPEG-, PPM-, PNM-, PGM-files. All are absed on the image-reading framework of Qt**qfe_dataexportbasics_xlsx**: export data-tables to Microsoft Excel (r) XLSX-files**qfe_nidaqmxreader**: allows to sample analog input channels of a National Instrument DAQ-card using the NI-DAQmx driver package (if available on your computer).**qfe_fcssimulator**: plugin, which controls an open-source FCS/FCCS simulator, available in this installation and under https://github.com/jkriege2/FCSSimulator.

**QuickFit**- plotter widgets:
- every single image plot may be saved as a rendered image (PNG/JPEG/BMP/...) via the context-menu
- improved autoscaling/zoom behaviour if data contains NANs
- bugfix: copy images didn't work in some cases
- you can now also copy the color palettes of an image plot to the clipboard
- bugfix: barcharts (bar widths) now also work for unsorted category data
- bugfix: copy to clipboard as image now works better on Windows (before it was not that easy to paste into PowerPoint!)
- added context-menu entry that allows to add plot curves to a curve RDR (e.g. for later data-fitting)

- expression parser:
- added vector creation functions ones(), zeros(), linspace(), logspace(), vector() meshgrid2d_x(), meshgrid2d_y()
- added function for real-values Faddeeva function used in TIR-FCS fit models: faddeeva_real()
- added function comment(), which does nothing and ignores any number of parameters
- added functions repeat() and repeatstring()
- added comments (single line with
`//`, or multi-line`/* ... */`. - bugfix: functions randvec(N,v1,v2) and randintvec(N,v1,v2) now work properly if more than 1 parameters are given
- bugfix: savefor() didn't work correctly for
`savefor(i,0:3,if(i%2==0,i,"bla"))` - improved function
`fitfunction_init(), fitfunction_fix()`, so parameters can be altered by parameter name - added functions:
`fitfunction_setparam(), fitfunction_setparammin(), fitfunction_setparammax(), fitfunction_parammins(), fitfunction_parammaxs(), fitfunction_paramabsmins(), fitfunction_paramabsmaxs(), fitfunction_fitranged(), fitranged()` - added functions:
`binomial(), factorial(), poissonpdf(), binomialpdf()` - added a new datatype "list", which is a list of (possibly different) values
- added a new datatypes "boolmatrix" and "doublematrix"
- added functions:
`list(), listappend(), listinsert(), listremove(), size(), sizecolumns(), sizerows(), dimensions(), doublematrix(), boolmatrix()` - added functions:
`reshape(), mat2vec(), vec2mat()`

- online-help:
- bugfix: the DOI's in the help texts should be linked now again!
- bugfix: in some cases the equations in a tooltip were displayed wrong (mixed up with old renderings!)
- bugfix: fixed an endless loop of the preparation of online-help pages in some cases
- added help-page on how to write a QFRawDataRecord plugin

- QF 3 now compiles with Qt 5.4 on MacOS X!
- added Faddeeva Package to support real-valued Faddeeva-Function, which is required by some TIR-FCS fit modelss
- several dialogs now have a maximize+minimize button in their header
- improved rendering of LaTeX expressions
- added (optional) support for general objective function minimization to QFitAlgorithm (+ implementations in the NLopt and GSL fit algorithm plugins)
- added menu entry "Tools | Copy SDK For Dynamic User Fit Function Libraries ..." which copies the SDK for user fit functions in a dynamic library into a folder on your computer.
- added option to settings dialog that allows to choose between native and Qt/QuickFit-specific file-open dialogs
- added easter-egg (have fun finding it ;-)
- added an error message/dialog, when an evaluation editor window does not open after a project-tree double-click, because no applicable RDRs were found in the project.
- added functions to export data from tables into Matlab *.MAT files as matrices [if possible]/cell arrays [otherwise]
- improved error reporting for the save-project and zip-project functions
- zipped-projects now also contain a
`.readme.txt`-file, which explains the contents of the ZIP-archive - added link to GitHub repository to several places in QuickFit
- improved function "Copy selected cells as table RDR with result access parser functions" in evaluation editor results table context-menu
- added the "Hack" font for nicer/more readable code and expression editing
- added option to choose font for code-editing
- improved style-preview in settings dialog
- bugfix: QFFunctionReferenceTool: behaves nicer, when selecting several characters in a parser expression (before, several small help-prepare windows appeared in fast succession)
- added option to settings-dialog (View/General Settings), which allows to choose a nonlinear scaling of the color-coding in VAR-COV-matrices (with a gamma-transform and user-selectable gamma!)
- extended QFitFunction with functions to estimate a specific parameter from an XY-location in a plot (also supported by library fit functions in a DLL/SOLIB...)
- "compound-result" in any RDR are accessible over the QFRDRCurvesInterface-interface, i.e. by curves-evaluations like the new curve_fit plugin
**FCS/DLS**- bugfix: corrected ALV-700X parser, which now can also properly read files, which only contain two FCCS-curves.
- bugfix: CSV import did not work, when tgegege is selected, but the file only contains 2 columns
- added support for reading PicoQuant exported ASCII FCS correlation curves (*.dat files) [thanks to Martin Seefeld, Uni Heidelberg]
- added support for reading PicoQuant *.cor ASCII files
- improved error reporting while importing data: there will be error messages now, when trying to import a non-existent file.
- added check-box to correlation editor, which allows to retain the current zoom-level when changing between runs and/or RDRs
- added Confocor2 import

**FCS fit**- added additional fit statistics parameters: AICc (also weighted), BIC (also weighted), max. rel. parameter error, bayesian model probability
- improved documentation of fit statistics
- added tutorial for model selection
- bugfix: the "show key" checkbox works now
- added overlay plots of the runs in a single RDR
- the fit statistics now display the var-cov-matrix of the fit with color-coded entries
- LMFit is now the default/proposed fit algorithm. It is comparable to levmar, but significantly fatser! Also it now calculates parameter errors from the Var-Cov-Matrix and so no reason exists to use the slower levmar.
- added option to general settings-dialog (View/General Settings), which allows to choose a nonlinear scaling of the color-coding in VAR-COV-matrices (with a gamma-transform and user-selectable gamma!)
- added context-menu that allows to estimate fit parameters from the mouse-position in the main plot (if the model supports it)

**imaging FCS fit**- added additional fit statistics parameters: AICc (also weighted), BIC (also weighted), max. rel. parameter error, bayesian model probability
- improved documentation of fit statistics
- bugfix: the "show key" checkbox works now
- added overlay plots of the runs in a single RDR
- the fit statistics now display the var-cov-matrix of the fit with color-coded entries
- The imFCS Calibration Wizard now shows an additional plot with the final wxy(a)/wxy(delta) curves and indicates the final result for wxy in the plot.
- added option to general settings-dialog (View/General Settings), which allows to choose a nonlinear scaling of the color-coding in VAR-COV-matrices (with a gamma-transform and user-selectable gamma!)
- added context-menu that allows to estimate fit parameters from the mouse-position in the main plot (if the model supports it)

**FCCS fit**- added additional fit statistics parameters: AICc (also weighted), BIC (also weighted), max. rel. parameter error, bayesian model probability
- improved documentation of fit statistics
- fit statistics are now save as global (for the complete fit) and local (for each curve in the global fit set separately). Note: The local fit statistics give limited information, because it does not take into account the other curves!!!)

**imaging FCCS fit**- improved documentation of fit statistics
- fit statistics are now save as global (for the complete fit) and local (for each curve in the global fit set separately). Note: The local fit statistics give limited information, because it does not take into account the other curves!!!)

**imaging FCS**- bugfix: selections and masks are no longer lost, when the data files are not found and the "fix file pathes" toll has to be used!
- extended imaging FCS simulator:
- added a second set of particles (with different D)
- diffusion is now either simulated on the whole space, or on the lower half-space only
- flow can be limited to the right-half of the simulation plane
- more automatic string-replaces in the output filename
- Now should use tinytiff-reader automatically for correlation
- added runtime and ETA displays to simulator progress
- added 3rd green component
- added options for boundary conditions
- added possibility to store PSFs, MSDs, trajectories and jump length distributions from the simulation
- improved options to set the output filename
- added grids of barriers or traps as environment, which model different conditions in cellular membranes
- added two different PSFs (either 2D gaussian or 2D square pixel with gaussian PSF

- bugfix: correlator didn't recognize background image series from imFCS simulator.
- added display options for annotations of the imFCS RDR
- added model comparison function to "imagingFCS Tools" menu, entry "Annotate Model Comparison", which can also calculate model probability maps from (non-normalized) Bayesian model probabilities
- implemented blocking method to estimate the standard error of the correlation function for some correlators and segments=1
- several results of the correlation process (e.g. bleach correction fit results, blocking transform results, ...) are now readable as RDR results and thwipus displayable as parameter images. Note: If you delete one of these results, it will be regereated/reread when reopening the project!!!
- bugfix: segment number and length were switched in evalsettings.txt files
- aded a wizard that allows to correlate (several) files and add the results to the project, also may add evaluation objects
- added wizard to add imaging FCS evaluation objects to the project
- added explicit project-wizard menu entry for "imFCS calibration wizard
- added correlation amplitude as metadata
- added metadata parameter-image for the correlation amplitude

**number and brightness**- bugfix: When using the wizard several times, old files were re-inserted!
- bugfix: selections and masks are no longer lost, when the data files are not found and the "fix file pathes" toll has to be used!

**FCS MaxEnt evaluation**- DLS-model: changed preset of offset A=1 to A=0 and renamed A to "Offset A"
- bugfix: fixed handling of offsets Ginfty and added offset to simple confocal FCS model
- bugfix: only run/index 0 was accessible, if more runs were available in an RDR, they were not displayed (thanks to Martin Wolff, Uni Potsdam)
- bugfix: MaxEnt parameters and data cuts are now enabled/editable, when an unfitted record is selected.
- added overlay plots of the runs in a single RDR
- bugfix: If a fit was once canceled, all following fits were also canceled after the first run/file, until QuickFit was closed and reopened
- bugfix: the overviewplot of ACF+fit now should work
- MaxEnt distributions are now stored as "compound-result" and are accessible over the QFRDRCurvesInterface-interface, i.e. by curves-evaluations like the new curve_fit plugin
- added improved and very extensive MaxEnt tutorial

**FCS MSD evaluation****MAJOR BUGFIX:**Before this versions, all 2D-diffusion MSD models returned an MSD, which was a factor of 2/3 too high! This was fixed now. See the documentation for the correct models. [Thanks to T. Wohland for pointing me to that]- bugfix: correlation function range edits are now enabled/editable, when an unfitted record is selected.
- added overlay plots of the runs in a single RDR
- bugfix: corrected the model equations in the online-help (there was a wxy^2 instead of a gamma^2wxy^2!)
- added an offset G
_{∞}to all models - bugfix: If a fit was once canceled, all following fits were also canceled after the first run/file, until QuickFit was closed and reopened
- "get N from fit results" tool can now also read imagingFCS fit results (i.e. from results that are stored as vectors which are index by the run/index/pixel)
- MSD curves are now stored as "compound-result" and are accessible over the QFRDRCurvesInterface-interface, i.e. by curves-evaluations like the new curve_fit plugin

**Diffusion Coefficient Calculator**- bugfix: D20W was not calculated correctly, when a D at arbitrary conditions with viscosity factor !=1 was given!
- added button to maximize window (thanks to Norbert M.)
- added an option for user-defined partial specific volumes for globular particles (+ presets for proteins, DNA, ...)

**SPIM-FCS fit models****MAJOR BUGFIX:**some of the 2-pixel FCCS models has an additional factor of 1/a^2, which was wrong. Therefore the particle number estimate from these models was wrong! [Thanks to F. Taheri]- added model for SPIM-FCS autocorrelation with diffusion and flow
- added 2-color FCCS model for 3D anomalous diffusion
- added 2-pixel FCCS 3D anomalous diffusion model

**TIR-FCS fit models****MAJOR BUGFIX:**The TIR-FCS fit models with square-pixels had an additional factor 1/a^{2}, which was wrong in the code (NOT IN THE DOCUMENTATION!). This is fixed now!- added model for TIR-FCS autocorrelation with diffusion and flow (pixel-detector)
- added 3D/2D anomalous diffusion model for confocal TIR-FCS
- added 3D/2D normal diffusion model for confocal TIR-FCS
- added 3D/2D normal diffusion model with variable moleculr brightnesses for confocal TIR-FCS
- added 2-pixel FCCS 2D anomalous diffusion model
- added 2-pixel FCCS 2D normal diffusion model

**2-focus Confocal FCCS fit models**- added 2-focus FCCS 3D anomalous diffusion models

**confocal FCS fit models with parameter distributions**- added model with normal distribution of D and numerical integration

**simple TCSPC reader**- added reader for Text files generated by Picoquant

**TCSPC importer**- added fluorescence liftetime (TCSPC microtime) histogram preview
- added an option for time-gate/lifetime-filtered FCS/FCCS to the correlator [thanks to Martin Seefeld, Uni Heidelberg for providing test-datasets]
- bugfix: countrate is now saved in the correct units (kHz instead of Hz) in the correlator output file (before it was a factor 1000 too high!)
- bugfix: fixed a small bug in the normalization of the TTTR correlator that could have an influence at low count rates
- FCS countrate binning is no longer set automatically from measurement length in file
- more metadata on the processing is written to the results files (and subsequently loaded into the FCS RDR)
- bugfix: it is now possible to set the number of segments to >100
- bugfix: there were some counter overflows when calculating the binned countrate for FCS files.
- bugfix: countrate RDRs were imported into the project without setting the proper group.
- new: sgements can either be defined by their number (during the meausrement duration), or alternatively by a fixed segment duration
- new: may create lifetime-histograms now
- new: added FRET Burst Analyzer
- improved error reporting when selecting a file that cannot be read
- added example dataset
- added input widget for Foerster-radius, so the DA-distance is calculated from the E
- if "Save to Project" is used, the created tables now allow to recalculate E (and rDA from it) dynamically with a user-selectable gamma-factor and Foerster-radius R0

**Table**- added Tools menu entry to quickly calculate and plot boxplots from columned data
- added Tools menu entry to quickly calculate and plot indexed statistics from columned data
- improved import from clipboard/file: data may be pivoted/rotated now in the import dialog (by a button above the table)
- fixed tab-order of plot/graph-settings widgets
- bugfix: sometimes, old column properties were strangely reappearing when removing columns
- bugfix: barcharts (bar widths) now also work for unsorted category data
- bugfix: sort function didn't work under some conditions and scrambled the undo/redo stack
- can read properties from CSV files
- the fit and regression tools show residuals only for the selected datapoints now
- improved import in case of whitepsace-separated ASCII-files, before empty columns were inserted when multiple whitespaces occured in a file
- improved parameter-widgets for hor/ver range graphs and added option to draw line-only or line+/-error
- implemented QFRDRCurvesInterface for compatible plots in a table RDR

**cairo graph exporter plugin**- added finer grained export options for different subformats (e.g. SVG 1.1&1.2, PDF 1.4&1.5, EPS2&3)
- license is now LGPL 2.1

**lmfit fit algorithm plugin**- some of the lmfit fit algorithms now estimate errors from the variance/covariance matrix of the fit (estimated numerically)
- fitalgorithm_lmfit is now licensed under the permissive BSD 3-clause license (taken from the underlying library)

**GSL fit algorithm plugin**- some of the GSL fit algorithms now estimate errors from the variance/covariance matrix of the fit (estimated numerically)

**Spectra Viewer**- spectra database is now loaded in parallel to the program startup, so you can immediately start using QuickFit, but the SpectraViewer plugin will be enabled only a few seconds later ...

