Aivia Software

Phenotyper

Owned by Nikitha.Kanumuri
Last updated: Jun 21, 2024 by Holger Fehlauer
5 min read

The Phenotyper is one type of object classifier that is introduced in Aivia 13. This is a more flexible varation of the User-guided object classifier. It allows you to create multiple Phenotypes based on intensity/morphological/spatial measurements. The Phenotyper uses a random forest algorithm to identify unique features (i.e. measurements) for classification.

This view can be accessed by selecting Object Classifier option in Layout options.


PhenotyperAccess

On this page:



Interface


The Phenotyper View has two sections: the image viewer on the left and the gallery on the right. Controls for the tool are found in the gallery section.



Phenotyper Interface

Phenotyper View 



Toolbar

The Classifier View toolbar is located at the top of the gallery on the right side of the Classifier View. The toolbar allows you to perform file actions related to the Phenotyper, such as selection, creation, and saving.


Phenotype ToolBar



The function for each item in the toolbar is summarized in the table below:
FunctionIconDescription

Classifier


The dropdown menu lets you select a loaded classifier to apply to your data.
Create New Classifier
This option allows you to create a new, blank pixel classifier for teaching.
Delete

This option removes the selected classifier from Aivia. This will not delete the selected classifier from its file.
Load

This option allows the user to load a pre-trained classifier (.classifier) from a file into Aivia.
Save

This option allows the user to save the current classifier to a file.
Export Classifier Data to CSV

This option allows the user to export the classifier data (trained objects and measurements) to an Excel-readable comma-separated value (CSV) file.
Reload Classifier

This option reloads the current classifier to its previously saved state, discarding any changes made to the classifier.
Toggle Multi-Selection

This option turns on the multi-selection cursor, allowing you to select multiple objects by clicking on each object in the gallery separately without holding down the Shift or Ctrl key on your keyboard.



The gallery shows a thumbnail of all objects on the image as well as the thumbnails of any objects that are taught during the current session. The gallery separates the thumbnails by phenotypes indicated by a colored header. Each Phenotype header has measurement and exclusivity selection. Standard measurements refer to channel mean intensity measurements and custom measurements refer to different morphological/spatial/intensity measurements. By toggling the exclusivity button PhenotypeExclusive, negative class is added/removed for the phenotype.

You can expand/collapse each phenotype separately. In the collapsed view, a generic icon (on the right) indicates the number of additional thumbnails/objects that are in the class. Clicking on the generic icon will fully expand the current class and collapse all others.


Phenotype Gallery

Phenotyper bar

The Phenotyper bar is located at the bottom of the gallery and provides a number of actions for teaching and applying the classifier on the image. + and - buttons add and remove phenotypes respectively whereas Assign objects is a drop-down menu button that is helpful in assigning selected objects to a phenotype in the list.




General usage

Apply a phenotyper

To apply a phenotyper, select the phenotyper to run from the Classifier dropdown menu and click the Apply button in the lower-right corner of the gallery. If the data has existing phenotype, applying a phenotyper will remove the existing classifications and create new ones. On apply, the phenotyper will look at each object and assign a phenotype. 

You can also view the objects by Phenotype in the Spreadsheet panel as subsets.










Create a new Phenotyper 

You will need to have analysis results, such as outlines and surfaces, to use Phenotyper View. You can generate results using one of the recipes or through manual editing. Tracks are currently not supported.

You can create a new Phenotyper from scratch by clicking on the Create New Classifier  button in the Classifier View toolbar. You will be prompted to enter a name, specify the Classification type as Phenotyper and object type (see right). If channel groups are available, these may by imported automatically - then phenotypes are created for each channel group, each having their channel intensity measurements selected as default. The general workflow for creating a classifier from scratch is as follows:

  1. Select the object type you wish to analyze using the Phenotyper View.

  2. Create phenotypes as needed for the Phenotyper.
  3. Select measurements and classes of objects (positive/negative) as needed for identifying each phenotype.
  4. Teach the classifier by selecting a few representative objects from each category and adding them to the relevant Phenotype gallery; click Teach when you have provided examples from each Phenotype.
  5. Update the classifier as needed by adding additional object examples.
  6. Apply the classifier to the image.

NOTE: Adding objects to relevant Phenotype can done in two ways.

  1. Using the assign objects button in Phenotyper bar.
  2. Select the objects on the image and right click to see to "Assign Objects to" Menu option.