FFS Data Processor. List of updates:

FFS Data Processor 2.7  (03.12.19)

Measurements database:

1. Import and processing of raw data (*spc files) of Becker & Hickl (B&H) cards SPC-140, SPC-144, SPC-150, SPC-154 is added;

2. Import and processing of raw data (*spc files) of Becker & Hickl (B&H) cards SPC-142, SPC-152 is added;

3. Add Files Group Wizard is extended by the possibility to copy all settings and parameters from the current record. It allows to import data much more quickly using this wizard;

FFS Data Processor 2.7  (22.08.19)

Main application:

1. Brightness correction in all FCS models (Triplet State, Conformational, ...) is extended to support also brightness ratio. It opens the possibility to perform the global analysis of ACFs and PCDs in a case if the brightness ratio q2/q1, q3/q1, ... is selected in the PCH model. The brightness ratio can be either fixed to know value or constrained to some reasonable boundaries that enhance the performance of the iterative fitting;

2. Improvement of automated creation of a global ACF + PCD analysis Three options, the type of the brightness correction, the dead time correction and fixation of the infinity term to unity were added. It allows to configure the analysis in details directly while its creation;

Measurements database:

1. Enhancement of the Raw Data Builder capabilities in a way of creation and handling of a big number of measured raw data. Automated creation of a set of curves (characteristics) ACFs, PCDs, FFCs with predefined parameters is programmed. It means one can initially define what characteristics one wants to calculate, define all needed parameters such as number of channels and time step, and finally calculate a number of sets of characteristics (e.g. at different time ranges in the raw data) one after another by clicking just one button. It allows to calculate coincident sets of ACFs + PCDs for their subsequent global analysis very quickly. One can also update the set of already calculated characteristics very quickly after e.g. changing the time ranges in the raw data. It is especially important in the analysis of data measured in living cells where just parts of measured traces are stationary and suitable for the analysis.

2. The naming newly calculated characteristics policy is changing. More options are added to the name that allows to sort them quickly.

3. Synchronization of calculated characteristics with the raw data from which they were calculated (while navigation among them) is added.

FFS Data Processor 2.6  (28.10.15)

Main application:

1. Automated creation of a global ACF + PCD analysis (FCS+PCH global analysis). Creation of necessary parameter groups and linking is done automatically;

2. Plotting of fit parameter histograms;

3. Normalization of ACFs is now performed by the maximum of correspondent theoretical curves (if they are available, i.e. after analysis);

4. The possibility to select the target chi2 criteria, standard global or weighted global (accordingly to Skakun et.al. 2011) is added;

5. The location (in Configuration dialog) of previously analysed data is memorized in registry;

6. The location of previously opened analysis (in Open/Save Analysis dialog) is memorized in registry;

7. Stored data are now listed in descending order (last analysis is first in the list) in Open/Save Analysis dialog.

Measurements database:

Direct (non-iterative) fast estimation of model parameters of measured (or calculated from raw data files) data. Fast estimation of model parameters is available for auto(cross)correlations, photon counting distributions and fluorescence cumulants. Triplet-state model is the default model for auto(cross)correlations, PCH with 1st order out-of-focus correction is used for photon counting distributions and FCA with 1st order out-of-focus correction is used for fluorescent cumulants (actually the same algorithm is used for parameter estimation for two last models).

FFS Data Processor 2.5  (16.02.15)

Measurements database:

1. Improved algorithm of bursts selection (in the intensity trace);

2. Bursts analysis. A possibility to select bursts in addition to reject bursts is added, i.e. to calculate ACF, PCD, etc. curves from the selected bursts (one curve per each burst);

3. Calculation of averaged ACF in a case of bursts analysis;

4. Possibility to interrupt the calculation of ACF, PCD, etc. curves in a case of processing of multiple raw data files, bursts analysis and if Multiple characteristic calculation regime is activated (calculation with increased bin time and sliding analysis);

5. Selection of time unit while import of already calculated curves (ACF, etc.) stored primarily in text files. Note: Data processor is independent from time dimension, it estimates parameters accordingly to the imported data. It is mostly for convenience purposes because lots of things (min/max settings, etc. are initially set assuming time in ms);

6. Acceleration of raw data processing in a case of calculation of ACF, PCD, etc. from parts of data (from bursts, in sliding regime);

7. Memorization of user settings in Raw data builder and Burst selection/rejection forms and in the Import data wizard;

8. Auto edit tables mode id added. It allows to edit all database tables without necessity to click Edit button in the database navigator each time before editing;

9. Enabling of resizing of Open and Save data dialogues;

10. Important. A data dependent problem in a calculation of crosscorrelation from two channel Confocor 2 raw data is fixed. This bug was introduced in the last versions. If a calculation of crosscorrelation from Confocor 2 raw data was interrupted with the error "Flow is incorrect" (this error is shown if next photon arrives before the current one), most probably you met this problem. In some cases depending on data some photons might be accounted in a wrong channel (respectively with assignment of arrival time which differ from the actual one in 1 - 3 clock-time events). Please ask for a free update of the Measurements database if you are working with two channel Confocor 2 data.

