Integration

Menu for adjustment of integration parameters. All commands can also be invoked using icons from the Integration toolbar.

All integration parameters are executed as a part of the Integration Table (for more details see also chapter Integration). All of these parameters are interval parameters, which means that it is possible to define the time frame of their validity and in particular to select various values for various parts of the chromatogram.

All interval operation follows the rule that with Time B = 0 operation will be applied from Time A to the end of the chromatogram. With both Time A and Time B set to 0, operation is applied over the whole chromatogram.

Integration commands in Baseline bar

Local Peak Width Defines minimum width of peak.
Local Threshold Describes the threshold of noise.
Local Baseline Slope Defines the position of automatically found peak starts and peak ends. The command is only available if Wave Integration Algorithm is used.
Integration Interval Sets the interval for the integration algorithm.
Detect Negative Detects negative peaks.
Minimal Area Sets the minimum peak area.
Minimal Height Sets the minimum peak height.
Minimal Half Width Sets the minimum peak width in half-height of the peak.
Detector Delay Shifts the signal on the time axis.
FFT Filter Applies/suspends the FFT Filter (Fast Fourier Transformation) for noise reduction.
Savitzky-Golay Filter Applies/suspends the Savitzky-Golay Filter for noise reduction.
Moving Average Filter Applies/suspends the Moving Average Filter for noise reduction.
Spike Filter Applies a filter that removes spikes to the selected region of the chromatogram. Only available in Clarity version 4.0 or higher.

Invoking this command or using the Local Peak Width icon opens the Peak Width dialog which defines the method of peak integration on a given time interval. Peak Width parameter should be set according to the narrowest peak of interest and influences the number of points used in the evaluation. The Value must be in the range of 0.001 - 10 minutes.

Peak Width

Caution:

Setting an excessively high value will distort the results.

The Local Peak Width command procedure:

  • You will be prompted to place the cursor lines to the beginning and the end of the interval and mark each by left-click of the mouse. The Local Peak Width parameter will be applied within this interval only.
  • Then the Peak Width dialog will open in which you may adjust the graphically set interval in the Start Time and Stop Time fields and enter the required peak width into the Value field.
  • Click the Suggest Value button to user is advised to interactively select the narrowest peak that still has to be integrated (again using the cursor lines). Suggested value will be transferred to the Value field.
  • Click OK to apply the selected value to the specified interval.

Note:

The value as well as the interval can be later edited in the Integration Table.

Start Time

Enables to edit the interactively set Start Time of the interval. The value set in the Value field will be applied within this interval only.

Stop Time

Enables to edit the interactively set Stop Time of the interval. The value set in the Value field will be applied within this interval only.

Value

Enables to edit the suggested value of theLocal Peak Width parameter. The value can be suggested by Clarity using the Suggest Value button.

Suggest Value

Clicking the button will display the cursor lines again and the user will be prompted to select the interval containing narrowest peak that still has to be identified. The suggested Peak Width value will be transferred to the Value field where it can be confirmed or edited.

Note:

The Peak Width value is not critical, so narrower peaks than the set value are also detected, but this may lead to an imprecise definition of the beginning and end of the peak and incorrect interlining of the baseline.

To adjust the Peak Width value for the entire chromatogram, use the Global Peak Width command (for more details see also chapter Chromatogram).

Invoke this command or press the Local Threshold icon to open the Threshold dialog which determines the noise threshold value for the specified interval. The Threshold parameter determines the sensitivity of the integration algorithm to distinguish between noise and peaks. The parameter also, unless overriden by Slope parameter value, determines the position of the starts and ends of peaks.

The height of all peaks (measured from the baseline to the apex) which you wish to detect should be at least twice this parameter. The Value must be in the range of 1 µV - 10 V.

