You can add additional measurements to your analysis results (from recipe apply or manual edit) for additional object characterization using the Measurement Tool. The tool contains a number of pre-defined measurements and can be extended through the advanced measurements tab.
Launch measurement tool
The Measurement Tool can be found in the Spreadsheet tab in the Content panel at the bottom of the Aivia window. Clicking on the Measurement Tool 
icon will launch a new modal window for selecting additional measurements on the current image. While the window is active, you will not be able to interact with the main GUI of Aivia.
Understand the measurement types
Aivia provides a plethora of measurement options depending on the objects that are available on the loaded image. You can find the measurement options that are available to you on the tabs at the top of the measurement dialog. Each measurement type correspond to a different type of analysis or different type of object.
There are twelve (12) types of measurements in Aivia:
| Measurement Type | Description |
|---|---|
| Objects | Morphological and intensity measurements for individual 2D object outlines |
| Whole Image Mask | Morphological and intensity measurements for 2D object outlines on the whole image as a single object |
| Tracks | Trajectory measurements, by individual time point as well as the whole trajectory, for each track objects |
| Lineage | Measurements for lineage trees of tracked objects |
| Mesh | Morphological and intensity measurements for individual 3D object surfaces |
| Neuron | Morphological measurements specifically for 3D neuron-type objects |
| Soma | Morphological measurements specifically for 3D soma-type objects |
| Dendrite | Morphological measurements specifically for 3D dendrite-type objects |
| Spine | Morphological measurements specifically for 3D spine-type objects, including spine head and spine neck subsets |
| Relations | Measurements for characterizing the relationship between two object sets |
| Colocalization | Measurements for characterizing the correlation between two image channels based on segmented regions (i.e. objects) |
| Advanced | Custom-defined measurements not included in the standard measurement types; please refer to the Advanced Measurement documentation for more information |
On this page:
Select measurements
You can select a specific measurement by first navigating to the tab of the measurement type you would like to measure. Click on the checkbox next to the measurement description to select or deselect the measurement. You can also select/deselect all the measurements of a given type by clicking on the Select All or Deselect All button.
|
| Measurement tabs and selection buttons |
Measure another object set
When you have multiple object sets on your image, it is possible to specify the measurements to generate for each object set separately. First, click on the Object Set selection dropdown menu and select a different object set. The main measurement selection table will refresh to show the measurements that are selected for the given object set. Select the desired measurements from the table.
Measure on another channel
Certain object types (objects, whole image masks and meshes) allow you to specify the image channel to measure the intensity on. Recipe apply will measure the channel intensity of the input channel for the detected objects by default. Click on the Channel selection dropdown menu above the intensity measurement table and select a different channel. The intensity measurement table will refresh to show the selected intensity measurements for the given object set and the selected image channel. Select the desired measurements from the table.
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| Object set and channel selection dropdown menus |
