- Scientific Software Technologies Center

- Scientific Software Technologies Center
Scientific Software Technologies Center
FFS Data Processor
Global analysis software in fluorescence fluctuation spectroscopy
User Manual
(Main Application)
SSTC contacts: www.SSTCenter.com; [email protected]
FFSDP User Manual
THEORETICAL BACKGROUND .................................................................................................6
Characteristics .............................................................................................................................................................................. 6
Models............................................................................................................................................................................................ 6
Custom model ............................................................................................................................................................................ 7
PCH model................................................................................................................................................................................. 7
FFC model ............................................................................................................................................................................... 10
Gaussian model........................................................................................................................................................................ 13
Correlation function models..................................................................................................................................................... 14
Methods ....................................................................................................................................................................................... 22
Global fit.................................................................................................................................................................................. 22
Sequential fit ............................................................................................................................................................................ 22
Initial guesses........................................................................................................................................................................... 23
Quality of fit............................................................................................................................................................................. 23
Exhaustive search .................................................................................................................................................................... 23
Standard errors......................................................................................................................................................................... 23
Simulator.................................................................................................................................................................................. 24
USING CUSTOM MODEL ..........................................................................................................24
Script programming language................................................................................................................................................... 24
Whitespace............................................................................................................................................................................... 24
Tokens...................................................................................................................................................................................... 24
Keywords ................................................................................................................................................................................. 25
Variable identifiers................................................................................................................................................................... 25
Variables .................................................................................................................................................................................. 25
Operators.................................................................................................................................................................................. 25
Built in functions ..................................................................................................................................................................... 28
Punctuators............................................................................................................................................................................... 31
Numeric expression ................................................................................................................................................................. 32
Expression................................................................................................................................................................................ 32
Parameters................................................................................................................................................................................ 32
Custom model configuration dialog box ................................................................................................................................... 32
button ............................................................................................................................................................................... 33
button............................................................................................................................................................................... 33
button ............................................................................................................................................................................... 33
button.............................................................................................................................................................................. 33
button ............................................................................................................................................................................. 33
Models list................................................................................................................................................................................ 33
Filter button.............................................................................................................................................................................. 34
Search button ........................................................................................................................................................................... 34
OK button ................................................................................................................................................................................ 34
Close button ............................................................................................................................................................................. 34
Help button .............................................................................................................................................................................. 34
Test button ............................................................................................................................................................................... 34
Add model by Wizard button................................................................................................................................................... 34
Initial settings table .................................................................................................................................................................. 34
Add button ............................................................................................................................................................................... 35
Delete button............................................................................................................................................................................ 35
Formula page ........................................................................................................................................................................... 35
2
FFSDP User Manual
Input variables list.................................................................................................................................................................... 35
External parameters list............................................................................................................................................................ 35
Functions combobox................................................................................................................................................................ 35
button ............................................................................................................................................................................... 36
button ................................................................................................................................................................................ 36
Model script rich editor............................................................................................................................................................ 36
Description page ...................................................................................................................................................................... 36
New model wizard ...................................................................................................................................................................... 36
Custom model integrity restore dialog box .............................................................................................................................. 38
USING FFS DATA PROCESSOR ..............................................................................................39
Starting FFS Data Processor ..................................................................................................................................................... 39
Main window............................................................................................................................................................................... 40
Main menu ............................................................................................................................................................................... 41
Main toolbar............................................................................................................................................................................. 42
Experiment window.................................................................................................................................................................... 42
Configuration part of the Experiment window........................................................................................................................ 43
Configuration toolbar............................................................................................................................................................... 44
Configuration treeview ............................................................................................................................................................ 45
Local menu of the Configuration treeview .............................................................................................................................. 46
Parameters table ....................................................................................................................................................................... 47
Properties table ........................................................................................................................................................................ 47
Local menu of the Properties table .......................................................................................................................................... 48
Analysis information window.................................................................................................................................................. 48
Parameters page ......................................................................................................................................................................... 48
Toolbar of the parameters page................................................................................................................................................ 49
Linked parameters treeview ..................................................................................................................................................... 50
Local menu of the Linked parameters treeview ....................................................................................................................... 51
Free parameters list .................................................................................................................................................................. 52
Local menu of the Free parameters list .................................................................................................................................... 52
Parameters settings table.......................................................................................................................................................... 53
Local menu of Parameters settings table.................................................................................................................................. 54
Unlinking parameters............................................................................................................................................................... 55
Linking parameters .................................................................................................................................................................. 56
2D Graphics page........................................................................................................................................................................ 56
Toolbar of the 2D Graphics page............................................................................................................................................. 57
2D Characteristics and Residuals charts .................................................................................................................................. 58
Local menu of 2D chart ........................................................................................................................................................... 59
3D Graphics page........................................................................................................................................................................ 59
Toolbar of the 3D Graphics page............................................................................................................................................. 60
3D Characteristics and Residuals charts .................................................................................................................................. 61
Local menu of 3D chart ........................................................................................................................................................... 62
Experiment configuration dialog box........................................................................................................................................ 63
Mesurements database page..................................................................................................................................................... 63
Simulator page ......................................................................................................................................................................... 65
Fit parameter dependence page................................................................................................................................................ 66
3
FFSDP User Manual
For Analysis table .................................................................................................................................................................... 68
Button "Hide/Show Source Data"............................................................................................................................................ 68
Button "DataBase" ................................................................................................................................................................... 68
Button "Ok" ............................................................................................................................................................................. 68
Button "Cancel" ....................................................................................................................................................................... 68
Button "Help"........................................................................................................................................................................... 68
Local menu of Configuration dialog box ................................................................................................................................. 68
“Open an existing experiment” dialog box............................................................................................................................... 69
Experiment Name .................................................................................................................................................................... 70
Previously saved experiments.................................................................................................................................................. 70
Button "Help"........................................................................................................................................................................... 70
Button "Open".......................................................................................................................................................................... 70
Button "Cancel" ....................................................................................................................................................................... 70
Button "Filter".......................................................................................................................................................................... 70
Button "DataBase" ................................................................................................................................................................... 71
“Save experiment as” dialog box............................................................................................................................................... 71
Experiment Name .................................................................................................................................................................... 71
Previously saved experiments.................................................................................................................................................. 71
Button "Help"........................................................................................................................................................................... 71
Button "Save"........................................................................................................................................................................... 71
Button "Cancel" ....................................................................................................................................................................... 71
Button "Filter".......................................................................................................................................................................... 71
Button "DataBase" ................................................................................................................................................................... 72
Export data dialog box ............................................................................................................................................................... 72
"File" edit................................................................................................................................................................................. 72
Button "Browse" ...................................................................................................................................................................... 72
"Target criterion value" check box .......................................................................................................................................... 72
"Related free parameters" check box ....................................................................................................................................... 73
"Data Sets" list ......................................................................................................................................................................... 73
Button "Check All" .................................................................................................................................................................. 73
Button "Clear All".................................................................................................................................................................... 73
"Parameters groups" group box ............................................................................................................................................... 73
"Arrays to be saved" group box ............................................................................................................................................... 73
Button "Export" ....................................................................................................................................................................... 73
Button "Help"........................................................................................................................................................................... 73
Button "Close" ......................................................................................................................................................................... 73
Create and save new template dialog box................................................................................................................................. 74
Button "Save"........................................................................................................................................................................... 74
Button "Cancel" ....................................................................................................................................................................... 74
Template name......................................................................................................................................................................... 74
Button "DataBase" ................................................................................................................................................................... 74
Button "Help"........................................................................................................................................................................... 74
Load and apply an existing template dialog box...................................................................................................................... 74
Previously saved templates ...................................................................................................................................................... 75
Template name......................................................................................................................................................................... 75
Button "Filter".......................................................................................................................................................................... 75
Button "Apply" ........................................................................................................................................................................ 75
Button "Cancel" ....................................................................................................................................................................... 75
Button "DataBase" ................................................................................................................................................................... 76
Button "Help"........................................................................................................................................................................... 76
"Fit parameter vs. external parameter view" window............................................................................................................ 76
Fit parameter combobox list .................................................................................................................................................... 76
4
FFSDP User Manual
External parameter combobox list ........................................................................................................................................... 76
Button "Help"........................................................................................................................................................................... 77
Button "Close" ......................................................................................................................................................................... 77
2D Chart................................................................................................................................................................................... 77
Local menu of 2D chart ........................................................................................................................................................... 77
"Separation of coincidence values histograms" window......................................................................................................... 78
Experiments list ....................................................................................................................................................................... 79
Options group box ................................................................................................................................................................... 79
2D Chart................................................................................................................................................................................... 79
Separation quality window ...................................................................................................................................................... 79
External parameters dialog box ................................................................................................................................................ 79
Table "External parameters" .................................................................................................................................................... 79
Button "Add" ........................................................................................................................................................................... 80
Button "Delete"........................................................................................................................................................................ 80
Button "Create new" ................................................................................................................................................................ 80
Button "Ok" ............................................................................................................................................................................. 80
Button "Cancel" ....................................................................................................................................................................... 80
Button "Help"........................................................................................................................................................................... 80
TERMS ....................................................................................................................................... 80
FCS............................................................................................................................................................................................... 80
FFS ............................................................................................................................................................................................... 80
Properties .................................................................................................................................................................................... 80
Parameters .................................................................................................................................................................................. 80
Structural parameter.................................................................................................................................................................. 80
Parameter group......................................................................................................................................................................... 81
Templates .................................................................................................................................................................................... 81
Local menus................................................................................................................................................................................. 81
Experiment .................................................................................................................................................................................. 81
Experiment properties:............................................................................................................................................................. 81
Data Set........................................................................................................................................................................................ 81
Data Set properties:.................................................................................................................................................................. 82
Data Source ................................................................................................................................................................................. 82
Data Source properties:............................................................................................................................................................ 82
Model ........................................................................................................................................................................................... 82
Noise............................................................................................................................................................................................. 83
REFERENCES TO LITERATURE..............................................................................................83
5
FFSDP User Manual
Theoretical background
Characteristics
Following characteristis can be analysed in FFSDP:
1. Autocorrelation function
2. Crosscorrelation function
3. Fluorescence factorial comulants
4. Coincidence values histogram
5. Photon Counting Distribution
Models
FFS technique is aimed to the investigations of the intensity fluctuations of fluorescent molecules excited
by a tightly focused laser beam. These fluctuations may arise from translational and rotational diffusion,
chemical reactions, deexcitation of the triplet-state, conformational and structural changes, etc [ 1, 2, 3, 4,
5, 15, 16, 26].
To take into account any phenomenon mentioned above while analyzing the FFS data the appropriate
mathematical model should be chosen. In the FFS Data Processor the mathematical models are
represented by the corresponding Model Objects.
Model Object can belong either to the Data Set or to the Simulation Data Source. In the first case Model
is used to generate the theoretical characteristic. In the second case it is used to generate noise-free source
characteristic.
Model icon is following: .
Now the following models are available to be used with FFS Data Processor:
Characteristics
Models
Correlation function
Pure-Diffusion
Triplet-State
Conformational
Protonation
FCS flow
Custom
Coincidence values histogram
Gaussian
Custom
Comulants
FFC
Custom
Photon counting distribution
PCH
Gaussian
Custom
(2D/3D free diffusion,
2D/3D anomalous diffusion,
2D/3D confined diffusion,
TIR-FCS are supported)
Identifiability
All models mentioned above (except Custom model and PCH with “FIDA-like” polynomial brightness
profile approximation) are totally identifiable, i.e. all parameters of the models can be uniquely
determined on the basis of only one measured characteristic. PCH with “FIDA-like” polynomial
brightness profile approximation at fixed background can have up to 3 equvalent sets of parameters each
of them can be used [27].
6
FFSDP User Manual
Custom model
Custom model is designed to perform the data analysis with user defined mathematical description. The
special Script programming language was developed for writing the user-defined models. Before
constructing new model some fit parameters should be created. The names assigned to the parameters can
then be used in the model script.
Custom model properties:
1. IG type
determines how the initial guesses of all model parameters are generated. See list of IG
type values for details.
2. Configuration provides access to Custom model configuration dialog box. Press the button on the
right side of the property value box to open this dialog box.
3. Subtype
provides quick selection of the needed custom model from the database.
Custom model parameters:
The parameters are defined by user. See Custom model configuration dialog box for more information.
To learn more about custom models see “Using Custom model” secton bellow.
PCH model
The PCH model is used to analyse Photon Counting Distribution (PCD).
The total PCD from a number of molecules is calculated by successive convolutions of a single molecule
PCD [ 23, 24, 25 ]:
(1)
where Poi(n, λ) denotes the Poisson distribution with the mean value λ, Veff is the effective volume and Q
is taken so that the product QVeff is large enough to completely include the illuminated volume. The total
distribution P(n) will be the weighted average of
convolved M times [25 ]
p (1) (0, Q, q ) = 1 − ∑ k =1 p (1) (k , Q, q ),
∞
(2)
⎧ 1, n = 0
p (0) (n) = ⎨
⎩0, n ≠ 0,
p ( M ) (n) = p (1) ⊗ p (1) ⊗ … ⊗ p (1) (n).