Analysis database:

1. Joining of several analyses stored in the database. Several analyses performed on the same sample (from repetitions, kinetic measurement, etc.) can now be joined in one analysis. After joining of global parameters (instrumental parameters and others expected to have same value across all analysis) one gets a 'super' global analysis;

2. Calculation of histograms of fit parameters is now possible;

3. Linking to other databases like it was done in the Measurements database is now possible also in the Analysis database.

FFS Data Processor 2.4  (25.10.13)

1. Direct (i.e. without merging) import, processing and analysis of data from two SPC 130 cards (SPC 132);

2. Calculation of red-to-blue (in addition to blue-to-red) crosscorrelation functions from the raw data. Calculation of averaged (blue-to-red + red-to-blue)/2 crosscorrelation function;

3. Burst rejection is updated by introducing user-defined gaps placed before and after of each selected busts. Vertical thresholds values can now be set by user. All settings are memorized in regestry.

FFS Data Processor 2.3  (20.05.13)

1. Import of new PiqoQuant Symphotime 64 (*.ptu) data is implemented.

FFS Data Processor 2.3  (02.02.12)

1. Import of 5 column ASCII data (X, Y channel red, Y channel red weight, Y channel blue, Y channel blue weight) is implemented;

2. Import of 7 column ASCII cross-correlation data (time-lag, ACF red, ACF red weight, ACF blue, ACF blue weight, CCF, CCF weight) is implemented;

3. Analysis of ICS (time correlation) data is now possible. Import of time correlation data exported from ImFCS software into three ASCII files: one column time-lag file, N-colunm ACF file, 2*N-column SD+AVG files is implemented;

4. Import/Export analyses stored in the Analysis database is now possible.

FFS Data Processor 2.3  (06.01.11)

1. Import of PicoQuant PicoHarp 300 data without the header (when the equipment is controlled LabView interface) is implemented;

2. Calculation of the Normalization value (required for PCD analysis) from data imported from the text files is added. See also the local menu item of the Files grid of the Measurement database.

FFS Data Processor 2.3  (01.11.10)

1. PCH model was extended:

• List of supported observation profiles is extended by the 2D Gaussian and squared Gauss-Lorensian profiles;

• Process correction list is extended by including a correction to the Conformation and Protonation processes;

• Motion correction list is extended by including a correction on the free 2D diffusion and anomalous 2D/3D diffusion;

• 1st and 2nd order out-of-focus correction is now available for the all (2D/3D Gaussian and squared Gauss-Lorensian) profiles (except for the polynomial profile);

• Normalization (scaling) is now available either to the effective volume (i.e. setting Veff=1) or by setting of both the first and the second moments of PSF to unity (FIDA-like normalization);

• For a two and more components model a ratio of both number of molecules and brightness could now be fitted, i.e. a list of four parameter combinations is supported: N1, q1, N2, q2,…; N1, q1, N2, q2/q1,…; N1, q1, N2/ N1, q2,…; N1, q1, N2/ N1, q2/q1,…;

• A range of available values of brightness and number of molecules is extended (to support larger values). The algorithm of PCH model calculation is updated;

• Initial guesses (IG) are calculated for all parameters of PCH model except afterpulses, dead time, process and motion correction parameters;

2. Analysis and manipulation of a large number of fitted curves is improved:

• The configuration dialog is updated to view more information about curves located in the database. Multiselection (with ‘shift’ or ‘ctrl’ keys pressed), selection by a number of criteria (type, range of ID, part of the name, kinetic number)and filtering are now possible (filter by selection is implemented);

• A manager of fit parameter settings is programmed. It allows to set values, minimum and maximum constraints, apply or remove fixing for a group of fit parameters selected by a name, type, range of values and name of the model. It allows searching parameters by a set of criteria and manipulation of their properties in automated way;

• Direct selection of any analyzed dataset in the 2D plot by double clicking the mouse button over the displayed curve (if several curves are displayed). This option simplifies the location and deletion of inappropriate data;

• Direct deletion of any dataset from the experiment tree without invoking the configuration dialog (one can delete any curve by simply selecting it and deleting it from the experiment);

• Dataset name and some measurement parameters like time step, repeat and kinetic number are displayed for each curve in the 2D plot if the mouse pointer is over the curve;

• Direct copy to clipboard and export to ASCII file is implemented from local menu of 2D plot.