Threshold

The Local Threshold command procedure:

  • You will be prompted to place the cursor lines to the beginning and the end of the interval and mark each by left-click of the mouse. The Local Threshold parameter will be applied within this interval only.
  • Then the Threshold dialog will open in which you may adjust the graphically set interval in the Start Time and Stop Time fields and enter the required threshold value into the Value field.
  • Click the Suggest Value button to interactively select the area with the "highest peaks" that still should not be integrated (using the cursor lines once more). Suggested value will be transferred to the Value field.

Note:

Keep in mind that the suggested value will be half of these "highest peaks" because only peaks twice the size of the noise threshold will be detected.

Note:

In the Wave integration algorithm, peaks that are lower than twice the threshold may still appear in the chromatogram if they are on the same baseline with valid (higher) peaks not to influence the course of the baseline. Such peaks can be hidden using the Peak - Hide function or the baseline can be modified to remove them using the Integration - Minimal Height operation set to twice the threshold value (baseline changes in the latter case).

  • Click OK to apply the selected value to the specified interval.

Note:

The Threshold value as well as the Local Threshold interval can be later edited in the Integration Table.

Start Time

Enables to edit the interactively set Start Time of the interval. The value set in the Value field will be applied within this interval only.

Stop Time

Enables to edit the interactively set Stop Time of the interval. The value set in the Value field will be applied within this interval only.

Value

Enables to edit the suggested value of the Local Threshold parameter. The value can be suggested by Clarity using the Suggest Value button.

Suggest Value

Clicking the button will display the cursor lines again and the user will be prompted to place an interval containing "highest peaks" that still should not be integrated. The suggested Threshold value will be transferred to the Value field where it can be confirmed or edited.

To adjust the Threshold value for the entire chromatogram use the Global Threshold command (for more details see also chapter Chromatogram).

Invoke this command or press the Local baseline Slope icon to open the Slope dialog which determines the expected signal curve slope value to detect peak starts and ends for the specified interval. The Slope parameter decides on the position of peak starts and peak ends in the Wave integration algorithm. If unused (value left at 0) the Slope is derived from the Threshold parameter (at 8 * Threshold at given area of chromatogram).

Slope

The Local Baseline Slope command procedure:

  • You will be prompted to place the cursor lines to the beginning and the end of the interval and mark each by left-click of the mouse. The Local Baseline Slope parameter will be applied within this interval only.
  • Then the Slope dialog will open in which you may adjust the graphically set interval in the Start Time and Stop Time fields and enter the required slope value into the Value field.
  • Click the Suggest Value button to interactively select the position of the expected peak start or peak end. Suggested value will be transferred to the Value field.

Note:

The suggested value will be exactly as the slope calculated at the position, but the peak start or peak end may be placed slightly differently - the expected slope is checked on the whole signal curve and there may be other areas which fulfill the slope condition closer to the peak apex.

  • Click OK to apply the selected value to the specified interval.

Note:

The Slope value as well as the Local Baseline Slope interval can be later edited in the Integration Table.

Start Time

Enables to edit the interactively set Start Time of the interval. The value set in the Value field will be applied within this interval only.

Stop Time

Enables to edit the interactively set Stop Time of the interval. The value set in the Value field will be applied within this interval only.

Value

Enables to edit the suggested value of the Local Baseline Slope parameter. The value can be suggested by Clarity using the Suggest Value button.

Suggest Value

Clicking the button will display the cursor line again and the user is prompted to point to a place where the expected peak start or peak end should be placed automatically by the integration algorithm. The suggested Slope value will be transferred to the Value field where it can be confirmed or edited.

To adjust the Slope value for the entire chromatogram use the Global Baseline Slope command (for more details see also chapter Chromatogram).

Invoking this command or using the Integration Interval icon allows to define the interval in which the integration algorithm is run. The course of the chromatogram outside of this interval will be ignored.

After using the function you are prompted to select the beginning and end point of the interval in the graph using the mouse. The starting time or ending time of the interval may be adjusted or directly set in the Integration Table on the Integration tab. When the Integration Interval command is not used, the integration algorithm is run on the whole chromatogram.