M −1 times
PCH model properties:
1. IG type
determines how the initial guesses of all model parameters are generated.
See list of IG type values for details.
7
FFSDP User Manual
IG type
Description
None
Generation of the initial guesses is not performed in any cases.
Method of moments
Generation of the initial guesses is performed by method of moments.
Phase plane method
Generation of the initial guesses is performed by phase plane method.
User-defined
The values defined by user will be used as initial guesses. In the case of
Custom model these values can be set via Custom model configuration
dialog box.
Predefined values
The predefined values will be used as initial guesses. These values are
specific for each type of the model and do not depend on the data of
characteristic associated with the model.
2. ComponentsCount
defines a number of molecular components with different brightness.
3. Dead time correction
determines if dead time correction (accordingly to Hillesheim at al., 2003)
is taken into account.
4. Process correction
determines if process correction (due to triplet-state intercrossing) is taken
into account.
5. Motion correction
determines if motion correction (due to diffusion) is taken into account.
6. Profile type
specifies the type of PSF(x,y,z). The following profile types are available:
3D Gaussian,
3D Gaussian 1-st corr.,
3D Gaussian 2-nd corr.,
Polynomial.
Common PCH model parameters:
1. Bg is the mean background count rate of detector.
2. Ni is the mean number of molecules of i-th brightness component.
3. qi is the mean number of photons detected in a time interval (brightness, cpsm) of i-th brightness
component.
4. Ti is the translational diffusion relaxation time of molecules of the i-th diffusion component (exists only
if Motion correction property is "true").
5. a is the structural parameter(exists only if Motion correction property is "true").
6. Ftrip is the fractional population of the triplet state (exists only if Process correction property is
"Triplet State").
7. Ttrip is the relaxation time of the triplet state (exists only if Process correction property is "Triplet
State").
8. Tdt is the dead time (exists only if Dead time correction property is "true").
9. Fit parameters of selected profile.
8
FFSDP User Manual
To find out more information about selecting the model and specifying related properties and parameters
see Experiment configuration box, Properties table and Parameters table , respectively.
3D Gaussian profile
Out-of-focus correction (3D Gaussian 1-st corr.; 3D Gaussian 2-nd corr.)
To improve the model, Perroud and Huang [ 23, 24 ] introduced additional fitting parameters Fk defined as
the relative difference between the integral of the k-th power χk of the normalized to unity actual
brightness profile function PSF(r) and that of its 3D Gaussian approximation χGk:
.
(3)
Fk can be also treated as an out-of-focus emission ratio. In the most cases only the first order correction
(all Fk equal zero except F1) is sufficient to get the best fit to the experimental data. The second order
correction (F1 and F2 are different from zero) is rarely needed. We use normalization to the effective
volume
in order to relate Ni obtained by both PCH and FCS.
Single molecule PCD with out-of-focus correction takes the form [ 24 ]
.
(4)
Specific PCH model parameters:
1. Fc1 is first order correction parameter.
2. Fc2 is second order correction parameter (for “3D Gaussian 2-nd corr.” profile only).
Polynomial profile
PSF(r) is approximated by an exponential function of one argument with polynomial transformation of
volume unit (further simply FIDA-like polynomial approximation) [ 21, 22 ]
,
,
(5)
where a1, a2 are instrumental parameters and PSF0 is the value of PSF(r) at r equal to 0. PSF0 and A0 are
calculated from a system of normalization equations:
(6)
9
FFSDP User Manual
(1) and
The total PCD is calculated by Eq.
(2) taking into account Eq.
(5),
(6).
Specific PCH model parameters:
1. a1 is the brightness profile parameter.
2. a2 is the brightness profile parameter.
FFC model
The FFC model is used to analyse a set of Fluorescence Factorial Cumulants [ 15, 20]. It is defined by the
following formula:
(7)
where qi is the mean number of photons (expressed in counts per second per molecule) detected in a time
interval T, Ni is the mean number of molecules of the i-th component in the open observation volume, Bg
is the mean background count rate of the detector and
is the diffusion correction term.
is the normalized correlation function of kth order [ 20 ]. For the limit of short bin times it takes the form:
.
We use normalization to the effective volume
in order to relate Ni obtained by both TIFCA and FCS. Factor γ2 that appears in Eq. 1 is due to this type of
normalization. γ-factors are defined as
,
,
where PSF(r) is the normalized to unity brightness profile function.
To correct for deviations of the actual observation profile from its ideal approximation three different
approaches can be used in FFC (see Profile type property of the model):
1) γ-factors (γ3, γ4, ...) can be fitted during the analysis (applicable only in the global analysis with linking
all fitted γ-factors);
10
FFSDP User Manual
2) FIDA-like polynomial profile [ 21, 22 ] can be used for the approximation of the actual PSF;
3) out-of focus correction of 2D/3D Gaussian or squared Gauss Lorenzian profiles [ 23, 24 ] can be used.
In the case of out-of-focus correction Eq. 1 becomes
,
where Fk are correction parameters defined as relative difference between integral of the kth power of the
actual observation profile χk and that of its approximation
.
In the most cases just first order correction is needed (all Fk = 0 except F1), and sometimes second order
correction (all Fk = 0 except F1 and F2) is necessary to get best fit to the experimental data.
FFC model properties:
1. IG type
determines how the initial guesses of all model parameters are generated.
See list of IG type values for details.
2. ComponentsCount
defines a number of molecular components with different brightness.
3. Motion correction
determines if motion correction (due to diffusion) is taken into account.
4. Profile type
specifies the type of PSF(x,y,z). The following profile types are available:
2D Gaussian,
2D Gaussian 1-st corr.,
2D Gaussian 2-nd corr.,
3D Gaussian,
3D Gaussian 1-st corr.,
3D Gaussian 2-nd corr.,
3D Gaussian fitted,
Squared Gaussian-Lorenzian,
Squared Gaussian-Lorenzian 1-st corr.,
Squared Gaussian-Lorenzian 2-nd corr.,
Polynomial,
FFC model parameters:
1. Bg is the mean background count rate of detector.
2. Nj is the mean number of molecules of j-th brightness component.
3. qj is the mean number of photons detected in a time interval (brightness, cpsm) of j-th brightness
component.
4. Ti is the translational diffusion relaxation time of molecules of the i-th diffusion component (exists only
if Diffusion correction property is "true").
5. a is the structural parameter (exists only if Diffusion correction property is "true" and Profile type
property is "3D Gaussian").
6. Fit parameters of selected profile.
11
FFSDP User Manual
To find out more information about selecting the model and specifying related properties and parameters
see Experiment configuration box, Properties table and Parameters table, respectively.
2D Gaussian profile
γ-factors are calculated by
,
where d is the dimensionality (d=2).
3D Gaussian profile
γ-factors are calculated by
,
where d is the dimensionality (d=3).
First order correction (2D Gaussian 1-st corr.; 3D Gaussian 1-st corr.; Squared GaussianLorenzian 1-st corr.)
all Fk = 0 except F1
Second order correction (2D Gaussian 2-nd corr.; 3D Gaussian 2-nd corr.; Squared GaussianLorenzian 2-nd corr.)
all Fk = 0 except F1 and F2
Specific FFC model parameters:
1. Fc1 is first order correction factor.
2. Fc2 is second order correction factor.
3D Gaussian fitted profile
γ-factors for two first comulants are calculated as
,
respectively. All other γ-factors (actually products γ2γ3, γ2γ4, …) are fit parameters.
Squared Gaussian-Lorenzian profile
γ-factors are calculated by
12
FFSDP User Manual
.
Polynomial profile
For the polynomial profile Eq. 1 becomes
,
,
where
,
and
,
(a1 and a2 are the fit parameters). A0 and B0 are chosen so that the normalisation conditions assumed in
) are satisfied.
FIDA (
Specific FFC model parameters:
1. a1 is the brightness profile parameter.
2. a2 is the brightness profile parameter.
Gaussian model
The Gaussian model is used to analyse coincidence values histogram [ 16 ] and photon counting
distribution. The model is based on the Gaussian distribution function:
,
where m is the mean, σ is the standard deviation.
Gaussian model properties:
1. IG type
determines how the initial guesses of all model parameters are generated.
See list of IG type values for details.
Gaussian model parameters:
1. M is the mean of the Gaussian distribution.
2. Sigma is the standard deviation of the Gaussian distribution.
To find out more information about selecting the model and specifying related properties and parameters
see Experiment configuration box, Properties table and Parameters table, respectively.
13
FFSDP User Manual
Correlation function models
The correlation function models [ 17, 18, 19 ] that are included in FFSDP are based on the following
general formula:
where:
is the level of autocorrelation function when
(by default
= 1);
denotes the average number of fluorescent particles;
denotes the background correction multiplier (
denotes background
is the uncorrelated background signal). Correction to
ratio, where is the sample signal and
background is performed if property Background correction is set on;
denotes some kinetic process;
describes the motion type of the particles.
. For each model with particular
The models are classified by kinetic term
types of motion are available trough the Motion type property.
several
The following motion types of the particles are implemented:
Free 2D Diffusion
Free 3D Diffusion
Anomalous 2D Diffusion
Anomalous 3D Diffusion
Confined 2D Diffusion
Confined3D Diffusion
TIRR-FCS
The fitting models designed in the FFSDP for the analysis of correlation functions are following:
Pure diffusion model
Triplet-State model
Conformational model
Protonation model
Flow model
Custom model
Free 2D Diffusion term
,
where and
are, respectively, fraction and translational diffusion relaxation time of molecules of the
i-th fluorescent component.
Fit parameters added to the model by Free 2D Diffusion term:
1. Fi is the contribution of molecules of the i-th fluorescent component. In the case if brightness of the
particles should be taken into account Fi is replaced by Ni (the number of particles for i-th component).
14
FFSDP User Manual
For more information see brightness correction.
2. Ti is the translational diffusion relaxation time of molecules of the i-th fluorescent component.
Free 3D Diffusion term
,
where and
are, respectively, fraction and translational diffusion relaxation time of molecules of the
i-th fluorescent component, a is the structural parameter.
Fit parameters added to the model by Free 3D Diffusion term:
1. Fi is the contribution of molecules of the i-th fluorescent component. In the case if brightness of the
particles should be taken into account Fi is replaced by Ni (the number of particles for i-th component).
For more information see brightness correction.
2. Ti is the translational diffusion relaxation time of molecules of the i-th fluorescent component.
3. a is the structural parameter.
Anomalous 2D Diffusion term
,
where and
are, respectively, fraction and translational diffusion relaxation time of molecules of the
i-th fluorescent component, denotes the anomality factor.
Fit parameters added to the model by Anomalous 2D Diffusion term:
1. Fi is the contribution of molecules of the i-th fluorescent component. In the case if brightness of the
particles should be taken into account Fi is replaced by Ni (the number of particles for i-th component).
For more information see brightness correction.
2. Ti is the translational diffusion relaxation time of molecules of the i-th fluorescent component.
3. alpha is the anomality factor.
15
FFSDP User Manual
Anomalous 3D Diffusion term
,
where and
are, respectively, fraction and translational diffusion relaxation time of molecules of the
i-th fluorescent component, a is the structural parameter, denotes the anomality factor.
Fit parameters added to the model by Anomalous 3D Diffusion term:
1. Fi is the contribution of molecules of the i-th fluorescent component. In the case if brightness of the
particles should be taken into account Fi is replaced by Ni (the number of particles for i-th component).
For more information see brightness correction.
2. Ti is the translational diffusion relaxation time of molecules of the i-th fluorescent component.
3. alpha is the anomality factor.
4. a is the structural parameter.
Confined 2D Diffusion term
,
where:
and
are, respectively, fraction and translational diffusion relaxation time of molecules of the i-th
fluorescent component, denotes the distance in lateral direction at which the intensity of the exciting
laser beam is dropped by , is the confined volume diameter.
Fit parameters added to the model by Confined 2D Diffusion term:
1. Fi is the contribution of molecules of the i-th fluorescent component. In the case if brightness of the
particles should be taken into account Fi is replaced by Ni (the number of particles for i-th component).
For more information see brightness correction.
16
FFSDP User Manual
2. Ti is the translational diffusion relaxation time of molecules of the i-th fluorescent component.
3. Y is dy/rxy.
Confined 3D Diffusion term
,
where:
and
are, respectively, fraction and translational diffusion relaxation time of molecules of the i-th
fluorescent component, a is the structural parameter, and are distances in lateral and axial direction at
which the intensity of the exciting laser beam is dropped by , and are the confined volume
diameters.
Fit parameters added to the model by Confined 3D Diffusion term:
1. Fi is the contribution of molecules of the i-th fluorescent component. In the case if brightness of the
particles should be taken into account Fi is replaced by Ni (the number of particles for i-th component).