**fit_levmar**- this fit algorithm is deprecated now, since fit_lmfit is a faster replacement, which has essentially the same features!

**basicimageexporter**- added exporter for Matlab MAT-files (using TinyMAT)

**picoquantimporters**- importers read more metadata from TCSPC files now.
- can now read v6.0 T3R files

**image_stack**- improved user-control over color-channel value-ranging

**fitfunctions_general****function changes:**modified all log-normal distributions to have log10(x)-log10(mean) as parameter!- license is now LGPL 2.1
- added fit function: Peaks: Multi-Component Gaussian function (1/sqrt(e) width)
- added fit function: Peaks: Multi-Component Log-Normal
- added fit function: Decays: Multi-Exponential
- improved estimation of multiple peaks (corrected wrongly estimated baseline for 2 or more peaks!)

**fcs_fitfunctions**- added code for single-parameter-estimation (from XY) and initial-parameter guessing

**qfe_dataexportbasics**- license is now LGPL 2.1

**rdrsettings**- license is now LGPL 2.1

**fitalgorithm_simanneal**- license is now LGPL 2.1

**Table**- license is now LGPL 2.1

**qfe_calculator**- improved user-interface with resizable (and always visible) editor for longer scripts
- bugfix: behaves nicer, when selecting several characters in a parser expression (before, several small help-prepare windows appeared in fast succession)
- license is now LGPL 2.1

**qfe_helpeditor**- license is now LGPL 2.1

**lights_b040laserbox**- added electronics description of B040 LaserBox (to control Cobolt lasers)

**shutter_servo_arduino**- added hardware description, PCBs, firmware, ...

**meas_b040resheater**- added hardware description, PCBs, firmware, ...

- plotter widgets:

**2015-03-18 (SVN: 3891)****new plugins:****qfe_plotterexportercairo**: additional export filters to PDF/EPS/PS/SVG, using the cairo graphics library**eval_cameracalibration**: new evaluation plugin for camera gain calibration**eval_beadscanpsf**: new evaluation plugin for the evaluation of beadscans (z-stacks), determines the PSF**eval_colocalization**: new evaluation plugin for a colocalization analysis**basicimageexporters**: new plugin, which allows to store image series in different standard formats (TIFF, RAW, ...)

**removed plugins:****qfe_defaultmathparserextensions**: functionality was incorporated into the QFMathParser standard library

**QuickFit**- plotter widgets:
- data table in plotter now has context menu entry to copy data as CSV
- changed appearance (default width of grid lines)
- improved speed of JKQtPlotter
- added rel. shift to error bars, as this allows to have shifted errorbars on bar charts
- added example for barcharts
- added asymmetric errorbars (different lengths to upper and lower bar.
- impulse-plots and filled_curve-plots now support a baseline-parameter
- bugfix: crash, when images have size 0 or NAN
- parametrized scatter plots now use the correct color palette
- axis tick labels can be rotated now
- key can also be layout as one row
- bugfix: fixed plotting of errorbars, that span below 0 in log-plots

- expression parser:
- added function findfirst()
- added function randvec_seed(), randintvec_seed(), randnormvec_seed(), randboolvec_seed()
- added functions cumsum(), cumprod(), diff(), mad(), nmad(), indexedmad(), indexednmad(), trapez()/trapz()
- added functions for date/time handling: now(), datenum(), datetimenum(), date2str(), datetime2str(), datediff2secs(), datediff2mins(), datediff2hours(), datediff2days()
- parser now supports user-defined functions, that have qfmpNode*'s as parameters, rather than qfmpResult's (this allows for constructs, like "for()" in user-defined functions
- bugfix: regular expressions functions now work correctly
- added functions for filename-handling: extract_filename, extract_basename, extract_complete_basename, extract_ext, extract_complete_ext, extract_file_path, extract_absolute_path, extract_absolute_file_path, clean_string_for_filename
- added function replace()/multireplace() for strings/vectors
- for() now also create string and boolean vectors
- added functions join(), split(), removeemptystrings(), ... for strings/string vectors
- added functions rdr_ids(), eval_ids(), rdr_getresult(), rdr_getresulterror(), rdr_getname(), rdr_getfolder(), rdr_getgroup(), rdr_getresultids(), rdr_getevaluationids() to access the current project
- added functions filterfor() and savefilterfor(), which allow to filter vectors according to an arbitrary expression/condition
- added type conversion functions strvec(), numvec(), boolvec(), bool(), double(), ...
- added functions, that allow to access data in a table RDR: table_...()
- bugfix: logical operations were not allowed for boolean vectors!
- added functions ensuresize() and ensuresize_start(), which cut/extend vectors to a given size
- added functions to access overview images (overview_...()), named image selections (imageselection_...()) and image masks (maks_...()) in RDRs
- bugfix: unary logic negation (!/not) was not implemented for boolean vectors!
- bugfix: corrected parser, so it understands [...] vector-expressions correctly, when they are preceded by a !/-/~/... (e.g. ![true,false])
- bugfix: regexpcontains(...) now works properly (i.e. works at all ;-)
- added functions isvoid(), isbool(), isnumber(), ... to check datatypes
- added function isvalid()
- improved algorithm of shuffle() to use the math parser random number generator (can be used in table-plugin expression without causing a compare error/"timeout")
- added functions that calculate histograms
- added functions that allow to access QuickFit's predefined fit functions
- added functions for model fitting (least-squares fitting)
- bugfix: function assignment now works properly
- bugfix: all median()/quantile()/min()/max() parser functions now should properly ignore NAN values.
- added functions to access run-selections
`runex_...()`in FCS,... records - You can use C-style escapes (
`\" \' \n \r \t \\ \/`) to add the delimiting characters to a string constant - added functions to the default lib, which were in the plugin qfe_defaultmathparserextensions before
- rangedhistogrambins() functions can now also be called without the data vector x as first argument.
- added function polyfit(), which obtains the least-squares coefficients of a polynomial from given data
- bugfixed crash of function shuffle() ... this function now also shuffles strings
- added functions: printexpression(), printexpressiontree()
- change in syntax: parser now also allows index-access to expressions (e.g.
`(1:10)[2,3] = [3,4]`)**note:**This change made expressions, like`3:-1:1`wrong now, they have to be reformulated with parantheses:`3:(-1):1`!!! - index access with [] now also works with boolean-indices
- added support for structs and functions: struct(), structget(), structsaveget(), structkexs()
- new functions: defaultfor(), quantile25(), quantile75(), itemorfirst(), firstinvector(), lastinvector()

- added context menu entry to tables, that allows to explicitly copy the table as "CSV", or to copy the table in a format suitable for "Excel", which depends on the current locale (e.g. for decimal separators)
- bugfixed "copy to Excel/CSV" in table view, which did not copy any data (regression?)
- improved LaTeX rendering
- improved rendering of math in online-help and plotter widgets
- results table export in RDR and evaluation now supports more file formats (via data export plugins)
- added newer version of the XITS fonts
- improved speed in JKQtPlotter, especially during resize (delayed plot)
- updated to Qt 4.8.6
- limited LOG-filesize to 50MB
- improved speed of search in online-help
- a right-click on any fit model selection combobox opens a context-menu with links to the model help and the model selector dialog
- added button "next of same role" and menu-entries to all RDR editors
- increased font size in online-help
- improved online-help
- bugfix in "copy table as image" (available in the context-menu of most tables in QuickFit3), the image now does not have a black background anymore (is no longer unreadable)
- bugfix of regression: online-help didn't display table of contents properly
- started adding a simple SDK for C fit functions
- the Tutorials page in QuickFit's main help now also lists all sub tutorials for each plugin!
- improved search speed in online-help search!
- select RDR dialog now has a completer for the filter string
- added Help-menu entry for citing QuickFit (this was a bit hidden in the copyright-help page before!
- added support for user-definable fit function in external shared libraries. This allows to write fit functions in C/Pascal/... or any other language, that can produce shared libraries. They will show much better performance, than user-defined fit functions using the internal expression parser. QuickFit now searches for these plugins in the sub-directory sdk_fitfunctions and sdk/sdk_fitfunctions.
- QuickFit now also searches for plugins in sub-directories
- Added citing tab to About QuickFit dialog, improved citing page in online-help
- fit algorithms should use the multiEvaluate() function of QFFitFunction now.
- prepared main window for (different) wizards
- online-help now supports a list of FAQs for QuickFit and for plugins
- Tools | Project Tools | set property in multiple RDRs: now can also set the name/rolw/folder/group of RDRs.
- added option dialog entry, which allows to set a global path for user-settings/config files
- added autolinks to the online-help system
- in results tables: parameter histograms now support a relaxed auto-ranging
- in results tables: parameter histograms now support a distribution fit to the histogram
- in results tables: parameter correlation now support a relaxed auto-ranging
- bugfix: in results tables: parameter histograms works correctly for auto-ranging
- bugfix: fixed possible crash, when loading a project, which contains an evaluation object, for which no plugin is installed.
- QFImporters can now return properties from the file
- added possible init()/deinit() methods to fit function, fit algorithm and importer plugins
- evaluation editors|results table: added checkboxes, which allows to show an additional column with the run/index/pixel of the result and a checkbox, which allows to hide all removed runs/indices/pixels
- FFitAlgorithm now supports error estimates via bootstrapping, in fit()
- added help page, which displays all registeres tooltips and autolinks
- added stylesheet (CSS) for main help formating
- added widgets to options dialog, which allow to set the font name and size in the main help
- added menu entry to RDR editor, which allows to export the contained data into a file (only enabled, if the plugin supports this function!)
- added preview plot to user fit-function editor
- added dialog to calculate RDR properties (Tools|Project Tools|calculate RDR properties) using the internal math expression parser
- bugfix: completer in editors of the evaluation editor widnows now work correctly and store the list of texts to disk
- added initial support for image file meta-data, such as OME or from ImageJ
- added support for zipped QFP-project files (*.qfpz)
- added function (File | Compress Project), which compresses the project file and all linked (and required) files into a single ZIP-archive
- bugfix: possible crash, when user adds a new property to an RDR
- added welcome screen, which allows to access common tasks (new Project/open project/wizards), the recent projects, the tutorials and some of the online-help
- added buttons "toggle selected"/"select selected"/"deselct selected" to the project tools "set/calculate RDR properties ..."
- bugfix: "set properties in multiple RDRs" now works correctly for name/folder/group/role (did not set the given string, but tried to convert it in some cases to a number/Boolean)
- added additional level of project backup file (*.qfp.backup_old)
- added menu entries to main window, which allow to duplicate items (RDRs/evals) and to copy/cut/paste items to/from the clipboard
- added button/menu entries to evaluation and RDR editors, which allows to view vector/list/matrix data from the results tables as a new table, where each cell is displayed in its own column. This displays any type of data (number, string, boolean, string lists, boolean lists, number lists, ...)
- added context-menu entries to evaluation and RDR editors, which allow to copy the RDR ID/result ID/evaluation ID or a rdr_getresult(...) template for the current cell into the clipboard.
- editing of RDR/Eval names in project tree can now be done using the systeme dit key (e.g. F2)
- bugfix: "duplicate evaluation" did not work correctly
- added View menu, which now allows to set the sort order of the current project.
- added context-menu entry to (most) tables, which alows to save the table as an image file (SVG/PNG/TIFF/...)
- added buttons for wizards to the toolbars of the main window
- added context-menu entry to files list in RDR editor window, which allows to open file with the associated system program
- online-help of fit functions and algorithms now show the function/algorithm ID in the header. Help pages for plugins show the plugin ID.
- added automatic parameter and fit function and algorithms property descriptions to the online-help system
- fit algorithms now support parameter transforms, if a special parameterType is specified in a QFFitFunction
- added menu entry to evaluation/RDR editors (result table tab), which allows to delete all results
- online-help system now supports the shortcut
`$(...)$`for`$$math:...$$`and`$[...]$`for`$$bmath:...$$` - automatic links for DOIs are added to the main help
- histograms show sub-plots for fit functions that support this (e.g. all single Gaussians in a double-Gaussian function)
- bugfix: online-help works correctly on Linux now (didn't recognize certain plugins correctly)
- bugfix (thanks to Jan Buchholz): cleaned up relative path handling in projects and project file names, especially on Linux
- CSV fileformat parameter dialog now have a button, which inserts a tab into the column separator field.
- Mask edit tools: added function "copy mask to RDRs"
- added Tools|Project Tools-menu entry, which allows to edit the groups, roles and folders of all RDRs in the project in a clear and concise manner
- added special FAQ lists for the expression parser
- fixed a crash, when exporting data from a table to an Excel97 (or another data) file
- improved CSV import dialog with table preview, parameter guessing and pre-saved configs
- QuickFit source code is compatible to Qt 5.x now!
- added libjpeg and updated cairo/pixman to newer versions
- added functions to libquickfcit, which allow to define 2D and 3D fit functions and to fit with these (implemented in QFFitAlgorithm)
- improved startup speed by improved search for plugins
- added possibility to write exporter plugins (QFExporter) and image series exporter plugins
- a category is now assigned to each fit function and they are displayed as a tree with these categories, where possible
- fixed some memory leaks
- added more status info outputs to the system log, when starting QuickFit
- improved rendering speed of online-help, using a caching strategy
- added save menu entry to the online-help window
- splash screen gives a better indication of loading progress/status now (with a progress bar)
- image reader plugins now support multiple channels
- added widget to configuration dialog, which allows to set the global config directory
- added context menu entry to evaluation results tab of evaluation editors, which allows to copy fit results to a table, where expressions are used to dynamically access the data (where possible).
- "open Project" button in Toolbar now has an arrow, which drops down a list of the recent files

