Aivia Software
How to add measurements to analysis results
- Hoyin Lai
- Aiden Maloney-Bertelli (Unlicensed)
You can add additional measurements to your analysis results (from applying a recipe or using other tools to generate objects) for further object characterization using the Measurement Tool. The tool contains a number of pre-defined measurements and allows you to add custom Advanced Measurements.
Launch the Measurement Tool
The Measurement Tool can be opened from the Spreadsheet tab in the Contents Panel at the bottom of the Aivia window. Click on the Measurement Tool icon (see below) to launch the Measurements window. While the window is active, you cannot interact with the main Aivia GUI.
Add pre-defined, general measurements
Aivia provides a plethora of pre-defined measurements depending on the objects that are available on the loaded image. Refer to the Measurement Definitions page for which measurements are available for which object types along with measurement definitions.
In the General tab of the Measurements window, first select the object set you would like to add measurements for using the Group and Set menus. Then, check the boxes for the measurements you would like to add. You may use the search bar to search for measurements or use the Morphology, Intensity, Position, and Count filter buttons to narrow down the measurement list. There are also Toggle All and Toggle Shown buttons that toggle whether the measurement checkboxes for all object groups and sets on the current image or all measurement checkboxes currently shown in the Measurements window are checked respectively. Once you have selected the desired measurements, click Finish to initiate calculation of the specified measurements; there is a progress bar for measurement calculation in the lower-right corner of the Aivia window. After calculation finishes, the selected measurements can be reviewed in the Spreadsheet tab or the Charts panel.
Intensity measurements include the measured channel in parentheses in their names; e.g., "Mean Intensity (GFP)."
Rename measurements
To rename a measurement listed in the General tab of the Measurements window, first double click on the measurement name. In the dialog that opens, edit the measurement name in the Name textbox. Click Finish to update the measurement name or Cancel to cancel any edits to the measurement name.
Add colocalization measurements
Colocalization measurements characterize the correlation between two image channels based on segmented regions (i.e., objects). You can add colocalization measurements in the Colocal tab of the Measurements window (see below).
First, specify the object sets and their associated channels to measure colocalization for in the Set 1, Ch 1, Set 2, and Ch 2 menus. Then, specify the desired measurements using the three levels of checkboxes; there must be at least one box checked on each level. The levels are as follows:
Level 1: Specify whether to measure over the regions where the objects in Set 1 and the objects in Set 2 intersect (Intersection) or measure over the full regions covered by the objects in Set 1 (Full Object).
Level 2: Specify whether to measure the Pearson's Correlation Coefficient (Pearsons), Manders' Overlap Coefficient (Manders), or Manders Overlap TM1/TM2.
Level 3: Specify whether to group all objects together for the measurement (Whole Image) or measure by individual object (Per Object).
Click Add to add the measurement(s) specified using the checkboxes, set menus, and channel menus to the list of colocalization measurements. Then, click Finish to initiate calculation of the specified measurements; there is a progress bar for measurement calculation in the lower-right corner of the Aivia window. After calculation finishes, the measurements can be reviewed in the Spreadsheet tab or the Charts panel.
Add custom, advanced measurements
Many custom measurements can be defined in the Advanced tab of the Measurements window (see below).
To add an Advanced Measurement, first type the name of the measurement into the Name textbox and specify the object set to measure in the Set menu. Then, type the measurement expression into the Expression field. You may insert another measurement into your expression by selecting the measurement in the Measurement menu and then clicking Insert. There are also several Advanced Measurement Functions available to use in your expression. Once you have set the measurement name, object set, and expression, click Add to add the measurement to the table of advanced measurements and click Finish to initiate calculation of the measurement. After calculation finishes, the measurement can be reviewed in the Spreadsheet tab or the Charts panel.
Please see the Advanced Measurements page for more information about adding and editing Advanced Measurements.