Integration

In integration, you can refine the data, and detect peaks.

../../../_images/integration.png

The view is made of three main parts:

Overview

../../../_images/integration_overview.png

It displays all your profiles data as a tree, ordered by HPTLC step / instrument and by wavelength (or illumination). You can select which step and wavelength you want to use in the evaluation.

Note

It is only possible to select one HPTLC step / instrument

If you need to use two or more steps, you should create new evaluation’s tabs for the other steps.

You can either select a whole HPTLC step / instrument, or only some of the wavelengths.

Important

Only selected data will be available in the next evaluation steps.

It is also possible to hide a specific track by switching the corresponding button from imgTrackOn to imgTrackOff

Note

For TLC Visualizer/TLC Visualizer 2 steps, you need first to generate profile data in Data View, and if not already done, the step will be marked with imgVisuWarn .

To the right of the track number, the type of sequence is displayed, imgReference for reference and imgSample for sample. The icons have tooltips displaying the application in details.

Peaks table

The peaks table has 2 modes:

  • When a single track is selected in the Overview, all the characteristics of the peaks of this track are displayed:

    ../../../_images/integration_peaks.png

    Note

    The peak table displays positions in 𝑅ꜰ or millimeter unit depending on the mode currently activated in the Profiles view.

    • Max 𝑅ꜰ or Max pos. (mm): the 𝑅ꜰ/mm position where the maximum height was found

    • Height: the maximum height of the peak

    • Height %: the height of the peak relative to the sum of the heights of all peaks detected for this track

    • Start 𝑅ꜰ or Start pos. (mm): the start 𝑅ꜰ/mm position of the peak

    • Start Height: the height at the start 𝑅ꜰ position

    • End 𝑅ꜰ or End pos. (mm): the end 𝑅ꜰ/mm position of the peak

    • End Height: the height at the end 𝑅ꜰ position

    • Area: the area of peak (obtained by discrete integration of all the profile points between Start 𝑅ꜰ and End 𝑅ꜰ)

    • Area %: the area of the peak relative to the sum of the areas of all peaks detected for this track

    • Assigned to: this field displays a combo box used to see and configure the substance associated to the peak. The combo box allows you to delete an existing assignment (– Not assigned – option), choose a substance already defined in the evaluation, or create a new substance (– Create substance – option). In this last case, the substance will have a generic name by default, modifiable in Definition.

    • btnDeletePeak : delete the peak (see Manual peak edition)

    • Manual peak: indicates whether the peak has been manually edited or not (see Manual peak edition)

On top of the peaks table, some peak-related actions are available (see Manual peak edition):

  • btnPeakAdd Add a new peak,

  • btnPeakClear Delete all peaks of the current track.

  • btnPeaksExport When a step or a wavelength is selected in the Overview, the peaks table only shows the number of peaks detected and also a CSV export button. The CSV export contains a simple table containing the following fields for each detected peak:

    • Wavelength or illumination,

    • The track number,

    • All the fields displayed when a track is selected in Overview.

Note about numbers range and significant digits

𝑅ꜰ is by definition in the range [0;1].

Absorbance, fluorescence and luminance are in arbitrary unit (AU), and the raw range depend of the instrument sensor and the quality requested. Therefore, each measure should be normalized to the same range. Contrary to previous software, the range used by visionCATS is the more common one of [0;1], same as for 𝑅ꜰ. The normalization range is arbitrary and will not affect results.

Significant digits of values are reduced for a more concise display, but all computations are done with the full precision available.

Important

If you need to do additional computations with these data, it is recommend to use the CSV export function to get values with maximal precision.

Note

The same value precision is available in the Report data, and therefore it is possible to create a report template with more significant digits (see Report templates).

Profiles view

The Profiles viewer can be used here in both 2D and 3D. Single tracks are available in 2D only.

Integration tools

On the right, you have the different integration tools. Different modes allow the settings of expert parameters:

  • btnEasy

    Easy : the main integration tools can be activated/deactivated but not configured, and the peak table is not shown. Use this mode when the default integration parameters work well.

../../../_images/toolsEasy.png

  • btnManual

    Manual : advanced baseline and peak detection features are enabled, and the peak table is shown. Use this mode to perform the integration manually.

../../../_images/toolsManual.png

  • btnExpert

    Expert : all available features are accessible. Use this mode to configure advanced features such as smoothing parameters and dual wavelength.

../../../_images/toolsExpert.png

Note

The default mode can be selected in User Options, see Default integration mode .

Bounds

Bounds will allow you to only use the data between the start and end bound (in 𝑅ꜰ unit).

  • Clip outside: will also hide data outside the bounds

Smoothing

Profile raw data usually have some noise, which can adversely affect the peak detection. With smoothing, you can remove this noise.

  • Savitzky Golay (SG)

  • Moving average (MA)

  • Gauss

For each algorithm, a window or width can be adjusted to specify the amount of noise filtered.

Baseline

Most plates don’t have a perfect background, therefore you should remove this baseline for better results.

You can display the detected baseline with the button btnDisplayBasline.

Profile Subtraction

In some cases, profile subtraction can be interesting as another option to correct profile and/or an alternative to baseline correction. visionCATS offers two modes:

  • Dual Wavelength: select a base wavelength in the combo box. Each track of the base wavelength will be subtracted from the tracks of other wavelengths in the step currently selected.

  • Track: select a base track in the combobox. For each wavelength, the values of the base track will be subtracted from the other tracks.

Peaks

  • Optional Quadratic Interpolation (OQI)

  • Gauss (Legacy): the implementation of Gauss peak detection as it was in visionCATS 2.4 and previous versions.

  • Gauss: the new and optimized version of the gauss peak detection, starting with visionCATS 2.5.

Peak detection can be adjusted with the Separation, Sensitivity and Threshold parameters.

Also, peaks can be manually adjusted with Manual peak edition.