- plotter widgets:
**imFCCSFit**- fixed a possible crash when selecting a new fit function by hand
- fit parameter names are more expressive now
- the tool to calculate the crosstalk-corrected rel. FCCS amplitude now supports background-correction
- replaced "run" by "pixel" to clear up the function
- added button "go to average pixel"
- added additional options for fit weighting (from standard deviation over 3,5,7,11 consecutive values of the curve, deviation from polynomial-smoothed version)
- added context-menu entries "copy Min/Max to all" to data-cut sliders
- added button "go to average run" to overview image
- added function to load/store custom global fit settings
- added example project for directed motion/flow
- new: added error estimation, using bootstrapping to curve fit (in plots)
- when removing a file, it is now possible to select the file that should be removed (default: last file)
- bugfixed possible crash, when applying the relative CCF amplitude tools to two different projects in the same instance of QF3
- bugfixed possible crash, when RDRs are deleted from the project
- bugfix: now it is no longer applicable to FCS data, only to imFCS data!
- added menu entry to set/reset fit parameters in all RDRs/runs (Tools Menu)
- improved fit speed by using multi-threading
- added "Reset Everything" button
- added menu entry "Check fitted filesets", which removes all fitted filesets, for which no fit results exist
- the menu entries "store/load global fit presets" also store and possibly (after a user-question) load the preset fit parameters, ranges and errors
- new/faster multi-threaded fit is default fit now

**FCCSFit**- fit parameter names are more expressive now
- bugfix: fixed possible crash, when trying to select anew fit model
- added additional options for fit weighting (from standard deviation over 3,5,7,11 consecutive values of the curve, deviation from polynomial-smoothed version)
- added function to load/store custom global fit settings
- new: added error estimation, using bootstrapping to curve fit (in plots)
- when removing a file, it is now possible to select the file that should be removed (default: last file)
- the menu entries "store/load global fit presets" also store and possibly (after a user-question) load the preset fit parameters, ranges and errors
- bugfix: shouldn't forget the cut-range any longer
- added menu entry to set/reset fit parameters in all RDRs/runs (Tools Menu)
- added "Reset Everything" button
- added fit repeats and global/local iterations controls
- added checkbox, that allows to NOT fit excluded runs
- added full tutorial to online-help

**General fit functions**- bugfix: some parameters in exp/dblexp were fixed initially
- "Waveforms: Sine" now also calculates the period=1/frequency
- added Cosine waveform
- added centered polynomial
- added Gaussian distribution function
- improved/bugfixed parameter estimation for Hill function and mod. Hill function
- added double log-normal function
- added skewed Gaussian distribution function
- improved estimation of width of distributions (it is now limited to ~2*data-distance)
- added fit function for segmented lines
- added fit function for segmented power-laws
- added fit function for a parabula with center and offset as parameters
- added fit function for properties (width/z-intensity) of a Gaussian beam
- added fit functions for several probability distributions (PDFs and CDFs) that are normalized, i.e. no amplitude and offset parameters

**dataexport_basics**- bugfix: the plugin did not export the headers properly

**FCS fit functions**- simple_exp: parameters are sorted by decay times now!
- added function for normal diffusion fit with different relative brightnesses of the species, which also supports up to four blinking components
- added fit function for anomalous diffusion with different molecular brightnesses
- added fit function for 2D normal diffusion
- added fit function for 2D normal diffusion with different molecular brightnesses
- added fit function for 2D anomalous diffusion
- added fit function for 2D anomalous diffusion with different molecular brightnesses
- added fit function for 2D normal diffusion with stretched exponential photophysics
- added fit function for 3D normal diffusion with stretched exponential photophysics
- added fit function for 3D normal diffusion with afterpulsing and C instead of N as parameter
- added fit function for 2D normal diffusion (xy) in TIRF-FCS ... these are just renamed versions of the 2D diffusion confocal model versions
- fit function with flow and v as parameter now supports up to three diffusing species and up to two non-fluorescent states

**DLS fit functions**- added fit functions for normal distribution of correlation times, which calculate the integral with numeric integration (improved accuracy over the old implementation with a sum!)
- added fit functions for log-normal distribution of correlation times, which calculate the integral with numeric integration (improved accuracy over the old implementation with a sum!)

**FCS fit functions with parameter distributions**- added fit functions for normal distribution, which calculate the integral with numeric integration (improved accuracy over the old implementation with a sum!)
- added fit functions for log-normal distribution, which calculate the integral with numeric integration (improved accuracy over the old implementation with a sum!)

**2-focus FCCS fit functions**- added fit functions for 2D diffusion and 2D diffusion+flow
- added documentation for all fit functions
- added fit functions for 3D diffusion without flow, but with C instead of N as parameter
- added flow angle, centered around 0° and 180° as calculated fit parameters to models with flow

**SPIM-FCS fit functions**- added presets to imfccsfit, which allows to perform a flow measurement with 4 neighboring pixels
- flow FCCS fit functions also calculate the angle of the flow now
- added FCCS fit function with flow and 1/e^2-width and new Veff
- added model of multi-component normal diffusion with different relative molecular brightnesses per species
- marked several 1/sqrt(e)-models as deprecated!
- added fit function for 2-pixel FCCS with 1-3 diffusing components (no flow)
- added fit function for 2-pixel FCCS with 1 diffusing+flow component and one diffusing global component (does not mind the shift!!!)
- added flow angle, centered around 0° and 180° as calculated fit parameters to models with flow
- 2-pixel FCCS fit function with flow now also support several diffusing species (with different diffusion coefficients, but a single flow velocity)

**TIR-FCS fit functions**- flow FCCS fit functions also calculate the angle of the flow now
- added model of multi-component normal diffusion with different relative molecular brightnesses per species
- bugfix: some models did not calculate the third component properly
- bugfixed: "TIR-FCCS: 2D Diffusion+Flow (1/e² radii)"
- added models for 2-color TIR-FCCS with anomalous diffusion
- added flow angle, centered around 0° and 180° as calculated fit parameters to models with flow
- added fit functions for 3D+2D diffusion
- 2-pixel FCCS fit function with flow now also support several diffusing species (with different diffusion coefficients, but a single flow velocity)

**imagingFCS**- bugfix: set background from selected pixels function didn't work correctly
- bugfix in "mask by image" dialog: sliders should be properly initialized now
- added additional button to GUI, that allow to access several functions from the menu quickly (copy mask to group, mask builder, copy fit result statistics, ...)
- added menu entries/buttons to mask by the overview image, channel 2 (so far only masking by channel 1 was possible)
- "set background from ..." functions stored the background divided by the frame time in the properties BACKGROUND and BACKGROUND_STD. Now the additional properties BACKGROUND_DIRECT and BACKGROUND_STD_DIRECT contain the same data, but without dividing by the frame time.
- bugfix "copy fit results statistics..." did not copy the results of the "relative imFCCS amplitude" evaluation tool
- simplified display of images (less ticks...)
- "copy fit result statistics to table": added possibility to copy from named selections
- displays average and background intensity for the selected pixels in the parameter image tab (near the bottom in the controll list on the rhs)
- bugfix: data-cut-sliders below correlation curve display in image editor tab do not disappear anymore
- added tool to correct CFs for an offset
- "copy fit result statistics to table" now also copies the overview image intensities
- the average+/-SD of both parameter images and possibly of both overview color channels is displayed in the text line above the images now + values should be updated now, when the fit parameter is reselected
- The function "Data|Insert Correlation Curves as new RDR into Project" now also creates two ACF+FCCS records from an FCCS imagingFCS record and can be configured more deeply!
- improved speed, when changing from one RDR to another
- imageingFCS correlator now only save lag times, that are smaller than the segment length (there is no data for larger lags anyways ;-)
- parameter correlation tab now has the possibility to color the scatter plot symbols according to a parameter image, coordinates etc.
- post-processing binning now supports a mode for overlapping/interleaved binning (i.e. no reduction of image size)
- masks now work when using post-processing binning
- histograms now support a relaxed auto-ranging
- parameter correlation now supports a relaxed auto-ranging
- parameter histograms now support a relaxed auto-ranging
- parameter histograms now support a distribution fit to the histogram
- added warning to the correlation dialog, when you try to correlate files, that are larger than 1GB, since this will require a lot of RAM!
- added initial support for image file meta-data, such as OME or from ImageJ (e.g. reads image stack size from file header, pixel sizes, ...)
- added "DCCF display" (correlation plot/selection display) mode for parameter image tab, which simply plots the correlation curves from all RDRs from the current group.
- added "Preview" button to correlation dialog, which will display the first frame from the image series in a separate window
- copy fit result statistics can now also add RDR properties to the output table!
- added menu entry to Mask/imagingFCS Tools menu, which allows to set the background from the mask in all imFCS RDRs in the project
- if a few (less than 5%) of the per-run/pixel errors of the CFs are 0, they are replaced with an average over the other errors ... this helps to overcome small glitches in the data, where one or two errors are close to 0
- excluding segments now does not delete the mask any more!
- correlator dialog: added entries to the crop-button, which allow to crop the left/right/top/bottom image halves.
- added context-menu entries and buttons to several widgets in the parameter image tab, which allow to reuse the current display settings in other RDRs.
- after correlation: N and B records are now split by color channel (when newly inserted into the project!)
- selection builder/mask builder can now be applied to a selectable list of records and can optionally save the selection to a named selection
- mask by intensity supports relaxed color-scaling for overview image
- improved bleach correction in correlator: In some cases, the background correction could lead to negative values in the intensity traces, which could lead to bad bleach correction. These values are filtered now!
- the plugin now exposes the time-averaged image as image stack No. 2, so we can e.g. use the colocalization plugin on this data
- improved resistance of bleach-correction to intensities, which are below the background intensity
- added tool (ImagingFCS Tools menu in RDR editor) to calculate FCS diffusion law
- overview images in tab "Images, Countrates, Videos" may be viewed as fit results (if they have the same size, as the imFCS acquisition in the same record
- mask may be copied also to records with different sizes (mask is rescaled then!), when "Mask | copy mask to ..." menu entries are used

**table**- added "QuickStatistics" and "QuickHistogram" tools, which show the statistics and histograms of the current selection (column-wise)
- added function to autoset column width ("Table" menu)
- added function to internal function parser: columntitle(), columntitles(), columnindexbytitle()
- in "column property editor" dialog: added context menu entries for relative column references to expression editor
- "edit column properties" dialog: added button that saves properties, but does not recalculate the expressions in the sheet
- added options to set key line width, line color, background color, ...)
- bugfix: several data access methods in function parser did not work properly for row>columnCount
- added more table export formats
- new format (XML) for graph settings templates
- added "Refit" option to fit and regression results (only works for fits/regressions calculated in QF3 version starting from this!)
- added special column with increasing number (1,2,3,...)
- axis labels can be set from table columns
- bar-charts now support errors
- date/time/date-time axis labels work properly now
- added parser functions colsavg(), colsstd(), colsmedian(), ..., which calculate a column of averages for each row in a set of columns
- massive speed improvement, when evaluating expressions in the table (column and/or cells)
- bugfix: in fit dialog the parameter ranges are editable now!
- table fit dialog now has a button for help on fit models and algorithms
- table fit dialog now has a button that opens a fit model selector
- table fit dialog allows to select weighted/non-weighted fit
- added button to configure fit algorithm parameters to table fit dialog
- bugfix: labels from column on plot axes were not displayed correctly (first label doubled!)
- added offset/baseline to barcharts, impulses, filled curves
- errorbars may be asymmetic now
- added checkbox do show/don't show the plot title
- added widgets for several parameters to format the key (offset, separation, margin, symbol length)
- added button to automatically set width/shift of bar charts
- when doing fit/regression, graph colors are set properly (either they are not changed, or set, as in the source graph, but darker!)
- bugfix: autocolumn 1,2,3,... is now truly 1,2,3,...
- plot magnification property is hidden now!
- added checkbox to hide the key entry for a graph
- added possibility to filter for a range of values
- newly inserted rows/columns ar not initialized as numbers (0.0) anymore
- bugfixed: some possible crashed, when insetring a row/column at the start/end of the table
- calculated fit parameters are now properly updated in fit dialog
- bugfix: range-editing widgets should be usable now and the tab-order of the widgets was corrected
- graph settings are now shown inside a scroll-area, if required
- bugfix: error is now displayed correctly in curve fit dialog
- new: a table can be made editable with an entry in the menu of the table RDR editor
- new: added error estimation, using bootstrapping to curve fit (in plots)
- bugfix: all fit properties (including errors) are now saved properly and fit parameter errors are displayed, in the graph editor of the fit function
- parametrized scatter plots now use the correct color palette
- added additional filters with logic operations connecting them
- added "import into table" function+button
- added option to rotate axis tick labels
- improved startup speed of column editor dialog
- data for plots can be sorted now
- added widgets to control the major and minor grids of a plot more finely (width/color/style separate for both grids and grids switchable along all axes)
- fit/regression now also minds strided and selected data
- column expression editor now is a multi-line edit widget
- added variable "thisrdr" to column/cell expression parsers, which references the current table RDR (as rdrID)
- added checkboxes to cell/column expression dialogs, which allow to switch off the preview calculation. The syntax check is still performed!
- bugfix: all median()/quantile()/min()/max() parser functions (column statistics!) now should properly ignore NAN values.
- bugfix: median/minimum columns were not shown for boxplots
- bugfix: auto-set buttons for X/Y-data in plots didn't work correctly
- in plots: symbol line width can be set now
- in keys: layout as one row is supported now
- fit dialog now allows to set bootstrapping options
- added more options for bootstrapping to the fit dialog
- added more weighting options to the fit dialog
- added menu entry to "import from clipboard", which is a paste, in which you can first inspect the pasted data and select, what you want to import
- improved CSV import dialog with table preview, parameter guessing and pre-saved configs
- added option to normalize data before plotting
- added copy/paste buttons for plot system settings
- bugfix: possible crash, when selecting incomplete axis label columns
- added widgets to set axis widths in points
- reordered menus a bit
- added mtuli-column properties editor
- added "Cells | set value in cells" function, which fills alls elected cells with a single value!
- added "Edit | Paste without expressions", which pastes the contenst of the clipboard into the table, but omitting the expressions
- improved error-reporting of column/data functions in parser
- improved error reporting in column/cell expression editor dialogs (now also errors during evaluation are reported!)

