Intercepts

The Intercept measurements compute the number of times that a pixel is "intercepted" in a given direction across the image. Intercepts describe something about the shape and size of objects. Intercept measurements can also be made per individual Object.

• 0° - Number of intercepts in the vertical directions.
• 45° - Number of intercepts in the upper-right and lower-left directions.
• 90° - Number of intercepts in the horizontal directions.
• 135° - Number of intercepts in the upper-left and lower-right directions.
• Mean - Average of the number of intercepts found along each of the four directions defined above.

Object Area

The sum of the Area measurements for each object. The Object Area result does not include holes.

ROI Area

The total area considered for measurement analysis. The ROI was defined in the Region Of Interest dialog from the Capture settings window, and can be any shape.

See also: ROI Width, ROI Height.

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Density

The ratio of Object Count over ROI Area, giving the count density per unit area. Density is used to compare the frequency of occurrence of objects between images where the ROI may change. Complements Object Count.

Fraction (Area)

The ratio of the Object Area to the ROI Area, which indicates the relative proportion of the ROI detected as objects. Area Fraction is measured as a percentage value, e.g. 52.4%.

Object Count

The number of separate objects found in the image. Object Count is used to compare the frequency of occurrence of objects between images where the ROI does not change. Complements Density.

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For normal images the gray scale range for intensity based measurements is 0-255. For images created with digital cameras, when the gray scale range can be greater than 0-255, the intensity measurements will be made using the full gray scale range available in the image.

Intensity Calibration Values

When creating calibrated intensity measurements using the non-linear curve fitting methods provided in the Density form within the Capture Pane, the intensities in the resulting linearized image have a calibration function:

• Dose Gradient - The slope of the non-linear intensity-to-dose calibration curve
• Dose Intercept - The Y-intercept of the non-linear intensity-to-dose calibration curve

Calibrated Dose = (Dose Gradient * Gray level) + Dose Intercept

This expression is used to calculate the Mean Dose and Total Dose object measurements described under Object Intensity/Color measurements. This expression can also be applied to any Field or Object gray level statistic measured to convert them into calibrated Dose measurements.

ROI Color Statistics

ROI Color Statistics are computed from the distribution of pixel intensity values over the entire ROI. By using the component RGB or HSI values, color indices can be created for other color standards by creating Custom Measurements that combine these values via appropriate weighting factors.

• Monochrome - see Mean Gray Level intensity
• Red - the average of the red-channel values of each pixel in the ROI.
• Green - the average of the green-channel values of each pixel in the ROI.
• Blue - the average of the blue-channel values of each pixel in the ROI.
• Hue - the average color value of pixels in the ROI after transforming RGB coordinates into HSI coordinates, representing the position of the pixel along a spectrum of pure colors.
• Saturation - the average saturation value of pixels in the ROI after applying a transform to convert to the HSI equivalent representation of the pixel, representing the purity of the color; objects with less pure colors which include more white light (from poor staining or illumination) have a lower saturation value.

ROI Intensity Statistics

ROI Intensity Statistics describe the distribution of pixel intensity values for every pixel in the measurement Region of Interest as defined in the Capture screen.

• ROI Mean Gray - the average intensity of each pixel in the ROI using the intensity component of the pixel after transforming into the HSI equivalent
• ROI Min - the minimum occurring gray level value
• ROI Max - the maximum occurring gray level value
• ROI Sdev - the standard deviation of gray level values
• ROI Range - the range of gray level values
• ROI Mode - the most frequently occurring gray level value
• ROI Modef - the frequency of the most frequently occurring gray level value

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Field Class Number (FLD_Class_No.)

The number of the current measurement Class being measured. May be used when data is saved to a file, to allow selection of data based on Class. The Field Class Number is saved into data documents by default. This measurement is also available as an Object Measurement.

Hint: For .FCS data files, exported from Data Documents, it may be useful to include FLD_Class_No. as a data field.

Field Number (FLD_Field_No.)

The number of the current field being measured. The Field Number is saved onto data documents by default. This measurement is also available as an Object Measurement.

For .FCS data files, exported from Data Documents, it may be useful to include FLD_Field_No. as a data field.