For more information see brightness correction.
2. Ti is the translational diffusion relaxation time of molecules of the i-th fluorescent component.
3. Y is dy/rxy.
4. Z is dz/rz.
5. a is the structural parameter.
17
FFSDP User Manual
TIR-FCS term
F
Gmotion (τ ) = ∑ i
i 2
−1
⎛
t ⎞ ⎡⎛
t
2
a
1
1 − diff
+
⎜
diff ⎟ ⎢⎜
Ti ⎠ ⎢⎣⎝ 2Ti
⎝
⎛
⎞
t
⎟ erfcx ⎜⎜
diff
⎠
⎝ 4Ti
⎞
t ⎤
⎥
⎟⎟ +
π Ti diff ⎥⎦
⎠
,
where and
are, respectively, fraction and axial diffusion relaxation time (Tdiff z) of molecules of the
i-th fluorescent component, a is the structural parameter a = z0 ω xy , erfcx( x) = exp( x 2 ) erfc( x) is the
scaled comlementary error function.
Fit parameters added to the model by TIR-FCS term:
1. Fi is the contribution of molecules of the i-th fluorescent component. In the case if brightness of the
particles should be taken into account Fi is replaced by Ni (the number of particles for i-th component).
For more information see brightness correction.
2. Ti is the axial diffusion relaxation time of molecules of the i-th fluorescent component.
3. a is the structural parameter.
Brightness correction
Brightness correction for correlation function model determines if different quantum efficiency of each
component is taken into account. In the case of brightness correction the following replacement is made in
the motion term of a model equation :
,
is the
where qi and Ni are, respectively, brightness and number of particles for i-th component,
is the contribution of molecules of the i-th fluorescent
average number of fluorescent particles,
component.
N, Fi (in the case if brightness correction is false) and Ni, qi (in the case if brightness correction is true) are
fit parameters, where i=1,2,..., n (n - number of fluorescent components).
Pure-Diffusion model
For Pure-Diffusion model [ 1, 2, 6, 7 ] kinetic term
following equation:
in general formula is defined by the
.
Pure-Diffusion model properties:
1. IG type
determines how the initial guesses of all model parameters are generated.
See list of IG type values for details.
2. ComponentsCount
defines number of fluorescent components.
3. Background correction
determines if background correction is taken into account. If this property is
true the Data Set associated with the model should contain the external
parameter BG ratio.
18
FFSDP User Manual
4. Brightness correction
determines if different quantum efficiency of each component is taken into
account. See brightness correction for more details.
5. Motion type
specifies the motion term
formula ).
in the model equation (see general
Pure-Diffusion model parameters:
1. Ginf is the level of autocorrelation function when
.
2. N is the average number of fluorescent molecules in the detection volume(exists only if brightness
correction is not performed).
3. Fit parameters of selected motion term
.
To find out more information about selecting the model and specifying related properties and parameters
see Experiment configuration dialog box, Properties table and Parameters table, respectively.
Triplet-State model
For Triplet-State model [ 8 ] kinetic term
equation:
in general formula is defined by the following
,
where Ftrip and Ttrip are, respectively, the fractional population and relaxation time of the triplet state.
Triplet-State model properties:
1. IG type
determines how the initial guesses of all model parameters are generated.
See list of IG type values for details.
2. ComponentsCount
defines number of fluorescent components.
3. Background correction
determines if background correction is taken into account. If this property is
true the Data Set associated with the model should contain the external
parameter BG ratio.
4. Brightness correction
determines if different quantum efficiency of each component is taken into
account. If this property is true the Data Set associated with the model
should contain the external parameters Component i brightness, where
i=1,2,..., n (n - number of fluorescent components). See brightness
correction for more details.
5. Motion type
specifies the motion term
formula ).
in the model equation (see general
Triplet-State model parameters:
1. Ginf is the level of autocorrelation function when
.
2. N is the average number of fluorescent molecules in the detection volume(exists only if brightness
correction is not performed).
19
FFSDP User Manual
3. Ftrip is the fractional population of the triplet state.
4. Ttrip is the relaxation time of the triplet state.
5. Fit parameters of selected motion term
.
To find out more information about selecting the model and specifying related properties and parameters
see Experiment configuration dialog box, Properties table and Parameters table, respectively.
Conformational model
For Conformational model [ 3, 4 ] kinetic term
equation:
in general formula is defined by the following
,
where A is the pre-exponential factor, β is the "stretch" parameter, τ conf is the characteristic time of
conformational relaxation.
Conformational model properties:
1. IG type
determines how the initial guesses of all model parameters are generated.
See list of IG type values for details.
2. ComponentsCount
defines number of fluorescent components.
3. Background correction
determines if background correction is taken into account. If this property is
true the Data Set associated with the model should contain the external
parameter BG ratio.
4. Brightness correction
determines if different quantum efficiency of each component is taken into
account. If this property is true the Data Set associated with the model
should contain the external parameters Component i brightness, where
i=1,2,..., n (n - number of fluorescent components). See brightness
correction for more details.
5. Motion type
specifies the motion term
formula ).
in the model equation (see general
Conformational model parameters:
1. Ginf is the level of autocorrelation function when
.
2. N is the average number of fluorescent molecules in the detection volume(exists only if brightness
correction is not performed).
3. A is the pre-exponential factor.
4. beta is the "stretch" parameter.
5. tau is the characteristic time of conformational relaxation.
6. Fit parameters of selected motion term
.
To find out more information about selecting the model and specifying related properties and parameters
see Experiment configuration dialog box, Properties table and Parameters table, respectively.
20
FFSDP User Manual
Protonation model
For Protonation model [ 5 ] kinetic term
equation:
in general formula is defined by the following
,
where P1 and P2 are the pre-exponential factors, 1 and 2 are the decay constants, associated,
respectively, with the external and internal protonation processes.
Protonation model properties:
1. IG type
determines how the initial guesses of all model parameters are generated.
See list of IG type values for details.
2. ComponentsCount
defines number of fluorescent components.
3. Background correction
determines if background correction is taken into account. If this property is
true the Data Set associated with the model should contain the external
parameter BG ratio.
4. Brightness correction
determines if different quantum efficiency of each component is taken into
account. If this property is true the Data Set associated with the model
should contain the external parameters Component i brightness, where
i=1,2,..., n (n - number of fluorescent components). See brightness
correction for more details.
5. Motion type
specifies the motion term
formula ).
in the model equation (see general
Protonation model parameters:
.
1. Ginf is the level of autocorrelation function when
2. N is the average number of fluorescent molecules in the detection volume(exists only if brightness
correction is not performed).
3. P1 is the pre-exponential factor, associated with the external protonation.
4. P2 is the pre-exponential factor, associated with the internal protonation.
5. tau1 is the decay constant, associated with the external protonation.
6. tau2 is the decay constant, associated with the internal protonation.
7. Fit parameters of selected motion term
.
To find out more information about selecting the model and specifying related properties and parameters
see Experiment configuration dialog box, Properties table and Parameters table, respectively.
FCS flow model
For FCS flow model [ 19 ] kinetic term
in general formula is defined by the following equation:
,
21
FFSDP User Manual
is the motion term in general formula, τ fl is the average flow time of the fluorescent
where
particles through the detection volume.
Flow model properties:
1. IG type
determines how the initial guesses of all model parameters are generated.
See list of IG type values for details.
2. ComponentsCount
defines number of fluorescent components.
3. Background correction
determines if background correction is taken into account. If this property is
true the Data Set associated with the model should contain the external
parameter BG ratio.
4. Motion type
specifies the motion term
formula ).
in the model equation (see general
Flow model parameters:
1. Ginf is the level of autocorrelation function when
.
2. N is the average number of fluorescent molecules in the detection volume.
3. Tfl is the average flow time of the fluorescent particles through the detection volume.
4. Fit parameters of selected motion term
.
To find out more information about selecting the model and specifying related properties and parameters
see Experiment configuration dialog box, Properties table and Parameters table, respectively.
Methods
Global fit
The parameters of the models attached to the characteristics can be estimated by a global fitting
procedure, based on the Marquardt-Levenberg non-linear method of least squares [ 9, 10 ]. In the global
analysis, several measured and/or simulated characteristics are combined and simultaneously fitted.
Certain parameters can be linked. The values of parameters linked together are kept equal to each other.
Each parameter can be fixed into the predefined value. For each parameter the range of admissible values
can be set by defining the constraints.
Sequential fit
The parameters of the models attached to the characteristics can be estimated by a sequential fitting
procedure, based on the Marquardt-Levenberg non-linear method of least squares [ 9, 10 ]. In the
sequential analysis, several measured and/or simulated characteristics are fitted one by one. Each
parameter can be fixed into the predefined value. For each parameter the range of admissible values can
be set by defining the constraints.
22
FFSDP User Manual
Initial guesses
For correlation functions the initial guesses for parameters are generated by the phase plane method. For
other characteristics method of moments is used.
To find out more about how to generate initial guesses for parameters while working with FFS Data
Processor see button Initial guesses of the Parameters page toolbar or command Initial guesses of the
Parameters settings table local menu.
Quality of fit
The quality of fit is judged by
and fitted curves.
criterion and visual inspection of the residuals between experimental
Exhaustive search
Error estimation of the recovered parameters can be performed by the exhaustive search method [ 12] (see
button CI Analysis of the Configuration toolbar ). In this method the examined parameter is fixed at a
number of particular values in a predetermined range, while other parameters are allowed to adjust to the
values on the particular parameter is observed. Analysis
minimum of . Thus, the dependence of the
becomes higher than the
level obtained from the statistical F-test
stops when the calculated value of
(for that particular confidential probability and number of degrees of freedom) [ 9 ]. The value of the
examined parameter obtained by the procedure described above is taken as the border of the confidential
interval.
To set confidential probability use property CI Probability of the Experiment Object.
Standard errors
Error estimation of the recovered parameters can be performed by calculating asymptotic standard errors [
14 ] (see button CI Analysis of the Configuration toolbar ).
Confidential interval for the parameter pj, j = 0, 1,… is calculated according to the following equation:
In this equation:
1. pj - the value of estimated parameter j;
2. Cjj - the jj element of the inverted Marquardt matrix obtained after the analysis;
3. α=1−β (β is confidential probability (0<β<1));
4. tα /2,v - the upper percentage point of the t - distribution (Student distribution) with v=n-p-1 degrees of
freedom (n is the number of experimental points and p is the number of estimated parameters). It can be
calculated from the definitions of percentage point of Student distribution and its distribution function.
5.
- the value of
obtained after the analysis.
To set confidential probability use property CI Probability of the Experiment Object.
23
FFSDP User Manual
Simulator
Simulation tools are aimed to investigate the performance of the fitting procedures with respect to the
particular type of characteristic. Simulation consists of the numeric generation of the corresponding
characteristic distorted by statistical noise (see Simulator box of the Experiment configuration dialog box).
The characteristics of statistical noise are strongly dependent on the experimental methods and apparatus
tools. In the case of FCS measurements, for example, expressions, describing statistics of the obtained
correlation function, are known only for a limited number of particular cases. That is why we assume that
value in each sampling interval or channel is the random value with Gaussian probability function with
mean value equal to the true value of correlation function and empirically derived standard deviation:
, (7)
where α, γ and β are the adjusted parameters (parameters of simulator).
To find out more about how to chose the noise and how to input corresponding parameters in the interface
see Experiment configuration box and Parameters table, respectively.
Using custom model
Script programming language
The following topics provide a formal definition of Script programming language, which is used for
creating custom model scripts:
Lexical elements
• Whitespace
• Tokens
Variables
Expressions
Built in functions
Whitespace
Whitespace is the collective name given to spaces (blanks), horizontal and vertical tabs and newline
characters. Whitespace can serve to indicate where tokens start and end.
For example, the following two sequences are lexically equivalent:
var: a, x, y;
a = x+y;
and
var:
a, x, y;
a =
x+y;
Tokens
Tokens are word-like units recognized by a language. Script programming language recognizes five
classes of tokens.
24
FFSDP User Manual
Here is the formal definition of a token:
• keyword
• identifier
• operator
• built in function
• punctuator (also known as separator)
As the source code is scanned, tokens are extracted in such a way that the longest possible token from the
character sequence is selected. For example, external would be parsed as a single identifier, rather than as
the keyword extern followed by the identifier al.
Keywords
Keywords are words reserved for special purposes and must not be used as normal identifier names.
Keyword var: is used to declare new variables .
Example:
var: x, y, z;
In this example three variables (x, y, and z) are declared.
Variable identifiers
Identifiers are arbitrary names of any length given to variables.
Naming and length restrictions
Identifiers can contain the letters a to z and A to Z, and the digits 0 to 9. There is only one restriction:
The first character must be a letter.
Case sensitivity
Script programming language identifiers are case sensitive, so that Sum, sum and suM are distinct
identifiers.