Caution:

It is not true that the Integration Interval command is an opposite to the Baseline - Lock command. Although their logic is opposite (the first command will permit the integration in the interval and in the second will prohibit it) there is a significant difference between using the Integration Interval command (which directly defines where the integration algorithm will be used) and using the Baseline - Lock command (which only prohibits already integrated peaks). In other words: the Baseline - Lock command does not radically change the course of the baseline before and beyond the area with suppressed peaks.

Invoking this command or using the Detect Negative icon enables the detection of negative peaks in the defined interval. When the function is not active on the given part of the chromatogram, all negative peaks present are considered to be the correct course of the baseline (similar to the part of the chromatogram which uses the Reject Negative function).

Invoking this command or using the Minimal Area icon allows you to set minimum allowed area of the peak. Peaks with areas smaller than or equal to this value are excluded from the integration.

Minimal Area

Start Time

Enables to edit the interactively set Start Time of the interval. The value set in the Value field will be applied within this interval only.

Stop Time

Enables to edit the interactively set Stop Time of the interval. The value set in the Value field will be applied within this interval only.

Value

Enables to edit the suggested value of the Minimal Area parameter.

Invoking this command or using the Minimal Height icon allows to set the minimum height of the peak. Peaks with heights smaller than or equal to this value are excluded from the integration. Parameters and fields in the Minimal Height dialog are the same as in the Minimal Area dialog.

Invoking this command or using the Minimal Half Width icon allows to set the minimum half-width of the peak. Peaks with W05 parameter smaller than or equal to this value are excluded from the integration. Parameters and fields in the Minimal Half Width dialog are the same as in the Minimal Area dialog.

Invoking this command or using the Detector Delay icon allows to correct the time delay of a detector. You are advised to point and click the cursor on the desired peak of the active signal and then on a corresponding peak in the reference signal.

Invoking this command or using the FFT Filter icon allows to apply the FFT Filter (Fast Fourier Transformation) for noise reduction in the selected interval. If more than one type of the filter is set on the same time interval, only the last used filter on that interval is actually used. FFT Filter in Clarity is non-parametric and may create artifacts on the signal under certain conditions.

For the description of equations behind FFT Filter calculation please check publicly available resources (Wikipedia).

Invoking this command or using the Savitzky-Golay Filter icon allows to apply the Savitzky-Golay Filter for noise reduction in the selected interval. If more than one type of the filter is set on the same time interval, only the last used filter on that interval is actually used. Savitzky-Golay Filter in Clarity is parametric, ranging the parameter from 1 (no filter applied) to 500 (filter window is 500 points wide). The parameter for the filter may be changed in the Integration table for the given signal, found on the Integration tab in Chromatogram window. Savitzky-Golay filter may create artifacts on the signal under certain conditions.

For the description of equations behind Savitzky-Golay Filter calculation please check publicly available resources (Wikipedia).

Invoking this command or using the Moving Average Filter icon allows to apply the Moving Average Filter for noise reduction in the selected interval. If more than one type of the filter is set on the same time interval, only the last used filter on that interval is actually used. Moving Average Filter in Clarity is parametric, ranging the parameter from 1 (averaging actual point with the previous and next one) to 500 (filter window is 1001 points wide - 500 points to each side). The parameter for the filter may be changed in the Integration table for the given signal, found on the Integration tab in Chromatogram window. The equation to calculate the moving average filter used in Clarity is:

, where Ei is original signal of point i and p is the parameter entered in the Integration table.

Invoking this command or using the Spike Filter icon allows to remove the spikes on the chromatogram signal. The parameter of the command (that can be edited from the Integration table) describes how wide spikes will be removed (their missing points replaced by a calculated value). The usage of this function only available in Clarity version 4.0 and higher may be disabled by the use of the Disallow Spike Filter and Spike Removal parameter from the GLP Options dialog (for more details see also chapter GLP Options). Spike Filter in Clarity is parametric, ranging the parameter from 1 (no filter applied) to 100 (filters out spikes 100 points wide maximum). The parameter for the filter may be changed in the Integration table for the given signal, found on the Integration tab in Chromatogram window.