Field Scan Delay (FLD_Scan_Delay)

The pause between each series of images in a Scan in seconds, entered in the Scan Wizard.

Hint: In the case of an XY Scan, this delay represents the target time to wait between initiating each scan. This may be set to 3600 in order to run an XY scan once per hour. If the scan takes only 5 minutes, this delay will be used to pause the system before starting the next scan. If the scan takes an hour and a half, the delay will have no effect, the system will not pause, but will continue immediately to process the next Scan.

Field Time (FLD_Time)

The number of seconds elapsed at the moment the field was captured since the first image capture in a Scan's sequence of images.

Field Time Delay (FLD_Time_Delay)

The pause between each frame of a Scan sequence in seconds.

Field Time Delay Notes:

The Field Time Delay is the target delay, but the Field Time Increment records the actual delay between fields, as it is possible that the processing may take longer than the target delay.

Example: In the case of an XY scan where the Field Delay is set to be 5 seconds, and processing each field takes 2 seconds, the Field Delay will be used to pause the system before starting the next field. If the processing takes 10 seconds, the delay will have no effect, the system will not pause, but will continue immediately to process the next image on schedule. ( If the processing takes 6 seconds, all the fields will still be captured but while falling progressively farther behind the original schedule.)

Filed Time Increment (FLD_Time_Inc)

The number of seconds elapsed between successive image captures in a sequence of images captured using process control.

Field Time Increment can be used with Field Time Delay to compute the time for processing of each image in a sequence.

Field XYZ Origin

These values are the uncalibrated number of steps representing the travel of the motorized X, Y, Z controller from the origin as defined in the first image of a sequence.

• Field X Origin - first transverse axis motion
• Field Y Origin - second transverse axis motion
• Field Z Origin - vertical axis motion

Hint: To compute the absolute coordinates of individual objects in an automatic scan, use the object center of gravity, the calibration scale-factor, the step size (constant for a given stage) and the current XYZ field position in steps.

Field XYZ Steps

These values are the number of steps to move the automatic stage controller between successive fields of view for analysis, as specified in the CUSTOM RS232 menu for the XYZ stage controller.

• Field X Steps (FLD_X_STEPS) - first transverse axis motion
• Field Y Steps (FLD_Y_STEPS) - second transverse axis motion
• Field Z Steps (FLD_Z_STEPS) - vertical axis motion

Field Wavelength Transmission (FLD_Wavelength Transmission)

The wavelength at which a tunable filter was programmed when the field was captured. It is possible to run a wavelength scan through using a tunable filter to create spectral response data measurements. This parameter provides the peak wavelength value for the current field in nanometers.

Field Wave Steps Wavelength (FLD_Wave_Steps Wavelength)

The step or increment between fields in Nanometers. This is applicable when scanning the wavelength range of a tunable filter to create spectral response data measurements

Region Of Interest (ROI) XY Origin

These coordinates define the origin of the Measurement ROI within the full image. This enables the ROI size and position to be part of an expression defined in Custom measurements. For ROI shapes that are not rectangular, these coordinates are from the top left corner of the bounding box that confines the ROI shape.

• ROI X Origin - the horizontal coordinate of origin
• ROI Y Origin - the vertical coordinate of origin

Region Of Interest (ROI) Size

For ROI shapes that are not rectangular, these dimensions are from the top left corner to the bottom right corner of the bounding box that confines the ROI shape.

• Width - the horizontal size in pixels that the measurement ROI projects in the image
• Height - the vertical size in pixels that the measurement ROI projects in the image

Note: The ROI X and Y Origin coordinates coupled with the ROI Width and Height can be used in Qualify to create to exclude objects on the basis of their position in an image. A wide variety of rules can be implemented to exclude objects using the object position information of any coordinate from the object's bounding box. This can be used to create a guard region to avoid measuring truncated objects or measuring objects twice. Using this method objects can be deleted if they touch any of the ROI borders. The use of a guard region is supported by using Edge Removal options as described in the Qualify Menu; however, the use of these ROI parameters in custom measurements increases the flexibility for applying rejection rules to edge objects. Such rejection rules can be based on comparing an object's centroid coordinates, COFG coordinates, or extreme coordinates against the field's ROI values.