**B040SPIM**- added JavaScript functions to set preview acquisition camera parameters
- saving a movie now also saves measured values
- added JavaScript functions to set current preview settings
- added JavaScript functions to set acquisition camera settings
- added two filters for each of the two laser boxes
- filters/objectives are sorted by name now!
- added two additional preview configs to the acquisition tab
- added "overview series" acquisition, which allows to acquire a set of overview images with different camera settings and light pathes.
- added two separately configurable "alignment modes" to preview window (mode-specific parameters: colorscale, frame tranform, marginal fits)
- added center crosscorrelation coefficient to preview window (only crosscorrelates the center-half of the frame in left-right/top-bottom transfrom modes)
- added marginal position as plot parameters to graph
- added camera preview modes that equalize the intenisty in the left/right half images.
- added spinbox to camera preview, which allows to set the font size of the parameter table.
- added configuration dialog pane and removed config-tab from control window (now incorporated into config dialog pane!)

**FCS Fit**- fit parameter names are more expressive now
- added button to start model selector + some code refactoring (using QFFitFunctionComboBox now)
- added button "go to average run"
- added overlay plot feater ("Tools|Overlay plot" menu)
- added additional options for fit weighting (from standard deviation over 3,5,7,11 consecutive values of the curve, deviation from polynomial-smoothed version)
- bugfix: weights combo-box is correctly initialized, when starting the editor
- new: added error estimation, using bootstrapping to curve fit (in plots)
- added checkbox to switch key/legend on/off

**FCS/DLS**- fixed a possible freeze of QF3, if ACF-data is imported from CSV files and no countrate-trace is provided!
- import functions for correlator.com .SIN files
- added tool to set background countrates in several RDRs
- added tool (RDR editor menu "Tools"!) to set background rates from the rates in the current RDR
- added tutorial for the background tools
- added tool to correct CFs for an offset
- can now also handle internally saved countrate curves
- internally saved correlation curves and count rates are stored as base64-encoded arrays in the project now. This is smaller and faster to read, than CSV!
- added import filter for Carl Zeiss ConfoCor3 datfiles (*.fcs)
- fixed possible crash, when opening the "fit function simulator" dialog
- added generic internal ASCII data format for correlation data
- added option to export the current data into a file (currently only the QF3 ASCII Correlation Data Format)
- added import filter for QF3 ASCII Correlation Data Format
- added support for ALV-700x files (should work for most files, but may not be perfect yet!!!)
- bugfix: correlation curve/countrate editors remember configuration in a more understandable way
- bugfix [thanks to Corentin Le Nézet]: Tab-separated ASCII files were not read correctly as FCS records in some cases (too many columns)
- CSV fileformat parameter dialog now have a button, which inserts a tab into the column separator field.
- added functions to the internal expression parser, which allow for access to the FCS raw data (correlation curves and count-rate traces/averages)
- added cross-correlation (2-color FCCS) overlay plot with cross-talk-corrected correlation amplitudes
- added data export to arbitrary table-oriented data format
- count rate statistics in the countrate RDR editor is now displayed in a real table widget
- the countrate RDR editor omits all runs with countrate all 0 now (this often happens for ALV-data, since ALV only saves the countrate from the last run)
- the "filter CFs for outliers" function now accepts a lag-time range in seconds

**imFCS Fit**- fit parameter names are more expressive now
- added button to start model selector + some code refactoring (using QFFitFunctionComboBox now)
- added button "go to average run"
- improved dialog to set fit result from other RDR/file/...
- added overlay plot feater ("Tools|Overlay plot" menu)
- "set fit result from RDR/file/..." now supports image transfroms to perform a limited set of image processing operations (bluring, ...)
- bugfix: weights combo-box is correctly initialized, when starting the editor
- new: added error estimation, using bootstrapping to curve fit (in plots)
- added checkbox to switch key/legend on/off
- improved fit speed by using multi-threading
- new/faster multi-threaded fit is default fit now

**Online-Help editor**- added several buttons for advanced insert/editing functions
- improved past image dialog (now allows scaling and cropping of the image
- editor now uses line-wrapping
- improved selection of links (also shows files from current directory now)
- added autosave function
- added Tools menu entry to open a second (third, ...) help editor window
- added special dialog to add FAQ entries and function reference entries
- added dialog to insert a new table
- added option to select an image, which is already present in the help system
- improved "paste image"/"select image" dialog to allow fine cropping

**spectra viewer**- added FRET Foerster radius calculator
- added some DNA dyes: YOYO-1/3, TOTO, ... from Molecular Probes

**FCS MaxEnt evaluation**- added overlay plot feater ("Tools|Overlay plot" menu)
- bugfix: plugin now works for DLS data
- bugfix: D-axis is now properly calculated for DLS-fits
- added option, that allows to copy run-averaged MaxEnt distributions

**FCS MSD evaluation**- added overlay plot feater ("Tools|Overlay plot" menu)
- added overview plots for MSD/6tau, MSD/(P*D*tau), D(tau), alpha(tau), ... curves, calculated from the actual MSD
- bugfix: model display of SPIM/TIRF-FCS models now works correctly (particle number/amplitude was evaluated incorrectly!)
- Plugin now calculates intersection points between consecutive theory fits
- bugfix (thanks to Tabea Elbel): Overlay plots of MSD/6tau ... were copied with the wrong time-axis!
- the plugin may now also read the focus properties (wxy, wz, gamma, pixel_size) from FCS fits
- added confocal 3D diffusion model with triplet and blink component correction
- improved speed of "get N+other parameters from FCS fits" function a bit

**Diffusion coefficient calculator**- now also calculates the hydrodynamic radius of the particle from the diffusion coefficient at the experiment conditions.
- now calculates rotational diffusion oefficients and relaxation times
- added more diffusion coefficients to internal database (mostly different standard proteins)
- added images for some of the standard diffusion coefficients

**qfe_plotterexporterlatex**- added export filter option, which does not parse the LaTeX strings.
- bugfix: size of output file was not set correctly

**qfe_plotterexportercairo**- bugfix: size of output PDF/PS/... was not set correctly
- bugfix: polygons are now output correctly

**fit_lmfit**- now uses lmit-5.1
- tried to improve box-constrained LMFit, so it gets a second try at the fit, if parameters stick to their bounds

**fit_levmar**- tried to improve box-constrained LMFit, so it gets a second try at the fit, if parameters stick to their bounds

**picoquantimporters**- added support for PicoQuant PTU files

**tcspcimporter:**- improvements: now group+role of the output records are set properly (according to input file!)
- the tcspcimporter now create the new QF3 ASCII correlation data files and imports those into the project. This fixes different inconsistencies with groups, roles and count-rates, when creating FCCS datasets from TCSPC data.
- added initial support for TTTR correlator

**qfe_calculator**- a new set of plot-commands allows to generate graphs (somewhat working like the respective Matlab functions):
`plot(), bar(), scatter(), semilogx(), semilogy(), colorscatter(), errorbar(), xerrorbar(), yerrorbar(), ...`

- a new set of plot-commands allows to generate graphs (somewhat working like the respective Matlab functions):
**basicimageimporters**- added initial support for image file meta-data for TIFF images, such as OME or from ImageJ
- added support for metadata from QuickFit B040SPIM .configuration.ini files
- added multi-channel support for libTIFF importer
- added readers for RAW files

**image_stack**- now tries to read metadat (pixel size, deltaZ/T, ...) from file properties (e.g. OME)
- added wizards for SPIM lightsheet analysis
- added wizard for image stacks
- added functions to internal math parser, that allow to access image stacks.
- single-file image stacks may now load images with multiple frames
- added additional widgets to configure display in RDR editor
- image stacks may be exported from the RDR
- mask may be copied also to records with different sizes (mask is rescaled then!), when "Mask | copy mask to ..." menu entries are used

**fitfunctions_lightsheet:**- added Gaussian function with width specified as FWHM

**lightsheet evaluation:**- improved convergence of fits

**qfe_resultstools:**- added RegExp test tool to this plugin (Tools-menu in QuickFit's main dialog)

**number_and_brightness:**- added wizard, that allows to insert a N&B record from average+stddev files for the iamge and the backrgound
- improved RDR editor with a proper correlation plot, an intensity histogram and selections by N&B
- N and B records are now split by color channel (when newly inserted into the project!)
- added comboboxes for color scales
- added edit fields for the color ranges in the N&B RDR editor
- added functions to set user background by mask/selection
- added tab, which allows to change the settings of the N&B calculation
- added wizard, which allows to calculate N&B raw images (averages/StdDev.) from image stacks

**cam_andor:**- camera also writes
`.description.txt`files for RAW data output - camera also writes file with QE from driver
- camera alsoreads sensitivity now

- camera also writes

**2014-04-18 (SVN: 3157)****new plugins:****cam_server**: added this plugin, which allows to use a custom camera server (for CHSPAD server)**meas_spadmeasurement**: added plugin to read the SPAD surveilance circuit

**QuickFit**- added display of internal result/evaluation names and groups [i.e. common information] to result tables tooltips in rdr and evaluation editors
- bugfix: correlation view: regression parameters were not displayed correctly in plot key
- bugfix: correlation view: show more digits in plot keys
- bugfix: CSV export save at most quadratic tables!
- improved copy data from a table functions: when interacting with table-RDR (column names were not copied appropriately)
- bugfix: PDF/PS output on Linux was in greyscale, not in color mode
- several parts are more stable now, if large images are processed (>65535 pixels)
- plotter widgets:
- boxplots plot only parts of the whole box if some columns are missing
- added error boxes and error ellipses as additional error styles

- expression parser:
- now supports functions for regular expressions (regexpcap(), regexpindexin() and regexpcontains())
- now supports functions to convert strings (str2num(), cstr2num(), str2bool())
- added functions to use regular expression in case-sensitive and minimal version
- added function forsave() which is a save version of the for() construct (i.e. does not crash if any expressions evaluates to non-number)
- added function filterfinit() which removoves all nan/inf values from a vector of numbers

- QFExtensionMeasurementAndControlDevice now support string parameters
- added menu entry to directly open one of the contained example projects (like open, but starts in the directory containing the examples)

**MaxEnt FCS Fit**- added camera SPIM-FCS 3D diffusion model
- added camera TIR-FCS 2D diffusion model
- added overview image tab (to the residuals statistics tabs at the bottom of screen) for imFCS records
- added possibility to change the tau-axis with different modes (lin./log. range of times or diffusion coefficients)
- added user-defined distribution time axes

**MSD FCS Fit**- added camera SPIM-FCS 3D diffusion model
- added camera TIR-FCS 2D diffusion model
- added overview image tab (to the residuals statistics tabs at the bottom of screen) for imFCS records

**imFCCSFit**- added option to save ACF/CCF amplitudes when calculating crosstalk-corrected relative CCF-amplitudes

**FCS fit functions**- added model with exponential decays
- added simple (double) exponential decay
- added simple (double) ower law decay
- added normal diffusion model with afterpulsing component (using gamma or wz for wz, D as parameter)
- bugfixed parameter range for exponential decay

**SPIM-FCS fit functions**- all anomalous diffusion fit functions now calculate MSDs after a given timespan and the time to leave the focal effective area
- some normal diffusion fit functions now calculate MSDs after a given timespan and the time to leave the focal effective area

**TIR-FCS fit functions**- all anomalous diffusion fit functions now calculate MSDs after a given timespan and the time to leave the focal effective area
- some normal diffusion fit functions now calculate MSDs after a given timespan and the time to leave the focal effective area

**imFCS**- parameter image RDR editor: added Selection-menu entries:
- deselect all masked pixels
- select pixels by parameter images/overview image

- image editor: improved "copy fit result statistics" when interacting with table-RDR (column names were not copied appropriately)
- bugfix: in "copy fit results to table", the pixel count column was contained several times
- correlation dialog has a button with some preset croppings
- added mask and selection builder dialogs (+ menu entries in the imFCS RDR Editor, "Selection" and "Mask" menus), which allow to build a selection/mask from up to three conditions to parameter images/overview images (in-range/out-of-range/>=threshold/<=threshold)
- "copy fit results to excel" allows now to also save the results and to copy results from several (selectable) files.
- added option "Selection|set background from selection" and "Mask|set background from masked", which averages over the intensity of the selected/masked pixel and sets it as background intensity, which can be used for fitting -> imFCS/imFCCS fit
- added user background to countrate curve plot
- overview image color may be scaled between 5% and 95% quantile now
- added checkbox to RDR editors that allows to set, whether the image plots should keep an aspect ratio of 1 or not. In the latter case the image fills the available space, and pixels may be non-square shaped!
- added two functions (to data menu in fit parameter image RDR) that allow to copy the average CorrelationFunction and the selected pixels correlation function to a table RDR
- added function to bin correlation functions without recorrelation.
- bugfix: DCCF_DELTAX property was erronously set in FCCS records!