3. Other changes:

• The Poissonian model for fitting photon counting distributions is implemented. Now three models for fitting photon counting distributions are available: PCH, Poissonian and Gaussian;

• Export to ASCII file is updated. Local target fit criterion values can now be exported;

• The amplitude normalization of a set of correlation curves is implemented.

4. Measurements database was updated:

• Import Data Wizard is programmed. The main goal of this wizard is to simplify the import (all related things including calculation of characteristics from the raw data, calculation of average characteristics, their weights factors are now possible in frames of this wizard);

• Direct appending and/or selection of Sample and Guest information (without invoking of additional forms) is now possible in the Import Data Wizard;

• Import of a single characteristic from two- (without weight) and three-column (with weight) ASCII files either without or with a header (in form of “parameter name”=”parameter value”) is implemented. If the header is presented, the line just before data with an identifier “#Data:” is required. A number of files can be selected, imported and processed at one step. If the third column is not presented, the calculation of the weight factors for PCD is performed automatically during the import assuming binomial statistics. The import of two column data by the three column importer and vice verse is possible;

• Import of weight factors from one- and two-column ASCII file is implemented;

• Calculation of the average characteristic from a set of selected (filtered) characteristics (curves) with equal type and X-axis is programmed. Calculation of the weight factors for PCD is performed automatically if no weight factors are available.

• Calculation of weight factors from a set of selected (filtered) characteristic (curves) with equal type and nearly identical X-axis (Time Step can differ in 1%) is improved. Weight factors can now be calculated from a set of either selected or filtered files.

• Managing of a high number of files is improved. With this aim the Files Selection dialog is programmed. It helps to select a set of files in the Files grid by a number of criteria (type, range of ID, part of the name, kinetic number). Also the continuous (Shift+) and selective (Ctrl+) selection of a number of files in the Files grid is now possible.

• Filtering data is improved. Filter by Selection and Clear Filter options are now available for all database tables. Status of filtration is now displayed in all database grids.

• Import data dialogs are updated. The problem with selection of a single file in a folder is solved. The selection of a number of files (for their butch processing) is now available in the most import data dialogs (including ConfoCor2 import data dialog).

• Import of ConfoCor 3 (Zeiss) raw (*.raw files) and preprocessed data (ASCII *.fcs files) is implemented in frames of a single routine. Pairs of raw data files (f.e. in the cross-correlation experiment) are now selected by their unique identification number (but not by a name of the file).

• Import of photon counting distributions (PCD) from text files having either ConfoCor2 (Zeiss) or ALBA (ISS) dataformat is improved. Now PCDs, imported from these files, can be analyzed in a normal way (earlier versions could only preview such data). Weight factors are calculated automatically during the import assuming binomial statistics.

• Import of the column organized data is improved. Now parameters which are necessary for the analysis, like TimeStep, are calculated from the imported data where it is possible, Weight factors are calculated automatically during the import also where it is possible.

• Raw Data Builder is updated. Automated calculation of the average characteristic is programmed (except for PCD). Calculation of a number of photons from a selected region and displaying a total number of photons in the Intensity chart title is implemented. Filtering of calculated characteristics is updated.

• Sliding analysis of characteristics (PCD, AC(C)F, etc), calculated from the raw data either by the constant time shift or the constant amount of photons is implemented. Multiple characteristics can now be calculated not only with different Time Step but also with different Start and End times accordingly to the chosen sliding scheme. Automated calculation of a number of characteristics followed by either a sequential or a global analysis is now possible for the data measured for a long time.

FFS Data Processor 2.2  (01.06.09)

PCH model was updated. A ratio of both number of molecules and brightness could now be fitted for a two and more components model, i.e. a list of four parameter combinations is supported: N1, q1, N2, q2,…; N1, q1, N2, q2/q1,…; N1, q1, N2/ N1, q2,…; N1, q1, N2/ N1, q2/q1,…;

FFS Data Processor 2.1  (15.09.08)

Import of simple raw data formats is updated. Not it is possible to import raw data (sequence of photon arrival times) stored in TEXT files. One channel data and data with router are supported.

FRD.dll is updated.

FFS Data Processor 2.1  (01.05.08)

Import and processing of raw data of PicoQuant PicoHarp 300 and PicoQuant Time Harp 200 dataformats is supported.

