Intensity Calibration

Intensity Calibration

Menu: Measure > Intensity Calibration

Script intCal, loadIntCal, defIntCal

Use this command to edit and/or apply an existing intensity calibration scale to an image or to create a new scale. The intensity calibration scales pixel intensity values by mapping them to the engineering units of the physical world.

The Table mode allows you to create a custom calibration map by specifying reference points that define how the physical world values relate to the pixel values in the image. This is usually done by acquiring an image of a grayscale tablet (optical wedge) with documented reference values. The reference points of the calibration scale are used to build a calibration curve by utilizing a selectable Fitting method. The calibration curve is then transformed to the calibration map with a specified number of Bins representing different ranges of pixel intensities. During the intensity measurements each pixel from a calibrated image is mapped through the corresponding bin and assigned the calibrated value.

In the Logarithm mode the calibration map is created by using the standard inverse logarithm formula for optical density, which assumes an exponential drop of light passing through a transparent material. To build a calibration scale in this mode, you have to indicate the intensity values representing the Black level (no light is transmitted through the camera's lens) and White level (maximum light is transmitted). Note that ImageWarp's analysis functions provide optical density and transmission measurements that assume a standard intensity calibration (non-logarithmic one). If you calibrated the image in optical density units, do not activate optical density parameters in measurements, but rather use grayscale parameters for optical density calculations. See Point Measurements, Blob Measurements, and Contour Measurements for more details.

If you choose this command, the Intensity Calibration dialog box will appear with the following options:

Image

Displays the number of the image frame for spatial calibration. If you want to perform the intensity calibration for another image, type or select the corresponding value.

Name

Displays the name of the intensity calibration scale to be edited and/or applied. If you want to edit and/or apply another intensity calibration scale, select its name from the drop-down list of all of the intensity calibration scales that have been created and saved.

Reference table

Specifies the pairs of input and output values that are used to define the intensity calibration map. The Input column contains the actual pixel values (X values on the Calibration graph), while the Output column establishes the corresponding engineering values taken from the physical world (Y-values on the Calibration graph). The data in the Reference table are always arranged by the order of input values. You can edit the values in the table manually or by using the Sampling tool. The actual calibration map is calculated by approximating the data in the table with the selected Fitting method. Note that for a linear calibration only two pairs need to be specified.

Sampling window

Lets you select the size of the square area used by the Sampling tool. The size of side of the square is measured in pixels, and it can be set to the length from 1 to 15.

Sampling tool

Click this button to define the Input value for the Reference table by sampling the image. When you move the cursor over the input image, the cursor will take shape of a foresight. Position the cursor over the area whose average gray level you want to define as the Input for a new calibration pair and press the left mouse button. A blinking red circle will appear on the image and new row will be added to the Reference table with both fields equal to the average gray level in the Sampling window. At this point you should modify the Output field by typing the physical world value corresponding to the Input value. Clicking in a row added with the Sampling tool will make the corresponding marker on the image blink.

Insert pair

Click this button to insert a new calibration pair into the Reference table. Both Input and Output fields of the new row will be set to zero.

Delete pair

Click this button to delete a calibration pair pointed by the cursor from the Reference table. If the pair was added by using the Sampling tool, the corresponding marker on the image will be erased.

Calibration graph

Displays the curve representing the current calibration map. The X-axis of the graph represents the actual pixel values in the image, while the Y-axis represents the physical world values. In the Table mode the graph also shows the points corresponding to the calibration pairs from the Reference table. The scaling factor for X and Y axes is defined automatically so that the calibration curve encompasses the whole range of the calibration map for both input and output values. The intensity scale is displayed under the X-axis, providing the visual reference for input values.

Table mode

Select this option if you need to define the intensity calibration map by specifying the pairs of input and output values that define the shape of the calibration curve.

Logarithm mode

Select this option if want to create a calibration scale in accordance with the standard optical density curve. The standard optical density is defined by the light transmission formula:

where

I_x,y is the intensity for which the optical density is being defined,

I_min is the intensity corresponding to the black level black level (no light is being transmitted)

I_max is the intensity corresponding to the white level (maximum light is being transmitted)

When you select the Logarithm mode, the Reference table will be unavailable, and the Min and Max boxes will be used to establish the intensities for the black and white levels respectively.

Bins

Displays the number of bins in the intensity calibration map. By default this value is set to 256. Enter the new value, if you want to modify the size of the calibration map. Note that increasing the number of bins in the calibration map will generally increase the accuracy of the intensity measurements, but will cause a higher memory load for calibrated images.

Min

Displays the minimum input level for the intensity calibration map in the Table mode or the black level in the Logarithm mode. By default this value is set to 0 except for floating point images, for which it is set to the minimum of the display range. Enter the new value if you want to modify the minimum level. In the Logarithm mode you can use the Sampling tool to select the black level from the picture. Note that the pixels whose intensities are less than the minimum input level of the calibration map will be assigned the calibrated value corresponding to the minimum level.

Max

Displays the maximum input level for the intensity calibration map in the Table mode or the white level in the Logarithm mode. By default this values is set to 255 for 8-bit images, 65535 for 16-bit images, and the maximum of the display range for 32-bit and floating-point images. Enter the new value if you want to modify the minimum level . In the Logarithm mode you can use the Sampling tool to select the black level from the picture. Note that the pixels whose intensities exceed the maximum input level of the calibration map will be assigned the calibrated value corresponding to the maximum level.

Unit

Type the name for the intensity calibration units. This name will be used when ImageWarp reports the intensity-related parameters in the data tables or status bar.

Fitting

Lets you select a fitting method for building the intensity curve and calibration map from the pairs of points in the Reference table. Select one of the following methods:

Connect

Connects the sampling points with straight-line segments.

Liniear

Fits the sampling points to a straight line using the least-squares method

Square

Fits the sampling points to a quadratic equation curve using the least-squares method.

Cube

Fits the sampling points to a cubic equation curve using the least squares method.

Lagnange

Fits the sampling points to a curve using the Lagrange interpolation.

Add

Click this button to add a new intensity calibration scale to ImageWarp's list of calibration scales. When you click this button, the Add dialog box will appear. Type the name for the new intensity calibration scale under Enter new scale and click OK. (If you click Cancel, ImageWarp will close the Add dialog box without creating a new intensity calibration scale.) After you click OK, you will return to the Intensity Calibration dialog box.

Rename

Click this button to rename the current intensity calibration scale. When you click this button, the Rename dialog box will appear. Type the new name for the intensity calibration scale under Rename this scale as and click OK. (If you click Cancel, ImageWarp will close the Rename dialog box without renaming the active intensity calibration scale.) After you click OK, you will return to the Intensity Calibration dialog box.

Delete

Click this button to delete the active intensity calibration scale.

Default

Click this button to store the current intensity calibration scale as the default one for all new images acquired with the video device.

Apply

Applies the current intensity calibration to the selected image.

Save

Saves the current calibration scale for future references.

Close

Closes the dialog box without performing any action.