Module: ClassifyObjects

Classify Objects classifies objects into different classes according to the value of measurements you choose.
This module classifies objects into a number of different bins according to the value of a measurement (e.g., by size, intensity, shape). It reports how many objects fall into each class as well as the percentage of objects that fall into each class. The module asks you to select the measurement feature to be used to classify your objects and specify the bins to use. It also requires you to have run a measurement or CalculateMath previous to this module in the pipeline so that the measurement values can be used to classify the objects.

There are two flavors of classification:

Note that objects without a measurement are not counted as belonging in a classification bin and will not show up in the output image (shown in the module display window); in the object classification they will have a value of False for all bins. However, they are still counted in the total number of objects and hence are reflected in the classification percentages.

Available measurements

See also CalculateMath and any of the modules in the Measure category.

Settings:

Make each classification decision on how many measurements?

This setting controls how many measurements are used to make a classifications decision for each object:

Select the object to be classified

The name of the objects to be classified. You can choose from objects created by any previous module. See IdentifyPrimaryObjects, IdentifySecondaryObjects, or IdentifyTertiaryObjects.

Select the measurement to classify by

Select a measurement made by a previous module. The objects will be classified according to their values for this measurement.

Select bin spacing

You can either specify bins of equal size, bounded by upper and lower limits, or you can specify custom values that define the edges of each bin with a threshold. Note: If you would like two bins, choose Custom-defined bins and then provide a single threshold when asked. Evenly spaced bins creates the indicated number of bins at evenly spaced intervals between the low and high threshold. You also have the option to create bins for objects that fall below or above the low and high threhsold

Number of bins

This is the number of bins that will be created between the low and high threshold

Lower threshold

(Used only if Evenly spaced bins selected)
This is the threshold that separates the lowest bin from the others. The lower threshold, upper threshold, and number of bins define the thresholds of bins between the lowest and highest.

Use a bin for objects below the threshold?

Select Yes if you want to create a bin for objects whose values fall below the low threshold. Select No if you do not want a bin for these objects.

Upper threshold

(Used only if Evenly spaced bins selected)
This is the threshold that separates the last bin from the others. Note: If you would like two bins, choose Custom-defined bins.

Use a bin for objects above the threshold?

Select Yes if you want to create a bin for objects whose values are above the high threshold.
Select No if you do not want a bin for these objects.

Enter the custom thresholds separating the values between bins

(Used only if Custom thresholds selected)
This setting establishes the threshold values for the bins. You should enter one threshold between each bin, separating thresholds with commas (for example, 0.3, 1.5, 2.1 for four bins). The module will create one more bin than there are thresholds.

Give each bin a name?

Select Yes to assign custom names to bins you have specified.

Select No for the module to automatically assign names based on the measurements and the bin number.

Enter the bin names separated by commas

(Used only if Give each bin a name? is checked)
Enter names for each of the bins, separated by commas. An example including three bins might be First,Second,Third.

Retain an image of the classified objects?

Select Yes to keep an image of the objects which is color-coded according to their classification, for use later in the pipeline (for example, to be saved by a SaveImages module).

Name the output image

Enter the name to be given to the classified object image.

Select the object name

Choose the object that you want to measure from the list. This should be an object created by a previous module such as IdentifyPrimaryObjects, IdentifySecondaryObjects, or IdentifyTertiaryObjects.

Select the first measurement

Choose a measurement made on the above object. This is the first of two measurements that will be contrasted together. The measurement should be one made on the object in a prior module.

Method to select the cutoff

Objects are classified as being above or below a cutoff value for a measurement. You can set this cutoff threshold in one of three ways:

Enter the cutoff value

This is the cutoff value separating objects in the two classes.

Select the second measurement

Select a measurement made on the above object. This is the second of two measurements that will be contrasted together. The measurement should be one made on the object in a prior module.

Method to select the cutoff

Objects are classified as being above or below a cutoff value for a measurement. You can set this cutoff threshold in one of three ways:

Use custom names for the bins?

Select Yes if you want to specify the names of each bin measurement.
Select No to create names based on the measurements. For instance, for "Intensity_MeanIntensity_Green" and "Intensity_TotalIntensity_Blue", the module generates measurements such as "Classify_Intensity_MeanIntensity_Green_High_Intensity_TotalIntensity_Low".

Enter the low-low bin name

(Used only if using a pair of measurements)
Name of the measurement for objects that fall below the threshold for both measurements.

Enter the low-high bin name

(Used only if using a pair of measurements)
Name of the measurement for objects whose first measurement is below threshold and whose second measurement is above threshold.

Enter the high-low bin name

(Used only if using a pair of measurements)
Name of the measurement for objects whose first measurement is above threshold and whose second measurement is below threshold.

Enter the high-high bin name

(Used only if using a pair of measurements)
Name of the measurement for objects that are above the threshold for both measurements.

Retain an image of the classified objects?

Select Yes to retain the image of the objects color-coded according to their classification, for use later in the pipeline (for example, to be saved by a SaveImages module).

Enter the image name

(Used only if the classified object image is to be retained for later use in the pipeline)
Enter the name to be given to the classified object image.