Import of SIN files is implemented.

The problem with global analysis of a large number of datasets having large number of estimated parameters (usually leads to the error EOverflow) is fixed.

The problem with freezing of global analysis at the end is fixed. These problems were related to calculation of inverse Marquardt matrix of large dimension. Now it is calculated only when necessary (for the calculation of standard errors of estimated parameters and calculation of weight factors while secondary characteristic building).

FFS Data Processor 2.0  (16.04.07)

New methods:

PCH with correction for the out-of-focus emission

Following observation profiles are supported:

• 3D Gaussian
• 3D Gaussian with 1^st order correction for the out-of-focus emission (accordingly Huang at al., 2005)
• 3D Gaussian with 2^nd order correction for the out-of-focus emission (accordingly Huang at al., 2005)
• Polynomial (profile and normalization conditions are the same as in FIDA, Palo et al. 2000)

Following corrections are supported:

• Correction for diffusion and triplet-state intercrossing (idea is the same as in Palo et al. 2000 – two first factorial cumulants are exact)
• Correction for background.
• Correction for dead time (accordingly Hillesheim at al., 2003).

IG (method of moments) were developed for all types of observation profiles. This allows to fit data in just a few iterations.

TIFCA (according to Wu et al., 2005).

Following observation profiles are supported:

• 2D Gaussian
• 3D Gaussian
• Squared Gauss-Lorenzian
• 2D Gaussian with 1^st order correction (accordingly Huang at al., 2005)
• 3D Gaussian with 1^st order correction (accordingly Huang at al., 2005)
• Squared Gauss-Lorenzian with 1^st order correction (accordingly Huang at al., 2005)
• 2D Gaussian with 2^nd order correction (accordingly Huang at al., 2005)
• 3D Gaussian with 2^nd order correction (accordingly Huang at al., 2005)
• Squared Gauss-Lorenzian with 2^nd order correction (accordingly Huang at al., 2005)
• Polynomial (profile and normalization conditions are the same as in FIDA, Palo et al. 2000)

Following corrections are supported:

• Correction for diffusion
• Correction for background (like it is done in FIDA).

IG for all cases were developed (method of moments)

Main updates:

1. In addition to Global Analysis the Sequential fit of a number of datasets was implemented (see property Analysis Type of the Experiment. It can be set to either Global or Sequential).

2. Calculation and viewing of the local Target Criterion Value (TFC) (ChiSquare) for all data sets was implemented. It now allows to explore quality of fit of an individual dataset in the global analysis.

3. Automatic calculation of a number of any characteristics with different bin time (Time Step) from a number of raw data files was implemented.

4. Creation of a Fit Parameter Dependence (FPD) curve from a number of Experiments (opened experiment windows). The FPD was a dependence of certain fit parameter (for example brightness) on the external parameter (for example bin time). Weighting factors are assumed to be asymptotic errors of fit parameters derived from diagonal elements of variance-covariance matrix. The FPD can be created by using the interface elements of "Experiment configuration window" located on the page "Fit parameter dependence". Created FDPs can be added to the experiment and analyzed by the User-created model.

5. Import of ASCII file that contain of any column organized data was implemented. Possibility to choose separator, delimiter, start/end row, data type for each column is supported.

6. Calculation of crosscorrelation function with leaking correction was implemented.

7. The brightness parameters are available for the fit when the brightness correction is set on for FCS models.

8. The possibility to generate Initial Guesses, calculate TFC and analyze individual data set within the experiment was added. These options are available for the case of sequential analysis and can be accessed trough local menu of "Experiment configuration window".

9. Import of Confocor 3 raw data.

10. Rejection of unwanted bursts of intensity was implemented.

11. Simulator of Poisson and double stochastic Poisson (with exponentially decaying autocorrelation function) random point processes was implemented. It allows to simulate raw data with user-defined properties.

Fields "Fit Criterion" and "Analyzed" were added in the analysis database. It requires restructuring the analysis database. 

FCS Data processor was extended and renamed to FFS Data processor  (01.01.07)

FCS Data processor 1.4.2  (25.02.06)

1. Multicolumn data import was implemented;

2. Bugs with confidential intervals analysis and calculation of Chi2 were fixed;

3. 3D chart visualization bugs were fixed;

4. Automatic creation of statistical characteristics with varying TimeStep was implemented.

FCS Data processor 1.4.1 (01.04.05)

Main updates:

1. Models library for fitting auto(cross)correlation functions has been extended:

·        correction for brightness difference is added;