Uniqueness
Although identifier names are arbitrary (within the rules stated), errors are generated if the same name is
used for more than one identifier within the script.
Variables
Variable is a named storage location that can contain data that can be modified during script execution.
Each variable has a name that uniquely identifies it within script. The variable names are sometimes
referred to as identifiers .Variables can be of three types:
external variables - fit parameters, time and external parameters.
internal variables - can be defined by user in the script.
result variable - contains script execution result.
Internal variables declaration
Internal variables declaration is a list of variable identifiers . The declaration begins with keyword var:.
The identifiers are separated by commas and the list is terminated by a semicolon.
Example:
var: var1, var2, var3, ...;
where var1, var2, var3, ... are any sequence of distinct identifiers .
Operators
Operators are tokens that trigger some computation when applied to variables and other objects in an
expression.
25
FFSDP User Manual
The following operators are available in the Script programming language:
* Operator
/ Operator
+ Operator
- Operator
= Operator
= Operator
This operator assigns the value of an expression to an internal variable.
Syntax
varname = expression
The = operator syntax has following parts:
Part
Description
varname
expression
Required; any internal variable.
Required; any numeric expression .
Example:
var: Var, Var1, Var2;
Var1 = 5;
Var2 = Var1+10;
Var = Var1 + Var2;
+ Operator
This operator is used to sum two numbers.
Syntax
result = expression1+expression2
The + operator syntax has following parts:
Part
Description
result
expression1
expression2
Required; any internal variable .
Required; any numeric expression .
Required; any numeric expression.
Example:
var: MyNumber, Var1, Var2;
MyNumber = 2 + 2;
' Returns 4.
MyNumber = 4257.04 + 98112; ' Returns 102369.04.
Var1 = 34; Var2 = 6;
MyNumber = Var1 + Var2;
' Initialize variables.
' Returns 40.
- Operator
This operator is used to find the difference between two numbers or to indicate the negative value of a
numeric expression .
Syntax 1
result = expression1-expression2
Syntax 2
-expression
26
FFSDP User Manual
The - operator syntax has following parts:
Part
Description
result
expression1
expression2
expression
Required; any internal variable .
Required; any numeric expression .
Required; any numeric expression.
Required; any numeric expression.
Remarks
In Syntax 1, the - operator is the arithmetic subtraction operator used to find the difference between two
numbers.
In Syntax 2, the - operator is used as the unary negation operator to indicate the negative value of an
expression.
Example:
var: MyResult, MyVar;
MyResult = 4 - 2;
' Returns 2.
MyResult = 459.35 - 334.90; ' Returns 124.45.
MyVar = 2;
MyResult = -MyVar;
' Returns -2;
* Operator
This operator is used to multiply two numbers.
Syntax
result = expression1*expression2
The * operator syntax has following parts:
Part
Description
result
expression1
expression2
Required; any internal variable .
Required; any numeric expression .
Required; any numeric expression.
Example:
var: MyValue;
MyValue = 2 * 2;
' Returns 4.
MyValue = 459.35 * 334.90; ' Returns 153836.315.
/ Operator
This operator is used to divide two numbers.
Syntax
result = expression1/expression2
The / operator syntax has following parts:
Part
Description
result
expression1
expression2
Required; any internal variable .
Required; any numeric expression .
Required; any numeric expression.
Note
27
FFSDP User Manual
expression2 must be nonzero expression2 = 0 results in an runtime error. (You can't divide by zero.)
Example:
var: MyValue;
MyValue = 10 / 4;
MyValue = 10 / 3;
' Returns 2.5.
' Returns 3.333333.
Built in functions
Built in functions are used to perform mathematical calculations.
The following functions are available in the Script programming language:
abs
acos asin atan cos
erf
erfc exp
fact Gamma
log
log10 logGamma
pow
sin
sqrt tan
abs
Syntax
abs(x);
Description
Returns the absolute value of a number.
Return Value
abs returns the absolute value of x.
acos
Syntax
acos(x);
Description
Calculates the arc cosine.
Arguments to acos must be in the range -1 to 1. Otherwise a runtime error will occur.
Return Value
acos of an argument between -1 and +1 returns a value in the range 0 to pi.
asin
Syntax
asin(x);
Description
Calculates the arc sine.
Arguments to asin must be in the range -1 to 1. Otherwise a runtime error will occur.
Return Value
asin of an argument between -1 and +1 returns a value in the range -pi/2 to pi/2.
atan
Syntax
atan(x);
Description
Calculates the arc tangent.
Return Value
atan of x returns a value in the range -pi/2 to pi/2.
28
FFSDP User Manual
cos
Syntax
cos(x);
Description
Calculates the cosine of a number.
The angle is specified in radians.
Return Value
cos returns a value in the range -1 to 1.
exp
Syntax
exp(x);
Description
Calculates the exponential e to the x.
Return Value
exp returns e to the x.
The constant e is approximately 2.718282.
If the value of x exceeds 709.782712893, a runtime error occurs.
Note
The exp function complements the action of the log function and is sometimes referred to as the
antilogarithm.
log
Syntax
log(x);
Description
Calculates the natural logarithm of x.
If the argument x passed to this function is 0 or less than 0, runtime error occurs.
Return Value
On success, log returns the value calculated ln(x).
log10
Syntax
log10(x);
Description
Calculates the base ten logarithm of x.
If the argument x passed to this function is 0 or less than 0, runtime error occurs.
Return Value
On success, log10 returns the calculated value log base ten of x.
pow
Syntax
pow(x, y);
Description
Calculates x to the power of y.
, the overflow runtime error will occur. If the
If the result of this function is more than
argument x passed to pow is real and less than 0, and y is not a whole number, or you call pow(0,0),
29
FFSDP User Manual
runtime error will occur.
Return Value
On success, pow returns the value calculated of x to the power of y.
sin
Syntax
sin(x);
Description
Calculates the sine of a value.
The angle is specified in radians.
Return Value
sin returns a value in the range -1 to 1.
sqrt
Syntax
sqrt(x);
Description
Calculates the positive square root.
If x is positive, the result is positive. If x is negative, runtime error will occur.
Return Value
On success, sqrt returns the square root of x.
tan
Syntax
tan(x);
Description
Calculates the tangent.
Angles are specified in radians.
Return Value
tan returns the tangent of x, sin(x) / cos(x) .
fact
Syntax
fact(x);
Description
Calculates the factorial of x rounded to the nearest lesser integer.
If x is negative, runtime error will occur.
If the result of this function is more than
, the overflow runtime error will occur.
Return Value
On success, fact returns the factorial of x.
erf
Syntax
erf(x);
Description
Calculates the error function of x, e.i.
30
FFSDP User Manual
.
Return Value
erf returns the error function of x.
erfc
Syntax
erfc(x);
Description
Calculates the complementary error function of x, e.i.
.
Return Value
erfc returns the complementary error function of x.
Gamma
Syntax
Gamma(x);
Description
Calculates the gamma function of x, e.i.
.
Return Value
Gamma returns the gamma function of x.
logGamma
Syntax
logGamma(x);
Description
Calculates the natural logarithm of the gamma function of x.
Return Value
logGamma returns the natural logarithm of the gamma function of x.
Punctuators
The Script programming language punctuators (also known as separators) are:
()
,
;
Parentheses
There are two cases when open and close parentheses ( ) are used:
to indicate function calls and function parameters:
Example:
func();
/* function call, no arguments */
to group expressions and change operator precedence:
31
FFSDP User Manual
Example:
d = c * (a + b);
/* override normal precedence */
Comma
The comma (,) punctuator is used for:
separation of the elements of a function argument list:
Example:
func(i, j); /* call function with two arguments */
separation of the different variables while making variable declaration:
Example:
var: x, y, z;
Semicolon
The semicolon (;) is a statement terminator. Any legal Script programming language expression is
followed by a semicolon.
Numeric expression
Any expression that can be evaluated as a number. Elements of an expression can include any
combination of variables , built in functions and operators that result in a number.
Expression
An expression is a sequence of operators , operands, and punctuators that specifies a computation.
Syntax
variable part = numeric expression ;
Where variable part is any defined internal variable .
Note
The script must contain at least one expression with result variable as variable part.
Parameters
Parameters are the values that can be estimated during the analysis.
Custom model configuration dialog box
This dialog box provides all operations related to managing the custom model.
An example view of the Custom model configuration dialog box is given below:
32
FFSDP User Manual
Notes
To choose the necessary page while working with Custom model configuration dialog box you should
click on the corresponding Tab.
Bellow the brief description of main components of Custom model configuration dialog box is given:
button
Makes a copy of the current record.
button
Deletes the current record.
button
Inserts new empty record.
button
Saves the current record.
button
Cancels changes.
Models list
Contains the list of custom models available from the custom models database.
33
FFSDP User Manual
Filter button
Opens Filter dialog box that allows creating the filter that can be applied to the custom models table. If
this filter is applied, the only table records that correspond to the filter criteria will be displayed.
Search button
Displays a search box for the subtype field of the custom models database. If you want to find quickly the
necessary record you should type the first few characters and press Enter. In this case the application will
automatically select for you the first record that contains these characters at the beginning. To close the
search box press key Esc.
OK button
Finishes work with the Custom model configuration dialog box and changes the configuration of the
current model according to the dialog box settings.
Close button
Finishes work with the Custom model configuration dialog box without changing the configuration of
the current custom model.
Help button
Opens the help window that describes how to work with Custom model configuration dialog box.
Test button
Tests the script of the current model for errors.
Add model by Wizard button
Opens the New model wizard for simple adding new custom model.
Initial settings table
Displays the initial settings of the parameters related to the current custom model.
Icon column contains the parameter icon.
Name column contains the name of the parameter. It can be changed.
Value column contains the value that will be used as initial guess for current parameter. It can
be varied between the minimum value contained in the field Minimum and the maximum
value contained in the field Maximum.
Minimum column contains the minimum possible value of the parameter.
Maximum column contains the maximum possible value of the parameter.
Fixed column indicates whether curent parameter is initially fixed when new custom model of
current type is created. If Fixed is true then the value of the current parameter will be constant
during the analysis, otherwise the parameter will participate in the fit. The final state of the
parameter (fixed or not) is defined in the Parameters settings table.
Notes
The parameters order can be changed by dragging icon of corresponding parameter to new place within
34
FFSDP User Manual
the table.
Add button
Adds a new parameter to the given model.
Delete button
Deletes the parameter currently selected in the Initial settings table.
Formula page
This dialog box provides all operations related to managing the custom model.
An example view of the opened Formula page is given below:
Input variables list
Displays model parameters that can be used as variables in the model script. The name of any parameter
viewed in Input variables list can be double clicked with left mouse button to be added to the current
cursor position in Model script rich editor.
External parameters list
Displays the time and external parameters that can be used as variables in the model script. The name of
any parameter viewed in External parameters list can be double clicked with left mouse button to be
added to the current cursor position in Model script rich editor.
Functions combobox
Contains list of all built in functions .
35
FFSDP User Manual
button
Inserts function currently selected in the functions combobox to the current cursor position in Model
script rich editor.
button
Shows help about function currently selected in the functions combobox.
Model script rich editor
Allows to edit model script. The script is written with Script programming language .
Description page
The Description page contains the description of the selected model.
An example view of the opened Description page is given below:
New model wizard
This wizard provides simple adding new custom model. For more information see Custom model
configuration dialog box topic.
An example view of the New model wizard is given below:
36
FFSDP User Manual
Step 1
Step 2
37
FFSDP User Manual
Step 3
Step 4
Custom model integrity restore dialog box
Custom model integrity restore dialog box is used to restore the custom model integrity. Custom model
integrity means that custom model contents with given subtype must exactly correspond to the custom
model contents with same subtype stored in the Custom model database.
An example view of the Custom model integrity restore dialog box is given below:
38
FFSDP User Manual
Any time when the custom model integrity is broken it can be restored by one of the following ways:
1. By using custom model with same contents but different subtype. This option is available in the case if
Custom model database contains records with same contents as in current custom model but with
different subtype names.
2. By saving current custom model contents to Custom model database with new subtype.
3. By overwriting custom model contents with same subtype currently stored in the Custom model
database.
One of the ways mentioned above can be chosen by selecting the corresponding radio button.
Button "Ok" finishes work with the Custom model integrity restore dialog box and restores the
experiment integrity.
Button "Help" opens the help that describes how to work with Custom model integrity restore dialog
box.
Using FFS Data Processor
Starting FFS Data Processor
Fluorescence Fluctuation Spectroscopy Data Processor (FFS Data Processor) can be started via
Start button on the Windows Task Bar:
Go to the Programs/FFS Data Processor/ and click the FFS Data Processor item;
Choose Run and specify the path to FFSDP.EXE;
Windows Explorer:
Locate and double-click the FFSDP.EXE file (if you have performed a default installation, this file
is located in \Program Files\SSTC\FFS Data Processor\Bin).
