Aivia Software
Annotations
The Annotations tool provides a small set of tools designed to help you measure your image while you are in the 2D view. You can access a set of manual drawing tools for defining regions and lines on the image. The Annotations tool will measure the dimension of the drawn shape along with its intensity (if available).
Interface
The Annotations tool is one of the six tabs that are found in the Content panel on the bottom of the Aivia window. The Annotations tool interface is shown below.
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Annotations GUI |
There are two sections, the data table and the intensity profiler, highlighted in red and blue above respectively. Each section has its own toolbar that controls the functions related to the given section.
On this page:
Data table
The data table contains the measurement data of all manual annotations on the image. Each column represents a different measurement while each row represents a different annotation region. The data table toolbar contains a number of tools and options for interacting with the data table. The toolbar is shown below:
Description and function for each tool are summarized in the table below:
Name | Icon | Description |
|---|---|---|
Line tool | | Toggles the straight line tool for measuring distance between two points |
Freehand region tool | | Toggles the freehand region tool for measuring the area and dimension of a drawn region |
Rectangular ROI tool | | Toggles the rectangular ROI tool for measuring the area and dimension of a drawn rectangle |
Angle tool | | Toggles the angle measurement tool for measuring the angle between two drawn segments |
Copy selected data | | Copies the selected row in the data table to the clipboard |
Annotation options | | Toggles the Annotations options pop-up |
Display filter | | Filters the data table display by annotation type |
Intensity profiler
Line
When you create a manual annotation using the Line tool, the Intensity Profiler section will become active and plot the intensity value on the image along the line of the first selected channel of the image.
Area (Freehand region or ROI (rectangle))
When you create a manual annotation using the Freehand region or ROI (rectangle) tool, the Intensity Profiler section will become active and plot a Histogram or (if the image is a 3D or time series) a stack profile of the intensity values on the image within the area of the first selected channel of the image.
The toolbar for the intensity profiler is shown below:
The function for each item is summarized in the table below:
Name | Icon | Description |
|---|---|---|
Export chart image | | Saves the displayed intensity profiler chart as a snapshot image. |
Copy chart image to clipboard | | Copies the displayed intensity profiler chart as a snapshot image to the clipboard. |
Export chart data | | Exports the intensity profiler data to an Excel spreadsheet. |
Switch Histogram / Stack profile (3D or time series only) | | Switches between histogram and stack profile if stack profile is available (3D or time series only). |
Logarithmical scale (Histogram only) | | Plots counts (y-axis) of histogram logarithmically to enhance visibility of smaller counts (Histogram only). |
Using annotations
To launch the Annotation tool, click on the Annotations button below the image panel in Aivia. This will open the Annotations tool interface.