- parameter image RDR editor: added Selection-menu entries:
**table**- bugfix: saved negative row/col numbers into QFTableXML-File, if the whole table was saved
- boxplots plot only parts of the whole box if some columns are missing
- added button to autoscale X&Y axis at the same time
- when delete/adding a table column, the plot columns are altered accordingly, so the plots are no longer destroyed
- added error boxes and error ellipses as additional error styles
- added math parser functions to access rows rowdata(), rowstr(), rowbool()
- added math parser functions to get a column as string vector or boolean vector (columnstr(), columnbool())
- in graph settings: added buttons to clear each data column selection
- in graph settings: added buttons to automatically determine (by an educated guess ;-) data columns based on one selected column
- bugfix: remove unneeded delete buttons
- improved reading of table column header, when pasting to a table or loading from a file
- added control to magnify the current plot widget
- removed unnecessary questions for overwriting a column header with the same valuee
- added option to select data for a plot, based on the value in another column

**B040SPIM**- added methods to access measurement devices with JavaScripts
- added methods to create/write into text files from JavaScript
- more instructions for scripted acquisition:
- access to "acquisition description"
- bugfixed setLaserIntensity() and setBrightFieldIntensity()

- added two MeasurementDevice tabs to optics setup

**FCS Fit**- bugfix: countrate was read from RDR for some fit models
- added spinbox to set number of repeated calls of the fit algorithm for each run/pixel

**imFCS Fit**- bugfix: countrate was read from RDR for some fit models
- added spinbox to set number of repeated calls of the fit algorithm for each run/pixel
- bugfix: sometime the imaging FCS fit "fit all runs" crashed

**Diffusion coefficient calculator**- added "viscosity factor", which is multiplied to any solution viscosity (e.g. to estimate diffusion in cells with eta_cell=3*eta_buffer)
- diffusion coefficient of cylinder is estimated using the formula by [Hansen 2004] now. This has an extended range for the axial ratio 0.01<= L/d <=100

**picoquantimporters**- the import does not halt anymore, if a T3R file has a number of boards >1

**spectra viewer**- added "E2V: front-illuminated EMCCD sensor CCD97" detector spectrum
- added Andor Clara CCD camera detector spectrum

**light sheet analysis**- added function to save a cut through the lightsheet at different positions.

**2013-12-20 (SVN: 2991)****new plugins:****plg_qfe_dataexportbasics**: added this plugin with data export routines for Excel 97

**QuickFit**- plotter widgets:
- bugfix for wrong scaling of print preview (and print)
- changed default appearance of colobars (smaller + no outside-ticks and no minor ticks)
- bugfix: top colorbar distance to plot is now smaller
- also displays smallest and largest tick now
- set property by RegExp may now also set/create named RDR properties
- improved plotting by drawing linegraphs as a polygon, not a bunch of lines ... if possible ...
- plotter now also uses the data storage plugins to save data

- math parser:
- added functions mad() and nmad() ([nromalized] median absolute deviation about the media)
- added function runningaverage()

- bugfix: if a directory was deleted from a project, not all RDRs/evals in it were also deleted.
- correlation plot: added robust linear regression to the correlation plot tool
- correlation plot: added normal regression to the plot
- correlation plot: added checkbox to switch off the keys' visibility
- evaluationeditor: saving data from the table will now only save the selected cells, not always the whole table
- evaluationeditor, rawdataeditor: added context menu entries to copy expanded data to Excel and Matlab from results table. This allows to copy cells which contain a vector of numbers in expanded form, i.e. not as a single cell with text, but as a bunch of cells each containing one value of the vector.
- evaluationeditor: moved most parts of the implementation to a private class
- set RDR property by RegExp now supports saving configs under a given name
- table widgets: added save functions (expanded/not expanded, flipped/normal) to the context menu of the table widgets, supports all generally supported dataformats (including Excel97 using the new plg_qfe_dataexportbasics plugin)
- histogram views: added checkbox to change the visibility of the key

- plotter widgets:
**FCCSFit**- bugfix: could not select per-run-error

**imFCCSFit**- bugfix: could not select per-run-error
- bugfix: added spinbox to enter the displayed run

**imFCS**- bugfix: didn't save report PDF in imFCS RDR editor
- added correlation plot against correlation amplitude
- swapped axes in correlation plot
- bugfix: corrected FCCS amplitude (dashed line in FCCS correlation function plot) now minds the masked pixels
- correlation plot: added robust linear regression to the correlation plot tool

**table**- bugfix: empty rows in the middle of table columns were not saved correctly
- added new plot type: parametrized scatter plot (symbol/line color and/or size can be read from additional columns)
- bugfix: Ctrl+C, Del shortcuts in table now finally work!

**qfe_spectraviewer**- added mKate2 data

**B040SPIM**- added buttons to acquire and make an image stack for the "next cell" (= 1. press "next" 2. press "acquire")
- optics setup saves additional light source properties (description, ...) to the acquisition description file.
- added save image series button to camera preview dialog

**cobol_driver**- supports Cobolt MLD now!
- device description now contains operating hours, serial number, ...
- measurement device interface supports several data items

**2013-11-05 (SVN: 2877)****new plugins:****fitfunctions_tifcs**: fit functions for imaging TIR-FCS (so far: 2D normal and anomalous diffusion + 2D diffusion+flow and FCCS models all with a pixel-detector)**fitalgorithms_gsl**: this plugin makes the fit and minimization algorithms in the GNU SCIENTIFIC LIBRARY (GSL) available to QuickFit (implemented simplex, randomized simplex, BFGS2, steepest descent, conjugate gradient minimizer)**lights_coboltlaser**: plugin to control Cobolt lasers as lightsources via a serial interface**stage_pi863_2**: plugin to control PI Mercury stages, which allows several controllers to be connected to different ports**meas_b040resheater**: plugin to control our B040 Temperature Controller**servo_pololu_maestro**: plugin to control filterwheels and shutters built from servos connected to a Pololu Maestro controller (http://www.pololu.com/docs/pdf/0J40/maestro.pdf)**shutter_relais_arduino**: plugin to control our B040 Relais Shutter Driver**qfe_gslmathparserextensions**: added this plugin which encapsulates some of the GSL functions into the internal expression parser**qfe_plotterexporterlatex**: added this plugin, which registers special image export formats for JKQtPlotter, which output Pgf/Tikz LaTeX files.

**QuickFit**- updated online help for tools
- made histograms use less space by default
- improved print quality of fancy text/check marks in enhanced tables
- tables can be copied as image to clipboard
- can set network proxy in settings Dialog
- added automatic and manual (Help menu) updates check
- can select whether automatically check for updates in settings dialog
- added initial support for user-defined fit functions
- added tool to edit user fit functions
- QFMathParser:
- added functions find() and select() to QFMathParser => documentation still needed
- improved functions remove(), removeAll(), concat(), ... they all support vectors of all types now (not just numbers)
- implemented compare operations between vectors and single values
- all comparisons work on vectors element-wise now (where it makes sense, e.g. [1,2,3]>[1,1,1] will return [false, true, true])
- added functions countoccurences(), alltrue(), allfalse(), contains(), isnan(), isinf(), isfinite(), isnumok()
- comparisons == and !0 between vectors return a boolean vector now
- added more statistical function to expression parser: corrcoeff(), skewness(), moment(), ncmoment()
- added functions atanh, asinh, acosh
- added indexed statistics functions: unique, indexedmean, indexedsum, indexedsum2, indexedmin, indexedmax, indexedmedian, indexedstd, indexedvar, indexedquantile, indexedskewness, indexedprod, indexedcount, indexedmoment, indexedncmoment, indexedcorrcoeff
- added vector functions: item, last, first, returnlast, returnfirst
- added functions for polynomials: polyval(), polyder()

- evaluationeditor: results table: property columns may be copied and have a tooltip now (thanks to Tabea)
- evaluationeditor: results table: with of vertical header is limited to 750px now (so very long file names are elided)
- bugfix: "set property in RDR" did not work for boolean properties
- bugfix: set RDR property by RegExp didn't work for the %0,%1,... replace option
- set RDR property by RegExp: added more options for output-replacement, can use more than just "name" as input
- plotter widgets: symbols are plotted more precisely now (changed some params from int to double)
- histogram and parameter correlation view now have buttons to save/print a report
- histogram and parameter correlation view now have buttons to copy/save the data used for the histogram
- bugfix: fixed auto-range for histogram view, if multiple histograms are present!
- added functions to read user-defined color palettes from assets/colorpalettes (+documentation on this)

**imagingFCS**- added label with the relative CCF amplitudes to the FCCS-mode widgets
- bugfixes in "mask by image" dialog (mixed up selection names of modes)
- added sliders to "mask by image" dialog
- bugfix: could not copy image data from parameter image plot itself
- added "add bin 1+2" button to correlator dialog, which add two jobs, one with binning 1 and one with binning 2
- added menu entry "imagingFCS Tools|recorrelate" which load the input file belonging to the current record into the correlator.
- renamed "goodness of fit" image parameter to "parameter 2" and added configuration widgets (range, colorscale ...)
- added second histogramn for parameter 2
- added correlation plot between image intensity and/or parameter 1 and/or parameter 2, this plot can show a scatterplot + a histogram or kernel density estimate of the distribution (bandwidth==binwidth)
- improved which parameters are displayed initially
- bugfix: RDR did not display the bleach correction shift term in some cases
- added double-exponential bleach correction
- changed bleach correction in load-single-frame mode from divide by bleach-function to the more complex expression by Ries etal.
- residuals plot is now properly displayed also when there i no data (tau-axis visible)
- bugfix (thanks to Nikki): plugin crashed while performing bleach correction
- added possibility to copy number of pixels, used for the statistics in "Copy Result statistics to..."
- median/min/max/... omits NAN/INF/... now on "Copy Result statistics to..."
- bleach correction models exp(poly2) and exp(poly3) no longer have an offset term (e.g. A*exp(-(o+t+f2*t^2)) is now A*exp(-(t+f2*t^2)) ), as this offset term was superfluous (the amplitude A does the same!)
- added two bleach model with 4th and 5th order polynomials: exp(poly4) and exp(poly5) [USE WITH CARE, as they may overfit!!!]
- added the possibility to select a parameter image FROM ANOTHER FILE (from the same group) AND FILESET (also in the current file), instead of from the current file
- can now also plot correlation between any parameter and the x-coordinate/y-coordinate/pixel distance from center of image
- fixed correlation parameter vs. image, which didn't work (image-axis had wrong values!)

**table**- bugfix: controls were not correctly displayed, when plotting a function
- added 1D histogram tool, also supports Kernel Density Estimation
- added 2D histograms/Kernel Density Estimation
- all sizes in plots (line widths, tick lengths, font sizes ...) are now given in system-indipentent DTP-points (1/72 inch)
- added several options to format coordinate axes and plots
- 2D histogram also outputs image size as column properties, so image sizes can be read by the according button when plotting!
- plots: added mor plot symbols (star, asterisk, pentagon,...) and simplified error bars
- curve fit + regression now output the parameters+errors as label for the fit function
- curve fit + regression output the parameter errors in their own column
- bugfix: autoscale for axes didn't work anymore
- column-expression parser: column() command takes a second (optional) argument now, which specifies which rows to read
- the shortcut "=" starts expression editing in a cell
- added result preview to column and cell expression editors
- added options to load/save/copy/paste the (selected) table layout
- bugfix: column expression was overwritten with 0 on read
- bugfix: improved handling of plot colors
- added widgets to set error-bar width, error-bar linestyle, error linewidth
- improved regression and curve-fit dialogs (splitter and parameters are now besides the plots)
- added auto-checkboxes for fill-, error- and centerline-color (chen checked the color is set according to the graph's color, else it is user-defined)
- in column/cell expression editors: added context menu to expression editor edit, which allows to insert the column ID or 'column(ID)' by choosing a column from the menu!
- added undo/redo functionality to table editor
- added functions collength, colimagewidth, colimageheight to table expression parser
- bugfix: now plot key properties are no longer eratically reset

**qfe_calculator**- added multiline expression editor widget
- added widget to set the precision (significant digits) of the output
- added write()/writeln()/disp() functions to allow user to make additional outputs

**qfe_spectraviewer**- added spectra for simple compounds (PHE, TYR, TRP, FAH, NADH, anthracene)
- added chlorophyll spectra
- added mCFP, acGFP, citrine (YFP)
- made startup fast: initial database read is done in a thread
- added several Atto-dyes and some more Tsien fluorescent proteins
- added several Alexa dyes
- "delete" removes all selected items
- viewer may display additional data entries from .ini files now (e.g. pKa for some fluorescent proteins ...)
- added saveguard against possible crash while reading database
- bugfix: shouldn't crash on win32 anymore on startup

**imFCCSFit**- "calculate crosstalk-corrected relative CCF amplitude" now can also use the g(0) fit result as input data!
- added global-local iterations to QFGlobalFitTool
- image mask can be edited in the image preview widget
- added mask by image option to preview widget
- bugfix: guessed file sets didn't show up in some cases

**imFCSFit**- fixed possible crash

**spim_lighsheet_analysis**- now employs parameter guessingbefore fit!

**fitfunctions_lightsheet:**- all functions now support parameter guessing

**fitfunctions_fcs:**- added fitfunction with flow and v,D,wxy as parameters
- added functions for circle-scanning FCS

**fcs**- added some runselection tools to the correlation function tab (mask outliers ...)
- added fucntions to read Oleg Kriechevsky's internal binary dataformat

**fcsfit**- added option to automatically calibrate all runs of current record.
- the plot contains two data columns for the NORMALIZED correlation function (and it's transformed weights) now. Normalization is done ONLY if a fit parameter n_particle (N) or 1n_particle (1/N) is present in the current model. After a fit which gives a proper N the normalized data is there and can be copied (right-click plot and display data table or copy data ...). Normalization is done by multiplying the CF with the extracted N. For the transformed weights standard gaussian error propagation for the product ist used.