Take a look on a successfully loaded FFS Data Processor
39
FFSDP User Manual
Main window
The view of the FFS Data Processor Main Window without any experiments being opened is given on
the following figure:
Main Window contains Main menu and Main toolbar.
40
FFSDP User Manual
Main menu
Main menu consists of the following popup items:
Items
Description
File
View
Tools
Window
Help
Contains menu commands for managing the experiments.
Contains menu commands for opening some application windows.
Contains menu commands for configuring active experiment and opening Databases.
Contains menu commands for managing the view of opened experiment windows and
provides the ability to switch between them.
Contains menu commands for accessing the online Help system and information about the
copyright.
File menu
Use commands of the File menu for managing the experiments.
The File menu contains the following commands:
Commands Description
New
Open
Close
Save
Save As
Exit
Creates a new experiment.
Opens an Open an existing experiment dialog box for opening or finding an experiment.
Closes the active experiment without exiting the application.
Saves the active experiment. In the case if active experiment is saved for a first time, Save
experiment as dialog box is opened.
Opens Save experiment as dialog box for saving the active experiment with a different
name.
Finishes work with FFS Data Processor.
View menu
Use commands of the View menu for managing the experiments.
The View menu contains the following commands:
Commands
Description
CVH separation
Shows a Separation of coincidence values histograms window.
Tools menu
The Tools menu contains the following commands:
Commands
Description
Experimental configuration
Measurements Database
Analysis Database
Opens the Configuration dialog box for configuring the currently active
experiment.
Opens the Measurements Database.
Opens the Analysis Database.
Window menu
Use commands of this menu for managing the view of opened experiment windows and switching
between them.
The Window menu contains the following commands:
Commands
Description
Cascade
Tile
Resizes and positions all windows in an overlapping pattern.
Resizes and positions all windows in a non-overlapping pattern.
41
FFSDP User Manual
Arrange Icons
Minimize All
Window List
(all items below
the separator)
Arranges icons of all minimized experiment windows.
Minimizes all opened experiment windows.
Displays the list of currently opened experiments. One can switch to required
experiment by
clicking it's name.
Help menu
Use commands of the Help menu to access the help system and get information about the copyright.
The Help menu contains the following commands:
Commands
Description
Opens Help topic contents.
Displays the copyright and version number for FFS Data Processor.
Contents
About
Main toolbar
The Main toolbar provides shortcuts for menu commands.
The correspondence between buttons and menu commands is the following:
Button
Menu commands
File|New
File|Open
File|Save
Tools|Measurements DataBase
Tools|Experiments DataBase
View|CVH separation
Window|Cascade
Window|Tile
The Main toolbar has short Help Hints. Help Hint is the pop-up text that appears when the mouse pointer
passes over a toolbar button.
Experiment window
Components of this window are used for creating and configuring an experiment , executing the analysis
procedure and displaying the results.
Experiment window has two parts: Configuration part (left) and Analysis part (right).
An example view of the Experiment window is given on the following figure:
42
FFSDP User Manual
The Analysis part of the Experiment window consists of three pages:
Parameters page is used for working with parameters.
3D Graphics page is used for displaying correlation functions and weighted residuals in threedimensional space.
2D Graphics page is used for displaying correlation functions and weighted residuals in twodimensional space.
Note
To choose the necessary page while working with FFS Data Processor you should click on the
corresponding Tab.
Configuration part of the Experiment window
This part of the Experiment window provides the quick access to the properties and parameters of the
objects included in the current experiment and is responsible for displaying the information about the
analysis progress.
An example view of the Experiment window Configuration part is given below:
43
FFSDP User Manual
Configuration toolbar
Configuration toolbar contains buttons for experiment configuration, analysis execution and exporting
the data.
Button "Export data"
This button opens Export data dialog box that allows exporting the data from any Data Set within the
current experiment to the text file.
Button "Apply Template"
This button opens the Load and apply an existing template dialog box for applying the previously saved
template to the current experiment.
Button "Save Template"
This button opens the Create and save new template dialog box for creating a new template and saving it
to the Analysis Database.
Button "Simulate"
This button executes the simulation procedures to prepare the source data in the Simulation Data Sets.
44
FFSDP User Manual
Button "Execute"
This button executes the fit.
Button "Stop"
This button interrupts the fit.
Button "Chi-square"
This button calculates Chi-square for the current values of fit parameters. Also theoretical curves and
residuals curves will be built and displayed in the corresponding graphical windows.
Button "View Properties"
If this button is down properties and parameters tables are shown, otherwise they are hidden.
Button "CI Analysis"
If this button is down confidential intervals for the estimated parameters will be calculated after execution
of the fit.
Button "Configuration"
This button opens the Configuration dialog box for configuring the current experiment.
Configuration treeview
Configuration treeview displays the structure of the experiment and provides the access to any object
included in it.
An example view of the Configuration treeview is given below:
The objects that can be displayed in this treewiev are divided into the following classes:
Experiment
Data Set
Data Source
Model
45
FFSDP User Manual
Noise
The names of Experiment and Data Sets or additional information about Data Sources, Models and
Noises are displayed on the right of the corresponding object icon. A red dot on the left of any object
means that this object is modified. If the object is not modified the green tick is displayed on the left of
the given object. If the current object contains some child objects then it has one of the special indicators
or . Press this indicator to show or hide the child objects.
Properties and parameters of the object, selected in the Configuration treeview, are displayed in the
Properties and Parameters tables, correspondingly.
Local menu of the Configuration treeview
This local menu contains following items:
1. Rename
2. Export Data
3. Apply Template
4. Save Template
5. Simulate
6. Execute
7. Stop
8. Calculate Chi-square
9. Show Properties
10. CI Analysis
11. Configuration
Local menu command: Rename
This menu command allows to change the name of the Experiment or Simulation Data Sets. The Rename
menu command appears only if the Experiment or Simulation Data Set object is selected in the
Experiment configuration treeview. After you have chosen this menu command the inplace editor will be
displayed instead of the selected treeview node.
Local menu command: Export Data
This menu command opens Export data dialog box that allows exporting the data from any Data Set
within the current experiment to the text file.
Local menu command: Apply Template
This menu command opens the Load and apply an existing template dialog box for applying the
previously saved template to the current experiment.
Local menu command: Save Template
This menu command opens the Create and save new template dialog box for creating a new template and
saving it to the Analysis Database.
Local menu command: Simulate
This menu command executes the simulation procedure to prepare the source data in the Simulation Data
Sets.
Local menu command: Execute
This menu command executes the fit.
46
FFSDP User Manual
Local menu command: Stop
This menu command interrupts the fit.
Local menu command: Calculate Chi-square
This menu command calculates Chi-square for the current values of fit parameters. Also theoretical curves
and residuals curves will be built and displayed in the corresponding graphical windows.
Local menu command: Show properties
If this menu item is checked properties and parameters tables are shown, otherwise they are hidden.
Local menu command: CI Analysis
If this menu item is checked confidential intervals for the estimated parameters will be calculated after
execution of the fit.
Local menu command: Configuration
This menu command opens the Configuration dialog box for configuring the current experiment.
Parameters table
This table is used to display the names and the values of the parameters related the object currently
selected in the Configuration treewiev.
An example view of the Parameters table is given below:
Note
To choose the Properties table you should click on the properties tab.
Properties table
This table is used to display the names and the values of the properties related the object currently selected
in the Configuration treewiev.
An example view of the Properties table is given below:
47
FFSDP User Manual
Note
To choose the Parameters table you should click on the parameters tab.
Local menu of the Properties table
This local menu contains following items:
1. Apply to all similar objects
Local menu command: Apply to all similar objects
This menu command allows to set the value of the currently selected property to the same properties of all
similar objects within the current experiment.
Analysis information window
This window monitors the information about the analysis progress.
An example view of the Analysis Information window is given below:
The new information in this window appears in the following cases:
after Chi-square was calculated;
while the fit is running;
while the analysis of the confidential intervals is running.
Parameters page
This page is used to manage the settings of the fit parameters and parameters linkage.
An example view of the Parameters page is given below:
48
FFSDP User Manual
The following components are related to the Parameters page:
Parameters toolbar
Linked parameters treeview
Free parameters list
Parameters settings table
Click the corresponding item to get more information about it.
Toolbar of the parameters page
Toolbar contains buttons for exporting the parameters settings, managing the parameters and parameter
groups within the Linked parameters treeview and setting the initial guesses of the parameters.
The Parameters toolbar has short Help Hints. Help Hint is the pop-up text that appears when the mouse
pointer passes over a toolbar button.
Button "Export parameters"
This button executes the export procedure that exports all values from Parameters setting table to the
standard MS Excel file. After pressing this button Save dialog box will be opened in which the path and
the name of the target MS Excel file can be specified.
Button "New Group"
This button creates new parameter group within the current experiment.
49
FFSDP User Manual
Button "Delete selected parameter group"
This button deletes parameter group selected in the Linked parameters treeview. All parameters of this
group will be moved in the Free parameters list. This action is equivalent to the unlinkage of all
parameters of this group.
Button "Link mode"
This button sets the Link mode for the drag-drop operation within the Linked parameters treeview.
This mode is used to relink the parameters related to the current experiment. If you drag any parameter
from one parameter group to another then this parameter will be moved from the source group to the
target group. If you drag any parameter group to another parameter group then all parameters from this
group will be moved to the target group and the dragged group will be deleted.
Button "Order mode"
This Button sets the Order mode for the drag-drop operation within the Linked parameters treeview.
This mode is used to order the parameters related to the current experiment. If you want to change the
position of any parameter within the given parameter group or the position of any parameter group within
the current experiment, you should drag this parameter or parameter group and drop on the necessary
position.
Button "Initial guesses"
This button sets initial guesses to all parameters and parameter groups within the current experiment.
Initial guess for every parameter depends on the value of the IG type property of model that contains this
parameter.
Linked parameters treeview
Linked parameters treeview is used for linking parameters and displaying the linked parameter groups. To
find out more about how to link and unlink parameters see Linking parameters and Unlinking parameters
operations.
An example view of the Linked parameters treeview is given below:
Parameter groups are marked with the following icon:
Parameters are marked with the following icon:
The names of the parameter groups and parameters are displayed on the right of the corresponding icons.
If the current parameter group contains some parameters then it has one of the special indicators or .
Press this indicator to show or hide the parameters related to the current parameter group.
50
FFSDP User Manual
Local menu of the Linked parameters treeview
This local menu contains following items:
1. Rename
2. Empty
3. Delete
4. Expanded
5. Free
6. Link To
7. Find Model
8. View on graph
9. Position
10. New Group
Local menu command: Rename
This menu command allows to rename parameter group selected in Linked parameters treeview. After you
have chosen this menu command the inplace editor will be displayed instead of the selected treeview
node.
Local menu command: Empty
This menu command empties the parameter group currently selected in the Linked parameters treeview
and moves all its parameters to the Free parameters list. Execution of this command is equivalent to the
unlinking the parameters contained in this group.
Local menu command: Delete
This menu command deletes the parameter group currently selected in the Linked parameters treeview and
moves all its parameters in the Free parameters list. Execution of this command is equivalent to the
unlinking the parameters contained in this group and deleting the current parameter group.
Local menu command: Expanded
If this menu item is checked the parameters related to the current parameter group are visible.
Local menu command: Free (for parameters only)
This menu command unlinks the selected parameter in the Linked parameters treeview e.g moves it to the
Free parameters list.
Local submenu: Link To
This submenu contains local menu commands that provide the ability to relink the selected parameter or
parameter group to any other parameter group. The name of the submenu command is equivalent to the
name of the target parameter group.
Local menu command: Find Model
This menu command finds and selects the model in the Configuration treeview which contains the
parameter currently selected in the Linked parameters treeview.
51
FFSDP User Manual
Local menu command: View on graph
This menu command opens "Fit parameter vs. data set number view" window.
Submenu command: Position
This submenu contains local menu commands that are used for changing the position of the selected
parameter within the given parameter group or the position of any parameter group within the current
experiment. This submenu contains the following commands:
Move Up - moves the selected parameter or parameter group one position up.
Move Down - moves the selected parameter or parameter group one position down.
Place First - places the selected parameter or parameter group to the first position in the list.
Place Last - places the selected parameter or parameter group to the last position in the list.
Local menu command: New Group
This menu command creates new parameter group within the current experiment.
Free parameters list
Free parameters list displays all free (unlinked) parameters within the experiment.
An example view of the Free parameters list is given below:
The parameters that are displayed in this list are sorted by name. To change the sorting direction of the
parameters contained in the Free parameters list click on the list header. A small triangle located on the
right of the header name shows the sort direction.
The free parameters that are going to be linked will be moved from this list to the Linked parameters
treeview. The linked parameters that are going to be unlinked will be moved from the Linked parameters
treeview to Free parameters list.
To find out more about how to link and unlink parameters see Linking parameters and Unlinking
parameters operations.
