Well Scanning Data

If the test run contains well scanning data, an additional view button in the Microplate View will become visible. Pressing this button will show an overview of the scanned wells. The values are mapped to colors defined with the color settings window.

If more than one wavelength was measured (dual emission or multi chromatic test runs) you must choose which wavelength to view using the drop down menu found above the microplate grid.

You can double click on a well to see a zoomed view of the measurement values along with additional information. In this detailed view it is possible to change the scan diameter used for the well calculations and also exclude single scan points.

Clicking on the Excel button will export a scan matrix with the measured values of each well to excel.

3.18.1 Detailed View of Well Scanning Data for a Selected Well

Double clicking on the well in the Microplate View when the Well Scanning View Mode is active, will open the detail window for this well.

In this window a zoomed view of the selected well will be shown along with some other additional information. When moving the mouse cursor over a scan point, a hint will appear showing the measurement value of the point. The picture contains three circles (for round wells) or squares (for square wells) with the following descriptions:

The fat black line: Shows the scan diameter used for calculations on the well. All scan points that fall outside of this line will not be used and are marked to indicate them as not in use.

The fat gray line: Shows the physical scan diameter. This is the diameter used by the reader as a limit when the well is scanned. Only scan points of the defined matrix whose centers lie inside this area are measured. The scan diameter is selected in the protocol settings of a test run in the reader control software.

The thin black line: Shows the border of the well as defined in the microplate database.

When the mouse cursor is moved over one of these border lines, a hint will be displayed showing the identifier and size of the border.

Description of the Window Calculated Values:

Calculation method

Select a calculation method (average, median, sum...) used to calculate the result value for the wells. The selected method is valid for all measured wells and not only for the displayed well.

Result This is the calculated result value of all scan points used, based on the selected calculation method. It will be displayed in the Microplate View (value view mode) and used as the raw data value for further calculations.

Std. Dev The calculated standard deviation of the scan points used.

%CV The %CV is calculated by dividing the standard deviation of the scan points by the average of the scan points used, and then multiplying the answer by 100 to express the value as a the well. Excluded (unused) scan points have a checked pattern on them. each scan point to ‘used’, if its center lies inside the area defined by the Scan Diameter in use.

To define thresholds for excluding scan points, press the Define Thresholds button. For more details on how to

can be displayed in a readable size.

To change back to viewing the data in color mode select Show colors.

Press the Colors item to change the selected color mode and its settings (see chapter 3.15: Color Settings). The color legend shows the color gradient between the minimum value (Min:) and the maximum value (Max:) of a selected well.

To get a three dimension view of the well, select Show 3D chart.

The section Exclude Single Scan Points on the window is then replaced by the section Chart

Settings to change the zoom value, the rotation and the elevation of the chart.

BMG LABTECH OPTIMA Software Manual - Part IIIa: MARS Data Analysis Change Scan Diameter

Press Scan Diameter Used to change the diameter of the circle/square which defines the valid data points. The diameter used window will then open:

The Scan Diameter Used describes the diameter of a circle (for a round well shape) or of a square (for a square well) that defines the area within the measured data points are used for further calculation.

Changing the diameter size allows users to reduce this area to exclude

potential inaccurate readings from the edge of the well. The used diameter window contains a slider control to change the diameter using the mouse to move the slider changing the diameter. Data points falling outside of the selected area will be displayed in a gray pattern indicating, that these points will not be used for calculating the result value of the well scanned.

Note: Changing the diameter will affect all wells used, not only the well altered in the detail window.

Alternatively the border in the image can be moved by using the mouse to change the diameter. Move the mouse over the fat black line in the image until a hint showing diameter used xxx mm appears and the mouse cursor changes to two arrows. Press the mouse button and the color of the border will change to blue, it can then be moved to the desired size before releasing the mouse button. Note that the new diameter will apply to all wells!

To export the measured values to Excel press the Excel button. A matrix of the scanning matrix dimension will be generated in Excel and filled with the values of all the scan points measured.

To print the window, press the Print button. A window to define the print destination (printer, pdf or html file,...) print orientation, page margins and header or footer contents will be opened (see chapter 3.16: Printing Your Data).

Click the Save button to save the well scan detail as a bitmap file or to the clipboard.

Using thresholds to exclude scan points

Beside reducing the used scan diameter and clicking on single scan points, there is a third way to exclude scan points from further calculation. You can define thresholds to exclude single scan points with the window that is show after pressing the Define Thresholds button:

There can be four threshold values which can be combined. One to exclude values below a certain number, one to exclude scan points above a certain number and two to exclude scan points between these numbers.

To use a certain threshold, activate the according control by checking its check box.