**fitalgorithm_lmfit**- speed improvement by removing several malloc/free calls

**diffusion coefficient calculator**- bugfix: corrected the displayed units for solution components (nM was wrong ... I meant mM of course) -> thanks to Tabea

**spim_fcs_fitmodels**- bugfix in new "D for every channel" model: THe D2 of the red channel was not used correctly!
- added fit function with one and two D's per channel, not per species
- FCCS fit function have been renamed (clearer notation)
- dded counts/molecule as second calculated parameter, in addition to counts/nM
- all CFs (ACFG, ACFR, CCF) have all applicable focal volumes as calculated fit parameter now
- added fit function for 2-component 2D diffusion (xy) with separate diffusion coefficients per channel
- added fit function for 2-component 2D diffusion (xz) with separate diffusion coefficients per channel
- all fitfunctions with D1/D2 per channel sort the diffusion coefficients now (D1>D2)
- all 1/e^2-widths should be w and all 1/sqrt(e) width should be sigma now
- bugfix: sorting of D-s was corrupted in some models [sorted also if one of the Ds was fixed] (thanks to Agata)

**fitfunctions_fccs**- added fit function with one and two D's per channel, not per species
- FCCS fit function have been renamed (clearer notation)

**fcsfit_msd**- added 2D and 3D model with triplet correction

**image_stack**- bugfix: mask editing works again
- added 3D viewer (in "Stack Tools" menu) ... THIS FEATURE IS EXPERIMENTAL AND NOT GUARANTEED TO BE STABLE!!!

**qfe_helpeditor**- made new/open/save/saveAs more like standard editors!
- new icon
- added several templates

**2013-08-22 (SVN: 2602)****new plugins:****general_fitfunctions**: several general fit functions (exponential, power law, polynomial, distributions, sigmoidals ...) for fits in table plugin. These mostly also include routines to guess initial parameters for the fits!**importers_simpletcspcimporter**: added this plugin to import simple TTTR files that are made up of 64-bit records which contain channel/special record flags in the first 7 bits and a macrotime with given resolution in the rest.

**QuickFit**- bugfix: fixed crash when clicking on the HELP button in a RDR editor
- QFFitFunction has function to extimate initial parameters and function to calculate numerical jacobian (using the 5-point stencil rule)
- added spinbox to set repeats of the optimize run in QFGlobalFitTool during gloabl fitting
- added random vector functions to QFMathParser
- QFPlotter should now be able to copy EVERY image plot to a table (also if data was not saved in columns!)
- JKQtPlotter: added additional color palettes
- added tool to set RDR properties using a regular expression and some other property as input
- you can add new colors to a color combobox with a right-click (context-menu)
- color combobox remebers newly added colors
- JKQtPlotter: improved export to vector formats (PDF, PS, SVG): e.g. font size is now the same as on screen
- JKQtPlotter: improved display of keys
- added several new library versions: GSL 1.16, Eigen 3.2.0, CImg, libtiff 4.0.3, ...

**imagingFCCS fit**- fixed crash in "calc relative CCF amplitude" tool
- added "don't fit masked pixels" checkbox
- started tool to inspect chi2 landscape
- bugfix: "reset current" does not reset all pixels now!
- now save g(0) as additional fit parameter (on default)
- added "reset all" button
- added tool to calculate relative intensities
- added tool to calculate the relative crosscorrelation amplitude with crosstalk correction

**spectra viewer**- added possibility to display detector spectra
- added a few common image sensors/SPADs
- added additional lamps and QDot/TetraSpec beads spectra
- added sunlight spectra as lightsources
- added additional fluorophores (EtBr, mApple, PA-GFP, SYBR Gold, SYBR Green, TagRFP, Hoechst 33258, Hoechst 34560, Quinine, wtGFP)
- added several standard filter spectra
- added combobox with common laser lines
- added edits to set plot range (wavelength)
- all fluorophores, lightsources, ... are now organized in folders
- currently selected spectrum is highlighted now

**ImagingFCS**- added more bleach correction functions (exp(poly2), exp(poly3)) to correlator
- now save g(0) as additional fit parameter (on default)
- added lateral shift of foci to simulation
- "copy CFs from group to table" now also copies single CFs!
- added possibility to display ACF0+ACF1+FCCS for FCCS-record. This also calculates the corrected CCF-amplitude.
- improved mask-by-image dialog
- bugfix: frametime was not correctly read/set/stored, when data from another microscope than the B040SPIM was used (missing configuration.ini file leads to non-set frametime), thanks to Philipp Struntz, Uni Bayreuth for the bug report
- improved import of DualView-correlation data (if imported from file, not from correlator dialog: now splits the data correctly!

**spim_fcs_fitfunctions:**- bugfix in anomalous diffusion, c as parameter: c is a fit parameter now

**FCS maximum entropy evaluation:**- added widgets to enter two ranges over which the relative particle numbers are calculated

**spim_fccs_fitfunctions:**- added 2-component diffusion models
- added fit function for 2-pixel crosscorrelation with diffusion only
- added SPIM-FCCS fit-functions for 1-comp. normal diffusion with Db=Fb*Da and Dab=Fab*Da
- SPIM-FCCS-models now support linking all D's per channel!
- BUGFIX: there was a typo in all SPIM-FCCS models if dx!=0 and/or dy!=0!!! ... a + instead of - leads to too high CCF-amplitudes if shifted laterall!!! This is corrected now.
- added fit models for SPIM-FCCS where not every species, but every channel has two Ds (D1, D2) => simplified model for complex FCCS applications.
- BUGFIX for all fit functions for global fitting: In the ACF-term, the focus distance has to be 0 always (used the dx, dy, dz parameters). Now the distance only plays into the crosscorrelation terms G_rg/G_gr!

**fccs_fitfunctions:**- FCCS-models now support linking all D's per channel!
- BUGFIX for all fit functions for global fitting: In the ACF-term, the focus distance has to be 0 always (used the dx, dy, dz parameters). Now the distance only plays into the crosscorrelation terms G_rg/G_gr!

**number and brightness plugin:**- bugfix: sometimes the acquisition background file was loaded, not the overview!

**table**- improved curve fit tool with progress dialog and threaded fit (may be canceled)
- bugfixes in fit®ression (improved collection of dataset for fit)
- added function to autocolor graphs from a colorbar
- plot can be given a custom size (uses scrollbars for display, if needed)
- reorganized graph settings into several subtabs
- added horizontal/vertical range plots
- added residuals to regression dialog
- added residuals to curve fit dialog
- added "guess parameters" button to curve fit dialog
- bugfix: fixed possible crash in residuals dialog
- the fill style may be set now

**imFCS Fit**- added tool to plot chi2 landscapes
- bugfix: "reset current" does not reset all pixels now!
- "calibration wizard" now also supports calibration by shifting two foci with respect to each other
- now save g(0) as additional fit parameter (on default)

**FCS Fit**- added tool to plot chi2 landscapes
- now save g(0) as additional fit parameter (on default)

**FCCS Fit**- added "reset all" button
- added "fit all filesets" menu entry
- added "reset all" button

**lmfit**- added IRSL-LM implementation (robust fit using iteratively reweighted least squares = IRLS)

**FCS**- ALV5000 import should be able to read inf/nan/...
- ALV5000/6000 import now supports a property "ALV_TIMEFACTOR" that is multiplied to the time in the file (e.g. if seconds instead of ms are written into the file, use ALV_TIMEFACTOR=1000). It's default value is 1, i.e. it does not affect the data!

**Diffusion coefficient calculator**- added possibility to give a diffusion coefficient in the current solution at ANY temperature -> renormalizes the temperature!

**SPIM B040 control plugin**- started to implement a parser for optSetup files (so far only as test code, no functionality yet!!! ... wait for next release)
- acquisition now also save preview background images
- image stacks now save a background image before the stack

**2013-06-20 (SVN: 2383)****Bugfix release****imagingFCS**- simulation now supports crosstalk and different sizes of red and green focus

**qfe_spectraviewer**- some bugfixes (crash if filter spectrum is used for spillover), sometimes the spectra got deleted when editing a filter, ...
- add short-, longpass and notch filters

**qfe_defaultmathparserextensions**- added function for arithmetics with errors

**table**- added power-law regression

**imfccs_fit**- "calculate relative correlation amplitude" tool had a bug which lead to a crash and is fixed now.

**2013-06-17 (SVN: 2368)****new plugins:****qfe_resultstools**: plugin with tools to work with rdr results (currently only a calculator Tool in the Tools menu)**qfe_defaultmathparserextensions**: plugin to extend the main math parser woth more functions (e.g. regression, model fit, ...)**fccs_fit**: plugin to perform a global FCCS fit for non-imaging FCS data (e.g. confocal FCS data/DLS data)**qfe_spectraviewer**: new plugin to display and compare fluorophore, lightsource and filter spectra

**QuickFit3:**- "copy plot data to table RDR" has an additional checkbox now that allows to copy only the data really used for the plot!
- "copy plot data to table RDR" can take a prefix for the column names now
- added print option to tables
- expression parser has basic support for string and bool arrays
- improved rendering in JKMathText: (- added italic correction in sub/superscript - corrected whitespace handling in math mode (now ignores them just like LaTeX, use "\ " to get an explicit whitepsace))
- increased lib version
- evaluation and rdr plugins have an init() method now
- online-help now supports special tags for references
- added installer (using NSIS)
- improved plotters: now they may copy the current plot into a table record
- bugfix: App crashed sometimes when closing before closing all evaluation windows separately
- It is possible to edit folder, RDR and evaluation names in the project tree
- the project tree now has a context menu to delete and add records.
- added function to load only a selected subset of a project
- improved expression parser implementation, speed and documentation
- QFDoubleEdit now supports step up/down via mouse wheel
- rdrs may now have a group to which they are assigned
- project tree displays group using background color
- added button to RDR editors that allows to select the next record from a tree of the project.
- online help: added tooltips, which may be defined in special INI files
- plotter: error polygons are plotted as one large polygon now
- JKQTFASTPLOTTER: has a context menu to copy the current image to the clipboard now
- improved expression parser: supports binary/hex/oct number constants, number vectors and function assignments (e.g. f(x)=x^2) + several new functions and improved documentation
- removed some smaller memory leaks (found by valgrind)
- QFDoubleEdit supports log-scaled stepping now, mouse-wheel interaction fixed
- added tool to fix wrong file paths in RDRs to the main application
- result tables show more information in tooltips for boolean and string arrays
- improved saving of relative filepathes (should clean away symbolic links now)
- plotters have help context menu entry now
- added tools to QMake projects to install example files into examples subdirectory of installation, moved examples to new directories!
- added tool ("Tools|Project Tools" menu) to rename RDR groups

**qfe_calculator**- bugfix, online-help for expression parser displayed correctly now
- uses imrpoved expression parser now
- added options dialog entry to set custom database path

**table:**- bugfix, online-help for expression parser displayed correctly now
- asks now whether to delete a graph
- changed default font for graphs
- bugfix: deleting a graph lead to an endless loop
- now supports common interfaces to edit data in table and graphs
- bugfix: table-size not initialized on startup
- more options to layout the coordinate system (background, axis styles, ...)
- added RGB image plot
- added alpha/saturation/value "modification" channel to image plots
- added extra labels for G and B channel in RGBimages
- added tool to calculate (linear) regression of a plot
- added several new possibilities to function plot (QFFitFunction, polynomial, exponential, power-law
- started to implement curve fit tool for QFFitFunction
- added boxplots
- allows width and shift for bar charts
- added printing support in tables
- added possibility to add image plots wil colgraphs... interface, added this to QFPlotter
- implemented indexed statistics
- bugfixed visibility of Median/Q75/max comboboxes in table editor for boxplots

**imFCS:**- bugfixes, crash when no overview image is returned
- bugfix: didn't read 4e6 frames due to integer overflow
- now reads also 80s Radhard correlation runs
- added display of background image size to correlation dialog
- bugfix: updating avg. correlations works now properly with the "Mask" menu
- increased binary correlation file format ID version to 3.1 ... older data is scrambled in the segment data and if additional correlations are saved in each pixel (e.g. 4-neighbor-CCF)
- added tool to exclude segments from the ACF in each pixel
- bugfix when reading 4-neighbor-CCF from binary files
- added simulator for 2D diffusion (including DualView to simulate imFCCS)
- added buttons to correlator window that allow to load a file without counting the frames in it (e.g. for a larger set of measurements, where the number of frames is always the same) ... this makes selecting a file much faster!
- prepared for two-channel overview image
- continued preparations to load only one half of a full imageDV2-correlations into an imFCS RDR
- FCCS correlation works properly now
- added overview widget
- added too (menu entry in editor) to set a fit parameter from another file.
- bugfix: first pixel (run 0) always equalled averag/std
- count rate display now works, also with FCCS files and dual-channel videos
- dual-channel videos are supported
- added second set of range edit fields for second color channel of overview
- added function to automatically create ACF1+ACF2+FCCS-plot
- istogram update when selection changes works now properly
- color range selection for 2 color channels now works correctly
- added mask tool that allows to create a masked border around the
- made sure that the ACF from an FCCS dataset has two overview images and allows to read the countrate from both channels, although it's only ACF_g or ACF_r
- added "copy mask to files in group" menu entry
- imFCS simulation does no longer report its background offset back, as a background file is created that corrects for the background!
- "mask|mask outlier CFs": now giving lower and upper percentage (e.g. 5% & 5% leaves only 5%..95%)
- "mask|copy mask to group" now updates the average run properly!
- corrected bug in imFCS calibration: preset wz was not used in fits! the default value 620 was used instead (always!!!)
- added checkbox to "copy result statistics" tool to switch off copying of the headers