Local menu of the Free parameters list
This local menu contains following items:
1. Link all [parameter name]'s
2. Link To
3. Find Model
4. View on graph
52
FFSDP User Manual
Local menu command: Link All
This menu command creates new parameter group with name "[parameter name]'s Group" and moves all
parameters with the name [parameter name] to this newly created parameter group.
Note
[parameter name] - is the name of the first parameter in the selection.
Local submenu: Link To
This submenu contains local menu commands that provide the ability to link the selected parameter(s) to
any existing parameter group. The name of the submenu command is equivalent to the name of the target
parameter group.
Local menu command: Find Model
This menu command finds and selects model in the Configuration treeview which contains the parameter
currently selected in the Free parameters list. This local menu command is visible if only one parameter is
selected in the Free parameters list.
Local menu command: View on graph
This menu command opens "Fit parameter vs. data set number view" window.
Parameters settings table
This table displays the settings of the parameters and parameter groups related to the current experiment.
An example view of the Parameters settings table is given bellow:
Parameters settings table contains the following fields:
Field Name
Description
Name
Value
Minimum
Maximum
Fixed
Contains the name of the parameter or parameter group. It can be changed only for
parameter groups.
Contains the value of the parameter or parameter group. It can vary from the minimum
value contained in the field Minimum to the maximum value contained in the field
Maximum.
Contains the minimum possible value of the parameter or parameter group.
Contains the maximum possible value of the parameter or parameter group.
Indicates whether the value of the current parameter or parameter group should be
optimized during the analysis. If Fixed is true then the value of the current parameter
53
FFSDP User Manual
will be constant during the analysis, otherwise the parameter will participate in the fit.
CI Left,
CI Right
CI Analysis
Owner
Contain left and right bounds of Confidential Interval, which was obtained for the
current parameter or parameter group if Confidential Interval analysis was performed
for it. These fields are read only.
Indicates whether the Confidential Interval should be calculated for the current
parameter or parameter group. If button CI Analysis on the Configuration toolbar is
down and CI Analysis value is true then the Confidential Interval will be calculated for
the current parameter or parameter group while Confidential Interval Analysis is
executed.
Contains the Name of the model, which generated the current parameter (for parameters
only). It is read only.
Notes
Fields CI Left, CI Right, CI Analysis are visible only if button CI Analysis is down on the
Configuration toolbar.
The parameters that are displayed in this table can be sorted by any field. To perform the sorting by the
given field, click the header of the appropriate column. To change the sorting direction of the parameters
click a second time on the same header. A small triangle located on the right of the header name shows
the sort direction.
Local menu of Parameters settings table
This local menu contains following items:
1. Rename
2. Empty
3. Delete
4. Link all parameter name's
5. Link To
6. Find Model
7. View on graph
8. Initial guesses
9. Export Parameters
10. Optimize View
Local menu command: Rename
Allows to rename the parameter group currently selected in the Parameters settings table.
Local menu command: Empty
This menu command empties the parameter group currently selected in the Parameters settings table and
moves all its parameters to the Free parameters list. Execution of this command is equivalent to the
unlinking the parameters contained in this group.
Local menu command: Delete
This menu command deletes the parameter group currently selected in the Parameters settings table and
moves all its parameters in the Free parameters list. Execution of this command is equivalent to the
unlinking the parameters contained in this group and deleting the current parameter group.
54
FFSDP User Manual
Local menu command: Link All
This menu command creates new parameter group with name "[parameter name]'s Group" and moves all
parameters with the name [parameter name] to this newly created parameter group.
Note
[parameter name] - is the name of the currently selected parameter.
Local submenu: Link To
This submenu contains local menu commands that provide the ability to link the selected parameter to any
existing parameter group. The name of the submenu command is equivalent to the name of the target
parameter group.
Local menu command: Find Model
This menu command finds and selects model in the Configuration treeview which contains the parameter
currently selected in the Parameters settings table.
Local menu command: View on graph
This menu command opens "Fit parameter vs. data set number view" window.
Local menu command: Initial guesses
This menu command sets initial guesses to all parameters and groups within the current experiment.
Initial guess for every parameter depends on the value of the property Auto Init of model that contains this
parameter.
Initial guess for every parameter depends on the value of the IG type property of model that contains this
parameter.
Local menu command: Export parameters
This menu command executes the export procedure that exports all values from Parameters settings table
to the standard MS Excel file. After pressing this button Save dialog box will be opened in which the path
and the name of the target MS Excel file can be specified.
Local menu command: Optimize View
This menu command automatically sets most suitable width of Parameters setting table columns.
Unlinking parameters
To unlink any parameter and make it free you can follow one of the ways listed bellow:
1. Select the parameter you want to unlink in Linked parameters treeview, drag it and drop on the Free
parameters list.
2. Select the parameter you want to unlink in Linked parameters treeview, press right mouse button to
display the Linked parameters treeview local menu and select the Free local menu command.
To unlink all parameters related to the given parameter group:
Select the current group in the Linked parameters treeview or Parameters settings table.
Press right mouse button on the selection to display the local menu and select the Empty local menu
command.
If you want to delete the given parameter group while freeing all it's parameters, then you should use the
55
FFSDP User Manual
Delete local menu command instead of Empty local menu command. The same operation for the
parameter group currently selected in the Linked parameters treeview can be done using Delete selected
parameter group button of the Parameters toolbar.
Linking parameters
In this application the special object parameter group is used for linking parameters. The parameters that
belong to one parameter group are considered as linked to each other.
To link two or more parameters together you should perform the following steps:
1. Create the new parameter group. There are some ways to create parameter group:
Press the button Create new parameter group on the Toolbar of the Parameters page ;
Right click on the Linked parameters treeview to open it's local menu. Choose New group menu
command from this local menu.
2. Select the parameters you want to link in Free parameters list, drag them and drop on the newly created
group.
If you have previously created parameter groups you can add any free parameter(s) to any of these groups.
Also, you can use local menu commands Link To, Link all [parameter name]'s of Free parameters list or
Parameters settings table as an alternative way for linking parameters.
2D Graphics page
This page is used to display characteristics and weighted residuals in two-dimensional space.
The following components are related to the 2D Graphics pages:
Toolbar
2D Characteristics and Residuals boxes
An example view of the 2D Graphics page is given below:
56
FFSDP User Manual
Toolbar of the 2D Graphics page
This toolbar contains buttons for changing view of 2D Graphics page.
This toolbar has short Help Hints. Help Hint is the pop-up text that appears when the mouse pointer passes
over a toolbar button.
Button "AutoSize"
If this button is down, the size of the graphical boxes that belong to the 2D Graphics page is automatically
changed while the Experiment window resizes.
If this button is up, the vertical size of the Characteristics box and Residuals box can be changed manually
using the splitting line that lies between them.
Button "Show Characteristics"
If this button is down Characteristics box is visible.
57
FFSDP User Manual
Button "Show Residuals"
If this button is down Residuals box is visible.
2D Characteristics and Residuals charts
2D Characteristics chart displays measured (green) and theoretical (red) characteristics in twodimensional space. 2D Residuals chart displays weighted residuals in two-dimensional space.
2D charts display curves according to the selection in the Configuration treeview. If the Experiment
object is selected in the Configuration treeview then the curves related to all Data Sets within the current
Experiment are displayed in 2D charts. If any Data Set or child objects (Data Source, Model, Noise) are
selected then the only curves that belong to this Data Set are displayed in 2D charts.
On these 2D charts the values of the characteristic (in the 2D Characteristics chart) and residuals (in the
2D Residuals chart) are displayed along the vertical axes and arguments are displayed along the
horizontal axes.
In the case if all curves are displayed in 2D chart particular curve can be selected by double click on it.
On these 2D charts the values of the characteristic (in the 2D Characteristics chart) and residuals (in the
2D Residuals chart) are displayed along the vertical axes and arguments are displayed along the
horizontal axes.
An example view of the 2D charts is given below:
For 2D chart you can:
move curves in the box by keeping the right mouse button down and moving the mouse pointer through
the chart.
zoom in the image by dragging the cursor diagonally across the necessary area from left top corner to
right bottom corner.
restore whole view of the image by pressing left mouse button and dragging mouse pointer on some
58
FFSDP User Manual
positions to upper left.
Additional actions with 2D Chart available through the local menu.
Local menu of 2D chart
This local menu contains following items:
1. Default view
2. Save graph
3. Copy graph to Clipboard
4. Export data
5. Graph configuration
6. Save settings as default
7. Load default settings
8. Reset default settings
Local menu command: Default view
Resets a view of the current 2D Chart to the initial state.
Local menu command: Save graph
This menu command saves the current 2D Chart image to BMP file.
Local menu command: Copy graph to Clipboard
This menu command stores the current 2D Chart image to Clipboard.
Local menu command: Export data
Exports data for the dependences currently displayed in the 2D Chart.
Local menu command: Graph configuration
This menu command opens the 2D chart configuration dialog box for configuring the current 2D Chart.
Local menu command: Save settings as default
Saves current settings of the current 2D Chart as the default settings.
Local menu command: Load default settings
Loads and Applies the default settings to the current 2D Chart.
Local menu command: Reset default settings
Resets and Applies the default settings to the current 2D Chart.
3D Graphics page
This page is used to display characteristics and weighted residuals in three-dimensional space.
The following components are related to the 3D Graphics pages:
• Toolbar
• 3D Characteristics and Residuals boxes
An example view of the 3D Graphics page is given below:
59
FFSDP User Manual
Toolbar of the 3D Graphics page
This toolbar contains buttons for changing view of 3D Graphics page.
This toolbar has short Help Hints. Help Hint is the pop-up text that appears when the mouse pointer passes
over a toolbar button.
Button "AutoSize"
If this button is down, the size of the graphical boxes that belong to the 3D Graphics page is automatically
changed while the Experiment window resizes.
If this button is up, the vertical size of the Characteristics box and Residuals box can be changed manually
using the splitting line that lies between them.
Button "Show Characteristics"
If this button is down Characteristics box is visible.
60
FFSDP User Manual
Button "Show Residuals"
If this button is down Residuals box is visible.
Button "Rotate Mode"
If this button is down 3D image rotation will be performed if the left mouse button is pressed and mouse is
moved over the 3D Chart.
Button "Zoom Mode"
If this button is down 3D image zooming will be performed if the left mouse button is pressed and mouse
is moved over the 3D Chart.
Note: the mouse should be moved in vertical direction to zoom the 3D image.
Button "Move Mode"
If this button is down 3D image moving will be performed if the left mouse button is pressed and mouse is
moved over the 3D Chart.
3D Characteristics and Residuals charts
3D Characteristics chart displays measured (green) and theoretical (red) characteristics in threedimensional space. 3D Residuals chart displays weighted residuals in three-dimensional space.
3D charts display all curves within the current experiment. Here the curves sequence corresponds to the
Data Sets sequence in the Configuration treeview.
An example view of the 3D charts is given below:
61
FFSDP User Manual
For 3D chart you can rotate, zoom or move the 3D image by keeping the left mouse button down and
moving the mouse pointer through the 3D chart. The active transformation of 3D image depends on the
mode that is set through the Toolbar or the 3D chart configuration dialog box.
Additional actions with 3D Chart available through the local menu.
Local menu of 3D chart
This local menu contains following items:
1. Default view
2. Save graph
3. Copy graph to Clipboard
4. Graph configuration
5. Save settings as default
6. Load default settings
7. Reset default settings
Local menu command: Default view
Resets a view of the current 3D Chart to the initial state.
Local menu command: Save graph
Saves the current 3D Chart image to BMP file.
Local menu command: Copy graph to Clipboard
Stores the current 3D Chart image to Clipboard.
62
FFSDP User Manual
Local menu command: Graph configuration
Opens the 3D chart configuration dialog box for configuring the current 3D Chart.
Local menu command: Save settings as default
Saves current settings of the current 3D Chart as the default settings.
Local menu command: Load default settings
Loads and Applies the default settings to the current 3D Chart.
Local menu command: Reset default settings
Resets and Applies the default settings to the current 3D Chart.
Experiment configuration dialog box
This dialog box is used to change the configuration of the current experiment. It provides the ability to add
and remove the Data Sets within the experiment and select the model that will be employed to analyze the
data from the given Data Set.
The Experiment configuration dialog box consists of three pages:
Mesurements database page is used to add data sets from database.
Simulator page to add simulation data sets.
Fit parameter dependence is used to create data sets that contain dependence of some fit parameter on
external parameter. The fit parameters for this dependence can be taken from currently opened
experiments that contain analysed data sets.
Note
To choose the necessary page while working with FFS Data Processor you should click on the
corresponding Tab.
Mesurements database page
An example view of the Measurements database page of Experiment configuration dialog box is
given below:
63
FFSDP User Manual
Bellow the brief description of main components of Measurements database page is given:
Alias
Shows the alias associated with Measurements Database.
In Database box
In Database box is used for displaying and choosing the measured data from the Measurements Database.
