Pixel Classifier

The Pixel Classifier is an image enhancement tool that enhances specific features on an image based on user-input teaching patterns. A number of image transformations are applied to the user-defined teaching regions (and their respective adjacent pixels) internally to identify unique features (such as edges or speckles) for classification.

Interface

The Pixel Classifier is a tab in the Analysis Panel, which is pinned and found on the right side of the Aivia window by default. When you launch the Pixel Classifier, the tool selects the most recently used classifier or starts a new classifier with two (2) predefined classes to help you get started right away.

The main Pixel Classifier GUI is shown below. There are five (5) sections in the Pixel Classifier interface:

• The Classifier Toolbar along the top of the GUI allows you to perform file actions related to the Pixel Classifier.

• The Input & Training section allows you to specify the image channel(s) to use for training and applying the classifier.

• The Drawing section lets you select a tool for defining training regions in the Image Panel.

• The Classifier section lets you select the pixel class to teach as well as specify output options.

• The Apply Controls along the bottom of the GUI allow you to preview, teach, or apply a classifier and specify regions of interest (ROIs) for previewing and applying.
  
  

Open

Input & Training

The Input & Training section lets you select the image channel(s) to use for training when creating a new pixel classifier or to specify the image channel(s) to use as input for applying a previously trained and finalized (saved as a .pxclassifier file) pixel classifier. During training, the teaching images are automatically set as the input images. 

You may specify the number of channels to use as inputs for the classifier as well as the names of the channel inputs in the Input Definitions column. The table below describes the options available in the Input Definitions column.

In the Training Channels column, you may use the dropdown menu(s) to select which channel(s) on the current image to use as which input(s) for training the pixel classifier.

The Manage Training Set button opens a window with options for saving the annotations for the individual images in the training set as well as removing images from the training set. See the "Train a pixel classifier over multiple sessions" section of this page for more details about saving training data.

Only the Input section is displayed when you are applying a previously trained and finalized pixel classifier to an image. You may use the dropdown menu(s) to select which image channel(s) on the current image to provide as which input(s) to the classifier.

Select a location on the image for the Magic Wand to search from. A preview of the region to be painted is shown in blue (see right). Adjust the Sensitivity slider (or use hotkeys W and R) to change the tolerance for intensity differences. The narrowest range of accepted intensity levels is used when the slider is all the way to the left. Adjust the Search Range slider (or use Ctrl + Shift + Mouse Scroll over the Image Panel) to increase or decrease the area over which the Magic Wand will search. No pixels outside of the search region are included in the painted region. The search range is indicated by the green box around the cursor when the Magic Wand is used (see right). Check the Fill Multiple Z Frames box to extend the user-defined search range limits in the z-direction; when this box is not checked, the Magic Wand only searches on the current z-frame. Finally, click on Paint (or press E) to paint the region and assign it to the selected class.

With the Magic Wand in 3D View, click on the image to show a surface preview. You may adjust the search range using either the Search Range slider or the Ctrl + Shift + Mouse Scroll hotkey combination. To adjust the range of intensities included in the region, adjust the LUT of the channel being used for the Magic Wand and click again on the image. Regions do not have to be connected to be painted and assigned to the selected class when the Magic Wand is used in 3D. The Magic Wand paints to two (2) classes: one (1) is the selected class, and the other is what is presumed to be the background class. This means that the total search volume is painted. When you click on Paint, a yellow frame around the painted region appears in 3D View. Return to Main View (2D) to closely examine the resulting annotations.

Classifier section

The Classifier section is the primary space for interacting with individual pixel classes in the Pixel Classifier. To begin training a pixel class, select the class's row prior to drawing the regions in the Image Viewer. The Classifier section also lets you specify the output type and options for each pixel class and add additional training features.

To edit the name of the classifier, double-click on the classifier name above the "[s]elect pixel class" text and then edit the text.

The function and description for each item in the Classifier section are summarized in the table below.

Advanced Options

The Advanced Options menu lets the user specify the image features to use for creating the pixel classifier. Click on a feature name in the table to add the feature to the list; features with the GPU-Computed symbol (see below) can be processed on a GPU. 