**imFCSFit:**- added wizard for calibration + documentation
- added method to automatically execute the D-fits in calibration

**cam_rh2v2:**- now support NOT writing raw data (it's sent to /dev/null)

**B040SPIM:**- acquisition script may now set camera properties
- camera view now save camera configuration with images and has option to save to multiple image formats with one click
- additional info on camera is saved for image stacks
- prefix-linedits in acquisition settings tabs now have button to select from autocompleter
- all acquisition settings tabs have save/load template buttons now
- added common prefix to qcquisition description
- added configuration tab
- added "Test" buttons to the image stack and acquisition config tabs that allow to quickly test the choosen camera/lightpath settinsg while the button is pressed
- line measurements in the camera view window now works with dragging the mouse, not 2 clicks
- DualView filter select comboboxes are locked by the lock button now
- switches mainwindow to non-project mode, so project editing is disabled!
- added "sample name" input widget to acquisition description
- lightpath selection now moved from optics setup tab to top-level widget
- added button to unlock lightpath combobox
- removed some commented out code sections
- tried to improve speed of image stack acquisition

**image_stack:**- full support for mask editing
- added mask tool that allows to create a masked border around the
- added possibility to load DualView image stacks
- added possibility to do a selection and get avg/std from this selection

**lightsheet_analysis:**- fixed display error for column cuts
- now displays cut through image row/column for all channels

**fitfunctions_fccs:**- corrected a bug that lead to concentrations that were wrong by a factor of pi/2
- added cAB/max(cA,cB) property to FCCS models (SPIM and confocal)
- added fit function following the Ries/Schwille FCCS framework for normal and anomalous diffusion in confocal FCCS
- added 2-component normal diffusion model
- bugfix: concentrations were wrong by a factor of (pi/2)^3 ... this is corrected now. D and rel. concentrations were not influenced

**msd:**- bugfix: theory and curves calculated from theory are updated reliably now
- added new testdata of Puc18 plasmid
- D(tau) and alpha(tau) curves are now fitted with different methods (LM fit, regression and iteratively reweighted least squares regression)
- added tool to fit power law to msd (displayed as "theory curve")
- fit range and result is displayed in MSD-plot when mouse moves over D(tau)/alpha(tau) plot
- in line-fits dialog, the fit-range is set in real time-units now
- added possibility to get 1/N for all records with one click (extended "average first few lags for N" dialog)
- started to implement tool to read N from fcs_fit!
- added tool to read N from FCS fit results
- some minor bugfixes (theory results were not properly updated in edit widgets, when the run was changed)
- improved initial estimated for 3D-MSD-fit (now takes the result of the 2D-transformation as initial value)
- implemented fitting all theory data to MSDs
- added transforms of MSD-curve in lower plot

**cam_andor:**- bugfix: switched output format of some values from float to double, as QSettings seems to have problems writing floats in QVariants!
- added checkbox to allow advanced EMGain

**fcs:**- added property to allow to use one countrate (e.g. when only one is available in an ALV file) for all runs
- plugin can load correlation output from the diffusion4 FCS simulation tool
- Added and integrated parser for ALV-6000 files by cloning and modding the existing ALV-5000 parser sparsely (thanks to Benedikt Häusele)
- If an FCS record displays an autocorrelation measurement, but both color channels were acquired, the countrates for both channels are loaded and displayed. Still the countrate of the loaded ACF channel is returned as countrate channel 1 and the other one as 2, son in the red ACF record, the countrates are swapped

**helpeditor:**- added more formatting buttons
- added more buttons (math, code, ...)

**calc_diffcoeff:**- moved calculation of D of sphere from its own tab to the "spheroid" tab (where also cylinders and ellipsoids are calculated)

**fitfunction_spimfcs:**- added fit function for anomalous diffusion (+demo project +documentation)
- started fit function for 2-color SPIM-FCCS
- updated documentation to show background correction factor
- anomalous diffusion model and diffusion model with c and D as parameters now work properly
- implemented simple 2-color-FCCS model
- corrected sorting behaviour (rhos and fixes are sorted now too)
- added functions with new Veff and c,D as parameters with 1/e²-widths
- added anomalous diffusion with e² radii and with c as fit parameter and e² radii
- added fit functions for 2-color FCCS anomalous diffusion
- corrected description of equilibrium constants ... now dissociation constants and unit is correct!
- added display fields for the molar brightnesses of fluorophores a and b

**cam_testcamera:**- added DualView modes and a fixed grid testpattern

**2012-12-10 (SVN: 1959)****new plugins:****qfe_calculator**: a small math expression parser as Tool (see Tools-menu)**qfe_helpeditor**: editor for QuickFit online-help files**fitfunction_2ffcs**: fit function for 2-Focus-FCS with gaussian PSFs

**QuickFit3:**- LaTeX renderer now uses the Open Source XITS fonts for math (which are included as OTF in the QuickFit3 binary)
- table widgets: added function to print table and to copy selection as Matlab script to clipboard
- improved online-help with automated table of contents
- added histogram functionality to rdr and evaluation results table
- added checkbox to rdr and evaluation editors that allows to toggle the display of vector/matrix data with/without average+/-SD
- plot widget: improvement to axis scaling algorithm
- all evaluations may now support filtering of files list by regular expressions/wildcards
- improved about-box with OS information and more detailed QF version. added License tab.

**calc_diffcoeff:**- added more diffusion coefficients to database and more information to each dye (buffer, method, error, ...)

**imagingFCS-Fit:**- bugfix: crahsed when reseting a value to initial

**imagingFCS:**- added function to filter the correlation functions for outliers (amplitude outside a range defined by two quantiles
- added option to copy the current mask to all files (as selected from a list)
- correlator now creates multi-distance FCCS from a list of distances given in the configuration dialog
- now properly recognisez ROI-size for RH2 files

**fcs:**- improved FCS simulator (added button to add a record with current settings, but does not close the window)
- simulator got a Help button and is now a floating (non-modal) window.

**fitfunction_2ffcs:**- added fit functions for 3D diffusion + flow in 2fFCS
- added fit functions for 3D diffusion in 2fFCS

**tcspcimporter:**- added spin box to change FCS countrate binning
- bugfix: importing CCFs into project didn't work correctly due to missing countrate files
- improved online-help

**fitfunction_spimfcs**- added SPIM-crosscorrelation fit function with flow
- fixed some bugs in online-help (confusion on definition ot σ
_{xy}, σ_{z}, w_{xy}and w_{z}, but: Models were not changed and the model names (1/e² or 1/√e were correct!!!)

**fitfunction_fcs**- fcs_diff_d now calculates wz
- added model fcs_diff_d_wz where the focus is parametrized by wxy and wz (gamma is calculated), the diffusion is parametrized by the diffusion coefficient D
- added model with diffusion coefficient as parameter (not tauD)

**table**- added editor widget for expressions to table cells (opened, when double-clicking a cell): basically two buttons that allow to edit and to clear the expression
- improved editing: pressing return will move the cursor to the first cell in the next line
- added function to clear the expressions in selected cells
- added function to reevaluate all/selected expressions
- added buttons to move plots left/right
- added buttons to move graphs up/down
- added function to duplicate a complete plot
- added function to restore the default coloring of graphs
- added an option to access columns in a stride-pattern to e.g. only plot every 2nd datapoint
- now supports comments for each cell
- now supports function plots from a parsed function

**image_stack:**- now supports masks

**eval_spim_lightsheet:**- now supports masked pixels

**fitfunction_fcsdistribution**- added new fit function with gaussian diffusion coefficient distribution
- added new fit function with gaussian diffusion time/hydrodyn. radius distribution

**picoquantimporters**- now work with any TimeHarp 200 5.x file (t3r-mode)

**several fit functions:**- minor corrections in parameter names (no expressions were changed!!!)

**2012-11-08 (SVN: 1880)****bugfix release****QuickFit3:**- added function to set/change properties in several RDRs at once (see Tools|project tools")

**imagingFCS:**- added more options for statistics copying

**fcs:**- bugfix: CSV import was broken ... works again now!

**fcsMsd:**- bugfix: alpha/D display more robust now

**2012-10-29 (SVN: 1856)****QuickFit3:**- plotter widgets now display a context menu on a right-click
- improved about-box
- added dialog that is shown whenever a new QuickFit version is started and updates the user on news and the release notes.
- added help menu entries to contact the authors and write to the mailinglist
- updated online help
- pushed library version from 1.2 to 1.3 (to summarize some API-changes since the last release)
- added option to display property values in the evaluation results table
- added "reload current project" function to the File menu
- if RDR files are editable, they may now be moved up/down and all the features of the new editable files list API are used for the UI ...

**jkqtplotter:**- added button/action to display a table with the plot data in a separate (modal) window
- shows a settings dialog when copying to the clipboard

**msd:**- added function to copy run average to clipboard

**calc_difcoeff:**- improved plugin with the possibility to estimate acqeous solution viscosity with a set of solutes (1..5). (same method as in Sednterp ... values fit quite accurately with small deviations due to different fits to viscosity reference data!)
- dded possibility to calculate ellipsoid and cylinder diffusion coefficients
- improved documentation
- givenD data may be deleted now
- givenD user data is stored in config directory now.
- you may view different plots (viscosity, density, refractive index) for solutes

**imagingFCS:**- bugfix: selection/mask overlays in the countrate and correlation curve displays work now correctly, i.e. colors are displayed, not just blach and white (problem with alpha blending in the plotter!!!)
- added DualView mode
- replaced example data
- added tutorial for beads data
- added option to copy fit result statistics (over selected/non-masked pixels) as a table to the clipboard
- added copy/print/save actions for all subplots to the Data menu
- bugfix: color scaling is now correctly done for masked images/overview
- added menu entry to copy currently selected correlation curves into a new fcs raw data record and add it to the current project.
- new tinyTIFF importer can import more than 65000 frames from a TIFF file, but with very limited feature support.

**table:**- bugfixed the data access functions (accessed the wrong columns!)
- added numbers to the column titles in the table ... data access functions work on these numbers as row/column number!!!

**fcs:**- parsing internal fcs in formats tccc or tcecece according to parameterChanged
- bugfix when reading CSV files in mode tcecece
- improved CSV import (allows to specify start/end line string), possibility to save presets in CSV dialog
- fully supports loading of multiple files into one RDR (including menu item!)
- improved online help

**DLS fit functions:**- bugfix that caused crash due to new DLS fit function
- corrected unit of scattering vector q^2 from 1/nm to 1/nm²
- added fit models expressed in terms of D and not tau

**2012-09-25 (SVN: 1823)****imFCS:**- added pixel-by-pixel "countrate" display which displays the timeseries from "videos". For the uncorrected video also the background level and (if available) the bleach fit is displayed
- several bugfixes
- now creates and displays "uncorrected" video
- new estimation of bleach correction parameters by simple linear regression + estimation of lm-fit parameters for bleach correction by regression

**table:**- added column statistics functions to math parser
- bugfixes in loading colors (no preceeding 0 when color saved as HEX) and display of steps (filling did not go down to axis

- FCS_Fit: added more parameters that are read from raw data (dls scattering angle, wavelength, ...)
- DLS: the DLS G2 fit function now calculates diffusion coefficients from the fitted correlation time
- SPIM_FCS models: corrected documentation
- spim_lightsheet_eval: created nicer icon
- rdr_settings: tree may be filtered now
- PicoQuant: bugfix in measurement duration determination for PicoQuant PT3 files
- when converting to number at many places the locale group separator is ignored now

**2012-09-04 (SVN: 1794)**This bug has been fixed in this release.__important bugfix:__The background correction factor in all FCS fit functions was implemented wrong. The uncorrected and background-corrected count rates were mixed up. THIS DOES NOT PLAY A ROLE WHEN THE BACKGROUND WAS 0 AND IT WILL ONLY IMFLUENCE PARTICLE NUMBER, BRIGHTNESS AND CONCENTRATION, NOT THE DIFFUSION COEFFICIENT!- new plugins:
**fcs_msd:**extracts mean squared displacement from FCS measurements**calc_diffcoeff:**calculates diffusion coefficients in a given solution and at a given temperature**spim_lightsheet_eval:**evaluate SPIM lightsheet properties from a x-stack (taken with a 45° mirror in a SPIM)**fitfunctions_lightsheet:**fit functions (gaussian, slit function) for lightsheet cuts (see spim_lightsheet_eval)**number_and_brightness:**performs simple number and brightness analysis- more new plugins can be found in the separate SPIM plugins release!