This box contains Files groups list and Files list. The Files group list displays file groups available from
the Database, the Files list displays files contained in the selected files group.
To add measured data to the current experiment double click left mouse button on the selected file or the
file group. If the item from the Files list was double clicked, the data set with the same name will be
added to the For analysis table. If the item from the File groups list was double clicked, the procedure
described above will be repeated for every file related to this group.
Files group list
The Files group list displays file groups available from the Measurements Database.
Files list
The Files list displays files contained in the files group selected in the Files group list.
64
FFSDP User Manual
Button "Filter"
This button is used for filtering data in the corresponding list. After this button is pressed, Filter dialog
box will be displayed. This dialog box is used for creating and applying the filter to the corresponding list.
Button "Search"
This button displays a search box for the corresponding list. If you want to find quickly the necessary item
you should type the first few characters of its name and press Enter. In this case the application will
automatically select for you the first item that has the name with this few characters at the beginning. To
close the search box press key Esc.
Simulator page
Simulator page is used to create and include to the current experiment a new Simulation Data Set. This
box contains three combobox lists named characteristic, model and noise. Characteristic combobox list is
used to choose type of the characteristic that will be simulated. The model type and the noise type that
were chosen in the corresponding comboboxes will be used as default source model and source noise for
new Simulation Data Sets that will be created. To create and add a new simulation data set to the current
experiment click the Add simulation data set button.
An example view of the Simulator page of Experiment configuration dialog box is given below:
Bellow the brief description of main components of Simulator page is given:
65
FFSDP User Manual
Characteristic combobox list
This combobox list is used to choose type of the characteristic that will be simulated.
Model combobox list
This combobox list is used to chose model type. The model of this type will be used as default source
model for new Simulation Data Sets that will be created. To create and add a new Simulation Data Set to
the current experiment click the Add simulation data set button.
Noise combobox list
This combobox list is used to choose noise type. The noise of this type will be used as default source noise
for new Simulation Data Sets that will be created. To create and add a new Simulation Data Set to the
current experiment click the Add simulation data set button.
Button "Add simulation data set"
This button creates and adds a new simulation Data Set to the current experiment.
Fit parameter dependence page
An example view of the Fit parameters dependence page of Experiment configuration dialog box is
given below:
66
FFSDP User Manual
Bellow the brief description of main components Fit parameters dependence page is given:
Experiments list
This list displays the names of experiments currently opened in FFS DP. The experiments that contain
required data for creating dependencies of fit parameter on external parameter can be selected by checking
corresponding checkboxes.
Model list
This list displays the names of models that belong to experiments selected in the experiments list and
have type currently choosen in the Type combobox list. The models that contain fit parameters required
for creating dependencies of fit parameter on external parameter can be selected by checking
corresponding checkboxes.
Type combobox list
This combobox list is used to chose model type. The models of this type will be displayed in Models list
located bellow.
Button Add data set
This button creates new Data Set that contains the dependence of fit parameter on external parameter and
adds it to the current experiment.
67
FFSDP User Manual
For Analysis table
For Analysis table is used for displaying Data Sets within the experiment and the models, that
correspond to them.
This Table contains the following columns:
Data set displays the names of the Data Sets contained in the current experiment (The values in this
column can be changed only for Simulation Data Sets).
Source model displays the type of the source model (for the simulation Data Sets only).
Source noise displays type of the noise (for the simulation Data Sets only).
Analysis model name displays the name of the analysis model related to the current Data Set.
Analysis model type displays the analysis model type.
Button "Hide/Show Source Data"
This button hides/shows In Database box and Simulator box.
Button "DataBase"
This button opens Measurements Database. You can use this DataBase as more advanced way to navigate
through your data and add some of them to the current experiment for analysis.
Button "Ok"
This button finishes work with the Experiment configuration dialog box and applies all configuration
changes to the current experiment.
Button "Cancel"
This button finishes work with the Experiment configuration dialog box without changing the
configuration of the current experiment.
Button "Help"
This button opens the help window that describes how to work with Experiment Configuration dialog
box.
Local menu of Configuration dialog box
This local menu contains following items:
1. Rename
2. Select All
3. Source Model Type
4. Source Noise Type
5. Analysis Model Name
6. Analysis Model Type
7. Delete
8. Locate in source data
9. Find in Measurements Database
Local menu command: Rename
This menu command allows changing the name of the Simulation Data Sets. The Rename menu
68
FFSDP User Manual
command appears only if the name of any Simulation Data Set is selected. After you have chosen this
menu command the inplace editor will be displayed in the selected cell.
Local menu command: Select All
This menu command selects all Data Sets in the For analysis table.
Submenu: Source Model Type
This submenu contains local menu commands for specifying Source model type for selected Data Sets.
Submenu Source Model Type is only available if all currently selected Data Sets are Simulation Data
Sets.
Submenu: Source Noise Type
This submenu contains local menu commands for specifying Source noise type for selected Data Sets.
Submenu Noise Model Type is only available if all currently selected Data Sets are Simulation Data
Sets.
Submenu: Analysis Model Name
This submenu contains local menu commands for specifying Analysis model name(s) for selected Data
Sets.
There are two special local menu commands in this submenu:
Same New - applies the same newly created model names for all currently selected Data Sets.
Different New - applies the different newly created model names for all currently selected Data Sets.
Submenu: Analysis Model Type
This submenu contains local menu commands for specifying Analysis model type for selected Data Sets.
Submenu Analysis Model Type is only available if analysis model names are supplied for all currently
selected Data Sets.
Local menu command: Delete
This menu command deletes the Data Sets selected in For analysis table.
Local menu command: Locate in source data
Finds the currently selected Data Set in the Files list.
The File group that contains this Data Set will be found also in the File groups list.
Local menu command: Find in Measurements Database
This local menu command executes Measurements Database and forces it to find the currently selected
Data Set.
“Open an existing experiment” dialog box
Open an existing experiment dialog box is used to load a previously saved experiment.
An example view of the Open an existing experiment dialog box is given on the following figure:
69
FFSDP User Manual
Experiment Name
Is used for entering the name of the experiment you want to load from the Analysis Database.
You can quickly find the experiment you want to load by typing the first few characters of its name. In
this case the application will automatically select for you the first experiment that has the name with this
few characters at the beginning.
Previously saved experiments
Displays the experiments previously saved in the Analysis Database.
Button "Help"
This button opens the help window that describes how to work with Open an existing experiment dialog
box.
Button "Open"
This button finishes work with Open an existing experiment dialog box and loads the selected experiment.
Button "Cancel"
This button finishes work with Open an existing experiment dialog box without loading any experiments.
Button "Filter"
This button opens Filter dialog window , that allows to create the filter that can be applied to the
Previously saved experiments list. If this filter is applied, the only experiment names that correspond to
the filter criteria will be displayed.
70
FFSDP User Manual
Button "DataBase"
This button opens Analysis Database and sets the record selected in the Open an existing experiment
dialog box as the current record in the Database.
“Save experiment as” dialog box
Save experiment as dialog box is used to save the active experiment with a different name.
An example view of the Save experiment as dialog box is given on the following figure:
Experiment Name
Is used for entering the name for the experiment you are saving.
Previously saved experiments
Displays the previously saved experiments in the Analysis Database.
Button "Help"
This button opens the help window that describes how to work with Save experiment as dialog box.
Button "Save"
This button finishes work with Save experiment as dialog box and saves current experiment using selected
name.
Button "Cancel"
This button finishes work with Save experiment as dialog box without saving the current experiment.
Button "Filter"
This button opens Filter dialog window , that allows to create the filter that can be applied to the
71
FFSDP User Manual
Previously saved experiments list. If this filter is applied, the only experiment names that correspond to
the filter criteria will be displayed.
Button "DataBase"
This button opens Analysis Database and sets the record selected in the Save experiment as dialog box as
the current record in the Database.
Export data dialog box
This dialog box is used to export the target criterion value, parameter groups, free parameters and arays of
characteristics and residuals to the text file.
An example view of the Export data dialog box is given below:
Bellow the brief description of main components Export data dialog box is given:
"File" edit
This box contains the name of the file where experiment data will be exported.
Button "Browse"
This button displays the standard Open dialog box in which the path and the name of the file can be
chosen.
"Target criterion value" check box
If this check box is checked, the target criterion value will be exported.
72
FFSDP User Manual
"Related free parameters" check box
If this check box is checked, the information about unlinked parameters related to each data set selected in
the Data Sets list will be exported.
"Data Sets" list
This list is used to choose the Data Sets, the data will be exported from.
Button "Check All"
This button selects all data sets in the Data Sets list.
Button "Clear All"
This button unselects all data sets in the Data Sets list.
"Parameters groups" group box
This group box provides a possibility to export the data related to parameters groups.
The following information about the parameters groups can be exported:
Names
Values
Included parameters
"Arrays to be saved" group box
This group box is used to choose the arrays of values to be saved. Check the corresponding check box to
export the certain array.
The following arrays of values are available for the export:
X-axis values
Experimental data -- measured or simulated data
Theoretical data -- the data calculated with chosen theoretical model
Residuals
Button
selects all arrays.
Button
unselects all arrays.
Button "Export"
This button executes the export procedure.
Button "Help"
This button opens the help window that describes how to work with Export data dialog box.
Button "Close"
This button finishes work with Export data dialog box.
73
FFSDP User Manual
Create and save new template dialog box
This dialog box is used to create and save a new template.
An example view of the Create and save new template dialog box is given below:
Bellow the brief description of main components Create and save new template dialog box is given:
Button "Save"
This creates and saves the new template using selected name.
Button "Cancel"
This button finishes work with the dialog box without creating and saving current template.
Template name
Is used for entering the name for the template you are creating and saving.
Button "DataBase"
This button opens Analysis Database, runs the template viewer and sets the record selected in the Create
and save new template dialog box as the current record in the template viewer.
Button "Help"
This button opens the help window that describes how to work with Create and save new template
dialog box.
Load and apply an existing template dialog box
This dialog box is used to load and apply a previously saved template.
An example view of the Load and apply an existing template dialog box is given below:
74
FFSDP User Manual
Bellow the brief description of main components Load and apply an existing template dialog box is
given:
Previously saved templates
Displays the templates previously saved in the Analysis Database. If the filter is applied, the currently
displayed template names depend on the filter criteria.
Template name
Is used for entering the name of the template you want to load from the Analysis Database.
You can quickly find the template you want to load by typing the first few characters of its name. In this
case the application will automatically select for you the first template that has the name with this few
characters at the beginning.
Button "Filter"
This button opens Filter dialog box, that allows to create the filter that can be applied to the Previously
saved templates list. If this filter is applied, the only template names that correspond to the filter criteria
will be displayed.
Button "Apply"
This loads and applies the selected template. After pressing this button the progress bar window appears.
This progress bar window contains a number progress bars for displaying the progress of the template
loading procedure.
Button "Cancel"
This button finishes work with the dialog box without loading and applying any templates.
75
FFSDP User Manual
Button "DataBase"
This button opens Analysis Database, runs the template viewer and sets the record selected in the Load
and apply an existing template dialog box as the current record in the template viewer.
Button "Help"
This button opens the help window that describes how to work with Load and apply an existing
template dialog box.
"Fit parameter vs. external parameter view" window
This window displays the dependence of the value of the given fit parameter on the external parameter.
An example of the "Fit parameter vs. external parameter view" window is given on the following
figure:
Bellow the brief description of main components "Fit parameter vs. external parameter view" window
is given:
Fit parameter combobox list
This combobox list is used to chose fit parameter to be displayed on the graph.
External parameter combobox list
This combobox list is used to chose external parameter
Note:
The External parameter is parameter concerned with external conditions of the measurements.
76
FFSDP User Manual
Button "Help"
This button opens the help window that describes how to work with "Fit parameter vs. external
parameter view" window.
Button "Close"
This button closes the "Fit parameter vs. external parameter view" window.
2D Chart
This 2D Chart displays the Fit parameter vs. external parameter curve. The values of the fit parameter are
displayed along the vertical axis and the values of the external parameter are displayed along the
horizontal axis.
With 2D Chart you can:
move curve in the box by keeping the right mouse button down and moving the mouse pointer through
the box.
zoom in the image by dragging the cursor diagonally across the necessary area from left top corner to
right bottom corner.
restore whole view of the image by pressing left mouse button and dragging mouse pointer on some
positions to upper left.
Additional actions with 2D Chart available through the local menu.
Local menu of 2D chart
This local menu contains following items:
1. Default view
2. Save graph
3. Copy graph to Clipboard
4. Export data
5. Graph configuration
6. Save settings as default
7. Load default settings
8. Reset default settings
Local menu command: Default view
Resets a view of the current 2D Chart to the initial state.
Local menu command: Save graph
This menu command saves the current 2D Chart image to BMP file.
Local menu command: Copy graph to Clipboard
This menu command stores the current 2D Chart image to Clipboard.