Additionally, Aivia provides three (3) preset groups of features:

• Clear deselects all features; you will not be able to teach the Pixel Classifier until at least one (1) feature is selected.

• Standard includes the default features that are used in the Pixel Classifier.

• Line includes specialized features designed to highlight fine, line-like features.

The Kernel Size option lets you choose Small (micro), Medium, and/or Large (macro) kernels for applying the image feature transformations. Smaller kernels are more attuned to highly localized features, while larger kernels are more accurate for detecting major image features.

Specify regions of interest

Click on the ROI Processing Options icon to open the Regions Of Interest Table (see right). When the ROI Processing Options icon appears as nested squares, a ROI is selected. Check the box in an ROI's row of the Regions Of Interest Table to select it for previewing and/or applying. Use the topmost checkbox, which is in the header row, to (de)select all ROIs. See the Regions of Interest page for more information about using ROIs.

Teach

The Teach button creates a pixel classifier using the drawn training regions for all training images and the feature calculation from those regions. An asterisk to the left of the Teach button indicates that changes have been made to the pixel classifier since it was last taught. At least two (2) classes must have training regions and at least one (1) feature must be selected before a pixel classifier can be taught.

Apply

The Apply button applies the taught pixel classifier to the selected ROIs or, if no ROIs are selected, the whole image. You can choose to apply to the whole image sequence (over all of T and Z), just the current t-frame, or just the current t- and z-frame (except if you are creating 3D objects).

The downward-pointing triangle to the right of the Apply button provides additional options for generating pixel classifier output. Select one (1) of the output options from the dropdown menu to apply the pixel classifier. There are four (4) apply options:

• Apply applies the pixel classifier to the entire image sequence (over all of T and Z).

• Apply to the current time frame applies the pixel classifier to the current t-frame.

• Apply to the current time and depth frame applies the pixel classifier to the currently displayed t- and z-frame only.

• Batch apply the classifier opens a window where you can specify a collection of images to apply the pixel classifier to as well as an output folder for the results.

ROI Processing Options icon (bottom right) and Regions Of Interest (ROI) Table

Train a pixel classifier over multiple sessions

There are two (2) types of files that you can save and load back into Aivia for training at a later date: annotation files (.pxannotations) and training set files (.pxtraining). 

Annotation files

Annotation files contain the drawn teaching regions for an image. To save annotations for the displayed image and current classifier, click on the downward-pointing triangle next to the Save icon in the Classifier Toolbar and then select Save Annotations for the current image (see right); this opens a window where you may specify the location and name for the .pxannotations file. Another option is to click on the Manage Training Set button and then on the Save icon for the image in the training set whose annotations you would like to save; note that this method allows you to save annotations for an image in the training set that is not currently displayed in the Image Viewer.

It is assumed that when annotations are loaded, the image that they are from and the classifier that was being trained (with the same number of classes, class names, etc.) are already open and displayed. To load annotations, click on the Load icon in the Classifier Toolbar, navigate to the .pxannotations file, and then click on Open. The previously drawn teaching regions are then displayed and may be edited and used for previewing, training, and applying pixel classifiers.

Training set files

Training set files include the following:

• Paths to all images in the training set

• Drawn teaching regions (annotations) for all images in the training set

• Classifier settings

• The taught classifier, if the training set was saved with a taught pixel classifier

To save a training set file, click on the downward-pointing triangle next to the Save icon in the Classifier Toolbar and select Save Training Set; this opens a window where you may specify the location and name for the .pxtraining file. Another option is to not only save the .pxtraining file but also copy the images in the training set to another location. To do this, click on the downward-pointing triangle next to the Save icon in the Classifier Toolbar, select the Copy all the training fields and training data to one spot option, navigate to the folder where you would like to copy the training images and .pxtraining file to, and then click on Select Folder.

To load a training set, click on the Load icon in the Classifier Toolbar, navigate to the .pxtraining file, and then click on Open or drag and drop the .pxtraining file onto the Pixel Classifier interface; this will load all of the images in the training set into the workspace as well as load the previously drawn training regions and classifier settings for the in-progress pixel classifier. You may then continue drawing teaching regions, adding images to the training set, and otherwise building upon and/or using your pixel classifier.