**table:**- added plots (also image plots) for table plugins
- improved online-help
- improved clipboard and files handling, editing capabilities
- added function parser
- improved display of cells
- added displayed row numbers
- sorting of columns
- added function to init cells with linear/logarithmic value list

**FCS:**- added new plotstyles for errors (polygons)
- improved FCS simulator with some noise models (uniform, gaussian, Koppel)
- started online-help

**FCS fit:**- in the focal volume estimation dialog you may now display the online help and run the calc_diffcoeff plugin, i.e. select a diffusion coefficient from the "diffusion coefficient calculator" by double-clicking it there
- added more automatic fit parameters (pixel_width, pixel_height), improved documentation
- added new plotstyles for errors (polygons)
- added checkbox to show/hide plot keys
- added estimation of remaining processing time
- added multi-threaded fits (used as default!)
- added configuration widget to the main settings dialog

**imFCS:**- added option to do interleaved binning
- implemented averaging cropping
- added correlators which use 64-bit integers for multiplications/sums
- improvement to correlators: explicit typecasts to double ... but no effect on results ;-)
- improved documentation
- added support for data taken with DualView optics
- added statistics of uncorrected input sequence (NOT TESTED YET ... POSSIBLY DOES NOT WORK CORRECTLY)
- added more options to edit masks/selections (copy/past to/from clipboard)
- cleanup in UI, placed parameter widgets in vertical scroll area
- when loading: pixel will all-0 correlation function are masked automatically!
- added selection that may be stored/loaded to/from a drop-down list and are saved in the QuickFit project
- added option widgets for overview (color bar and range)
- added display for background statistics time series
- added button/menu entry to copy current data as table to the clipboard
- images contain an axis label at the color bar
- histograms have x-axis label now
- improved overview image display with selection histogram
- added output of stddev over whole image series in addition to average + support for this in raw data record
- added output of unscaled (float) average frame
- added histogram to image display in raw data record
- added counts/molecule to SPIM FCS models
- added corrdinate+value display to image display
- added option to preset the camera pixel size
- switching off exponential bleach correction for pixels where the fit failed
- when correlating, the plugin also inserts the (possibly) available acquisition settings as rdr_settings and the measured values as table RDR
- also when loading a Radhard2 correlation file, we search for experiment description
- displays more additional images
- correlator outputs image that shows whether the 1-exp fit in the bleach correction actually worked (1) or not (0)!
- added "add series job" button

**imFCS fit:**- now the pixel size is initially guessed from the pixel size saved with the acquisition and the binning saved as a property by the correlation dialog
- added online-help
- now has an option to only fit the non-masked pixels
- added checkbox to show/hide plot keys
- added estimation of remaining processing time
- added multi-threaded fits (used as default!)
- added configuration widget to the main settings dialog
- added menu entry to add several fits with varying wxy for SPIM-FCS calibration

**MaxEnt:**- improved online-help
- added possibility to change lag-time-axis in diffusion coefficient axis

**basicimageimporters:**- improved online-help
- libTIFF may create log files now (may be activated in the settings dialog)

- improvement to
**graph plotter widget:**- bugfix in scaling of gridPrinting plots
- user may select the columns to be exported/copied as data (CSV, SYLK, DIF, MatLab, ...)
- implemented storage system for user settings (print/export settings, selection of columns on export, ...)
- improved placement of key and outside-elements (color bars ...)

**basic raw data record/evaluation editor dialogs:**- now have menus (visibility changes with visible tab, added menus for help and results)
- added filters for the reults tables (with wildcards or regular expressions, added docu for regular expressions)
- added edit capabilities for files list in raw data records
- improved SYLK export in rdr/evaluation editors for results
- added flipped SYLK export in rdr/evaluation editors for results
- evaluation/rdr editors now have an option to also save the results with averaged vector/matrix fields
- property names and types may be edited in table
- added copy/cut/paste and set property suereditable to property table + context menu
- several small improvements (icons, context menus ...)
- added delete results to evaluation editor
- added a menu bar at the top of the raw data record and evaluation editor window, which also gives direct access to the respective plugin help. This menubar may change depending on the tab currently displayed.
- averages in the result table also averages over list/matrix data

**central QuickFit services:**- implemented --verboseplugin command-line option which outputs additional debugging information when loading the plugins (into the QuickFit log-file/pane)
- improved (math) text rendering and export in plots
- improved math rendering in online-help (anti-aliasing)
- speed improvement and multi-thread safety in QuickFit project code (allows for mult-threaded fits!)
- save to CSV/SYLK save vector/matrix results in additional columns
- exchanged options dialog with tabs by nicer version with an icon list
- log widgets may be searched now (Strg+F/Ctrl+F); log widgets prepend current date and time to each line
- speed improvement in saving project
- settings dialog may also be used by plugins
- added option to switch off automatic saving of project
- added performance test to Tools menu
- added function to replace substrings in the names and folders of raw data records

**QuickFit online-help:**- allows to search all available help files
- extended online-help
- added help page on file formats
- help window is an application level mainwindow now (may hover over several other windows!)
- added help page on help browser
- added remark on postcard-ware to copyright help-page and about box
- help viewer allows to search in the current page

- as always: many bugfixes and improvements,

**2012-05-25 (SVN: 1532)****bugfix release for SVN 1515!!!**- SPIM-FCS 3D diffusion model function: fixed some typos in the implementation
**NOTE; YOUR OLD FITS MIGHT BE WRONG!!!** - bugfix in the raw data record/evaluation results list editor: table items were scrambled
- added new copy to clipboard options for the raw data record/evaluation results list tables
- improved display of evaluation results in raw data record and evaluation editors:
- matrices/vector entries are shown if smaller than 10 entries, else only a type descriptor is displayed
- if the mouse hover over a table cell a tooltip is displayed with the cells mean and standard deviation (if the cell conatins a vector for which mean/SD make sense)

- added help button on mainwindow toolbar
- imFCSFit: evaluation group name now uses the user supplied name of the evaluation object

**2012-05-23 (SVN: 1515)**- new plugins:
- fitfunction_dls: implements Dynamic Light Scattering G2 correlation function
- image_stack: displays multi-channel/timepoint image stacks
- rdrsettings: display settings files in the standard INI format

- some bugfixes
- improvement of online-help (also LaTeX rendering in it)
- MaxEnt: new Models implemented
- fcs_fitfunctions: added oscillatory FCS autocorrelation model function
- imFCSFit: now is faster when resetting
- imFCS: implemented new exponential bleach correction as shown in Ries/Chiantia /Schwille (2009): BiophysJ 96(5),1999-2008
- imFCS: improved documentation
- imFCS fit: bugfix: now all runs are fitted (before the last one was skipped)
- imFCS: corrected an error in the binning code of the correlator: frame was read into a uint16 => there were overflows for high binnings
- imFCS: Radhard2 code now omits first channel

- new plugins:
**2012-04-19 (SVN: 1441)**- some bugfixes
- in nearly all plots: dialog to set the size of the output when exporting/printing the plots
- PicoQuant importers: now supports PicoHarp 300 PT3 files (T3 mode )
- TCSPC importers: now the correct experiment duration is stored in the result files
- FCS Maximum Entropy: added support for new models (still unfinished, so only partly working) and reports

**2012-03-30 (SVN: 1410)**- many bugfixes
- new plugin: FCCS fit functions
- new plugin: FCS Maximum Entropy evaluiation
- new plugin: photon count raw data record
- new plugin: TCSPC correlator
- new plugin: Picoquant importer
- new plugin: imFCS Fit
- pushed extlib CImg to 1.4.9
- imFCS: correlation dialog is no longer modal
- improved online help
- 64-bit Windows version
- folders in project to organize raw data records
- onle-help viewer now renders LaTeX expressions

**2012-02-13 (SVN: 1304)**- many bugfixes
- now uses Qt 4.8.0
- major speed improvement mainly for imFCS
- added "Copy To Matlab"/"Save to Matlab" functionality in many places (allows to save data of a plot as a Matlab script which defines a variable for every column)
- plots may be copied as an image to the clipboard
- added possibility to group QFRawDataRecords into folders (folder input field in raw data record windows, on the first tab)
- SPIM-FCS model: diffusion coefficients are now sorted in descending order
- FCS Fit Functions: added background correction factor to most models
- imFCS: selection/masking by rectangle, scribble, line, circle and ellipse are now possible
- imFCS: added "Copy To Matlab" functionality for images
- imFCS: updated PDF/PS/Printer-Report code so the fit parameter table is scaled with its size
- imFCS: added dialog to mask pixels by their value in param image, gof image and overview image
- imFCS: added more options to edit the masl (invert, clear, ...)
- imFCS: implemented bleach correction (normalize to frame average and normalize to exponential decay
- imFCS: implemented data explorer, which allows to have a look at the data before the correlation
- imFCS: added multi-tau correlator with implicit averaging (ACF is effectively convolved with a triangular kernel!!!)

**2011-12-15 (SVN: 1200)**- reworked part of the icons/artwork
- added copy data to clipboard action to plot toolbars and also to the FCS fit dialog
- imFCS: more information is saved in the project
- imFCS: correlator saves GnuPlot file to plot (and fit 1-exp) the statistics data file
- SPIM-FCS fit functions: extended diffusion model to <=3 components
- imFCS: added mask and selection display
- imFCS: use target symbol to display selected pixel
- imFCS: allow to edit mask in parameter image tab
- imFCS: added checkboxes to switch single image plots on and off
- imFCS: no more crashes when clicking on parameter images
- improved plot speed of images, when zooming in
- imFCS: added distance CCF, which allows 2color-FCCS
- imFCS: added method to read Radhard2 correlation yaid files into plugin
- correction in QFFitFunction lists in online-help system
- improved speed/stability
- mFCS: added binning (tested, still some problems at the borders -> recheck) and cropping to image readers/correlation dialog
- FCS Distribution Models: complete log-normal distribution
- added FCS fit functions for diffusion + flow
- added FCS fit functions for diffusion + rotation
- resorting of function inf FCS Fit plugin
- improved datacut sliders
- massive update of online-help and tutorial
- FCSfit: added buttons to copy to/reset all runs
- imFCS: video correlator now supports background image removal and calculates statistics after removal
- SPIM-FCS diffusion model: correction of mistake when calculating focal volume (factor 1000)

**2011-10-19 (SVN: 1069)**- FCS: improved support for CSV files with MacOS line endings
- added sort priority to QFRawDataRecord results
- corrected some export errors when saving result tables as CSV/SYLK
- improved sorting in results tables
- corrected display error of graph axis labels (sometimes 10^{-3} was drawn as 0)
- slight speed improvements, no more console window in release mode
- added SPIM-FCS fit model for 1-component pure-diffusion
- imFCS: parameter image editor supports saving of data and reports
- imFCS: added correlator for image series (reads TIFF and Radhard2 raw file format)
- imFCS: added parameter histogram
- FCSFit: residual correlation is now normalized by residual variance
- FCSFit: added more possibilities to copy a fit parameter to other files/runs
- imFCS: implemented fit parameter table (with colored byackground to indicate curve)
- imFCS: implemented goodness of fit plot
- imFCS: goodness of fit and image plot support set of transformations when reading data
- massive speed improvement of FCS fit and imFCS
- put some efforts into unifying double-to-string conversion for project using a QLocal::c() with disabled group separator!
- FCSFit: improved plotting speed for many ACFs (switch off anti-aliasing when plotting graphs)
- Lib: improved fit results table (now supports nicer formating of results)
- imFCS/FCS: selected graphs are plotted on top now
- imFCS/FCS: splitters are save to ini now correctly!
- minor error correction: (lag-time axis in seconds, not µs at different positions
- new splash screen and icon (multiple sizes ;-) design
- lmfit: added lmfit (fast Levenberg Marquardt implementation) as fit algorithm plugin
- added special copyright.html files to online-help
- added external lib/Icon copyright notices to the online-help
- no more autocreated files in online-help ... all files are created at install time / and then the information dynamically at run-time (we do no longer need write access to the assets direcory in order to have working online help!)
- plugin sources for QGPL-infected plugins are now distributed in the ./sources/ directory
- moved online-help from tabs to buttons that open an independent window which is also not influenced by window-modal dialogs
- massively improved online-help

**2011-08-30 (SVN: 940)**, a small bugfix-release!- some bugfixes with finding correct online-help file in raw data and evaluation windows
- main window has better resize properties now
- fixed count rate readout in FCS Fit!!!

**2011-08-30 (SVN: 939)**- "normal diffusion"+levmar are default model/algorithm in fcs_fit
- solved a bug (crash) when deleting records that are currently displayed in an evaluation
- massively improved and extended online-help
- added R^2 and TSS statistics to FCS Fit
- FCS Fit now saves statistics as fit results
- FCS Fit uses TabBar to distinguish between parameters & ranges (removed "Edit Ranges" button)
- added global configuration directory
- modified autoversioning -> Version reset to 3.0, now to distinguish releases: use SVN version!)
- error corrections when editing properties (possibly wrong property selected when deleting)
- now FCS & imFCS has an error series for every run (if available!), updated FCS Fit plugin to support this (shoose between stddev/avg from all runs, per-run-stddev), imFCS will really use it to have a stddev for every pixel/run
- added units to report of FCS fit plugin

**2011-07-05 (SVN: 772)**- added multi-diffusion (2D/3D, normal/anomalous) FCS fitting function
- corrections in the calculations of counts/particle in all FCS fitting functions, except normal diffusion

**2011-06-29 (SVN: 763)**- corrected an error when reading ALV5000 files with two header/identifier lines and a possible crash when parsing an FCS file failed

**2011-06-27 (SVN: 759)**- added recent projects menu
- fixed problem reading settings
- imFCS plugin now reads data correctly
- imFCS plugin now has a display for correlation functions (basically copied from standard FCS plugin)
- imFCS plugin now import auto- and crosscorrelation from video_correlator
- LIB/qt/JKQtPlotter: fixed problem with number of digits in axis labels
- improved FCS Fit reports
- improved imFCS plugin (can now read imFCS files from video_correlator)

**2011-06-24 (SVN: 751)**- started imaging FCS data plugin (incl. SPIM-FCS test data)
- FCS fit now supports moving average over residuals
- added support for per run error estimates, loaded from files (currently not usable, as this data may not be imported from any FCS data file)
- update help system (with text replacements)
- some more cleanup
- reorganization of assets files. They now reside in the same directory as the plugin and will only be copied to the output directory!
- reworked/tidied plugin API, added QF3Lib version header!