Local menu command: Export data
Exports data for the dependences currently displayed in the 2D Chart.
77
FFSDP User Manual
Local menu command: Graph configuration
This menu command opens the 2D chart configuration dialog box for configuring the current 2D Chart.
Local menu command: Save settings as default
Saves current settings of the current 2D Chart as the default settings.
Local menu command: Load default settings
Loads and Applies the default settings to the current 2D Chart.
Local menu command: Reset default settings
Resets and Applies the default settings to the current 2D Chart.
"Separation of coincidence values histograms" window
This window is used to calculate the separation quality for two coincidence values histograms that can be
choosen from experiments currently opened in FFS Data Processor.
An example of the Separation of coincidence values histograms window is given on the following
figure:
Bellow the brief description of main components Separation of coincidence values histograms window
is given:
78
FFSDP User Manual
Experiments list
Contains all expeiments currently opened in FFS Data Processor.
Options group box
Allows specify data sets containing coincidence values histograms that will be used for calculating the
separation quality.
2D Chart
Displays coincidence values histograms from selected data sets and allows visually estimate the separation
quality of them.
Separation quality window
Displays separation quality value.
This value is calculated according to the following equation:
where σ K1 and σ K2 are the standard deviations, <K1> and <K2> are mean values of the coincidence
values K1(n) and K2(n) for two samples.
External parameters dialog box
This dialog box is used to view and manage the extenal parameters of the current Data Set. It provides the
ability to add, remove and edit the external parameters within the Data Set and create new external
parameters.
An example view of the External parameters dialog box is given below:
Bellow the brief description of main components External parameters dialog box is given:
Table "External parameters"
This table is used for displaying external parameters within the Data Set.
79
FFSDP User Manual
It contains the following fields:
Name displays the name of the external parameter contained in the current Data Set.
Value displays the value of the external parameter.
Button "Add"
This button adds empty external parameter to the current Data Set which must be filled in.
Button "Delete"
This button deletes the external parameters selected in the "External parameters" table.
Button "Create new"
This button opens Parameters form.
Button "Ok"
This button finishes work with the External parameters dialog box and applies all changes to the current
Data Set.
Button "Cancel"
This button finishes work with the External parameters dialog box without applying any changes.
Button "Help"
This button opens the help window that describes how to work with External parameters dialog box.
Terms
FCS
FCS - Fluorescence Correlation Spectroscopy
FFS
FFS - Fluorescence Fluctuation Spectroscopy
Properties
Properties are the values that are used for configuring the corresponding object within the current
experiment.
Parameters
Parameters are the values that can be estimated during the analysis.
Structural parameter
The structural parameter is given by
,
80
FFSDP User Manual
where rxy and rz are the distances from the center of the laser beam focus in the lateral and axial
directions, respectively, at which the collected fluorescence intensity has dropped by a factor of
compared to its peak value for Gaussian beam profile.
Parameter group
In this application the special object parameter group is used for linking parameters. The parameters that
belong to one parameter group are considered as linked to each other. Parameter groups are displayed in
the Linked parameters treeview.
Templates
Template contains the all information (the types of the models and their properties, settings and links of
the parameters being estimated) that is related to the analysis of the Data Sets within the current
experiment. Template provides the quick way for analyzing the large amount of data with the same
analysis scheme.
Local menus
FFS Data Processor offers local menus (context menus) for several interface elements. All these menus
can be opened through a right mouse click when mouse pointer is over the element that contains local
menu.
Experiment
In the FFS Data Processor the notion Experiment means the numerical experiment. Within the FFS
Data Processor the Experiment is associated with a special object.
Experiment Object contains all other objects that are used for preparation of data and analysis execution.
Experiment icon is following: .
Experiment properties:
1. Configuration provides access to Configuration dialog box. Press the button on the right side of the
property value box to open this dialog box.
2. Analysis type allows to select a method for analysis. The following Analysis types are currently
available: Global and Sequential.
3. CI Probability specifies the value of confidential probability.
Minimum possible value is 0.001.
Maximum possible value is 0.999.
Default value is 0,67.
4. CI Analysis type allows to select a method for confidential intervals analysis. The following CI
Analysis types are currently available: Exhaustive search and Standard errors.
Data Set
Data Set Object contains all necessary information that describes the data, related to the one measured
(simulated) characteristic (autocorrelation function, crosscorrelation function, etc.) that corresponds to the
sample under study. Also this information defines the conditions under which the data of the given
characteristic will be analyzed.
Data Set icon is following: .
81
FFSDP User Manual
Data Set properties:
1. Local fit criterion displays a value of the Chi-square calculated separately for current data set.
2. External parameters provides access to External parameters dialog box. Press the button on the right
side of the property value box to open this dialog box.
3. Points count indicates the total number of points in the measured (simulated) characteristic. This
property is read only if Data Set contains measured data, otherwise it is changeable.
4. Start analysis at defines the initial point for analysis. The characteristic contained in the Data Set will
be analyzed starting at this point.
Minimum possible value is 0.
Maximum possible value is Points count - 1.
5. End analysis at defines the end point for analysis.
Minimum possible value equals to the Start analysis at.
Maximum possible value is Points count - 1.
Default value is Points count - 1.
6. Start criterion at specifies the initial point for the Chi-Square calculation.
Minimum possible value equals to the Start analysis at.
Maximum possible value is Points count - 1.
Default value equals to the Start analysis at.
Data Source
Data Source Object is used to prepare the source data for the analysis.
Data Source can be Measured or Simulation.
Measured Data Source is used for preparation of measured data.
Simulation Data Source is used to generate data on the bases of Model and Noise.
Data Source icon is following: .
Data Source properties:
This object does not have any properties.
Model
FFS technique is aimed to the investigations of the intensity fluctuations of fluorescent molecules excited
by a tightly focused laser beam. These fluctuations may arise from translational and rotational diffusion,
chemical reactions, deexcitation of the triplet-state, conformational and structural changes, etc [ 1, 2, 3, 4,
5, 15, 16].
To take into account any phenomenon mentioned above while analyzing the FFS data the appropriate
mathematical model should be chosen. In the FFS Data Processor the mathematical models are
represented by the corresponding Model Objects.
Model Object can belong either to the Data Set or to the Simulation Data Source. In the first case Model
is used to generate the theoretical characteristic. In the second case it is used to generate noise-free source
characteristic.
Model icon is following: .
Now the following models are available to be used with FFS Data Processor:
Characteristics
Models
Correlation function
Pure-Diffusion
Triplet-State
Conformational
82
FFSDP User Manual
Protonation
FCS flow
Custom
Coincidence values histogram
Gaussian
Custom
Cumulants
FFC
Custom
Photon counting distribution
PCH
Gaussian
Custom
Identifiability
All models mentioned above (except Custom model) are totally identifiable, i.e. all parameters of the
models can be uniquely determined on the basis of only one measured characteristic.
Noise
Noise Object adds noise to the correlation function curve generated by Model for Simulation Data Set. To
find out more about noise generation see the description of the Simulator.
Noise icon is following: .
Noise properties:
1. Initial Rando specifies the initial value of the random variable generator. (This value should be odd.)
2. Constant level defines the amplitude of the constant noise component.
3. Variable level defines the amplitude of the time-dependent noise component.
4. Time Power defines the noise distribution along the correlation function curve.
References to literature
1. E.L. Elson, D. Madge, 1974. Fluorescence correlation spectroscopy. I. Conceptual basis and
theory. Biopolymers 13, 1-27.
2. J. Widengren, R. Rigler, 1998. Fluorescence correlation spectroscopy as a tool to investigate
chemical reactions in solutions and on cell surfaces. Cell. Moll. Biol. 44, 857-879.
3. L. Edman, U. Mets, R. Rigler 1996. Conformational transitions monitored for single molecules in
solution. Proc. Natl. Acad. Sci. USA. 93, 6710-6715.
4. S. Wennmalm, L. Edman and R. Rigler, 1997. Conformational fluctuations in single DNA
molecules. Proc. Natl. Acad. Sci. USA. 94, 10641-10646.
5. Ulrich Haupts, Sudipta Maiti, Petra Schwille, and Watt W. Webb, 1998. Dynamics of fluorescence
fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy.
Proc. Natl. Acad. Sci. USA. 95, 13573-13578.
6. S.R. Aragon and R. Pecora, 1976. Fluorescence correlation spectroscopy as a probe of molecular
dynamics. J. Chem. Phys. 64, 1791-1803.
7. R. Brock, M.A. Hink and T.M. Jovin, 1998. Fluorescence Correlation Microscopy of Cells in the
Presence of Autofluorescence. Biophys. J. 75, 2547-2557.
8. Widengren J., Rigler R. and Mets U., 1994. Triplet state monitoring by fluorescence correlation
spectroscopy. J. Fluorescence 4, 255-258.
83
FFSDP User Manual
9. Bevington, P.R. Data Reduction and Error Analysis for the Physical Sciences. McGraw-Hill, New
York. 1969.
10. Grinvald, A. and I. Z. Steinberg, 1974. On the analysis of fluorescence decay kinetics by the
method of least squares. Anal. Biochem. 59, 583-598.
11. E.G. Novikov, A. van Hoek, A.J.W.G. Visser and J.W. Hofstraat, 1999. Linear algorithms for
stretched exponential decay analysis. Opt. Commun. 166, 189-198.
12. Beechem, J.M.; Gratton, E.; Ameloot, M.; Knutson J.R.; Brand L. In Topics in Fluorescence
Spectroscopy, Vol. 2, ed. J.R. Lakowicz. Kluwer Academic Publishers, New York, 2002, p. 241.
13. Johnson M.L., Faunt L.M., 1992. Parameter Estimation by Least-Squares Methods. Methods
Enzymol. 210,1-37.
14. Martin Straume, Susan G. Frasier-Cadoret, and Michael L. Johnson. In Topics in Fluorescence
Spectroscopy, Vol. 2, ed. J.R. Lakowicz. Kluwer Academic Publishers, New York, 2002, p. 177.
15. J.D. Muller, 2004. Cumulant Analysis in Fluorescence Fluctuation Spectroscopy. Biophys. J. 86:
3981-3992.
16. Katrin G. Heinze, Markus Rarbach, Michael Jahnz, and Petra Schwille, 2002. Two-Photon
Fluorescence Coincidence Analysis: Rapid Measurements of Enzyme Kinetics. Biophys. J. 83,
1671-1681.
17. Oleg Krichevsky and Gregoire Bonnet, 2002. Fluorescence correlation spectroscopy: the technique
and its applications. Rep. Prog. Phys. 65, 251-297.
18. Samuel T. Hess, Shaohui Huang, Ahmed A. Heikal, Watt W. Webb, 2002. Biological and Chemical
Applications of Fluorescence Correlation Spectroscopy: A Review. Biochemistry 41,697-704.
19. Petra Schwille and Elke Haustein. Fluorescence Correlation Spectroscopy: A Tutorial for the
Biophysics Textbook Online. 2002.
20. Wu B., and J.D. Muller, 2005. Time-Integrated Fluorescence Cumulant Analysis in Fluorescence
Fluctuation Spectroscopy. Biophys. J. 89, 2721-2735.
21. Kask, P., K. Palo, D. Ullmann, and K. Gall, 1999. Fluorescence-intensity distribution analysis and
its application in biomolecular detection technology. Proc. Natl. Acad. Sci. USA. 96,13756-13761.
22. Palo K., U. Mets, S. Jager, P. Kask, and K. Gall, 2000. Fluorescence intensity multiple distribution
analysis: concurrent determination of diffusion times and molecular brightness. Boiphys. J. 79,
2858-2866.
23. Perroud T.D., B. Huang, M.I. Wallace, and R.N. Zare, 2003. Photon Counting Histogram for OnePhoton Excitation. ChemPhysChem. 4, 1121-1123.
24. Huang B., T.D. Perroud, and R.N. Zare, 2004. Photon Counting Histogram: One-Photon
Excitation. ChemPhysChem. 5, 1523-1531.
25. Chen Y., J.D. Muller, P.T. So, and E. Gratton, 1999. The Photon Counting Histogram in
Fluorescence Fluctuation Spectroscopy. Biophis. J. 77,553-567.
26. Victor V. Skakun, Mark A. Hink, Anatoli.V. Digris, Ruchira Engel, Eugene G. Novikov, Vladimir V.
Apanasovich, Antonie J.W.G. Visser. Global Analysis of Fluorescence Fluctuation Data // Eur.
Biophys J. 34 (2005) 323–334.
27 V.V. Skakun, E.G. Novikov, V.V. Apanasovich, H.J. Tanke, A.M. Deelder, O.A. Mayboroda. Initial
Guesses Generation for Fluorescence Intensity Distribution Analysis // Eur. Biophys. J. 35(5) (2006)
410-423.
84
Was this manual useful for you? yes no
Thank you for your participation!

* Your assessment is very important for improving the work of artificial intelligence, which forms the content of this project

Download PDF

advertisement