7 Measuring With OMERO

The OMERO.insight client has tools to help you measure regions and distance in your images. This is done using the Measurement Tool in the image viewer.

7.1 Regions of Interest (ROIs)

Select an image in the workspace panel as shown below.

Double click on the image to bring up the image viewer.

In the image viewer toolbar click the icon to bring up the Measurement Tool.

• Select an image in the workspace
• Open it with the image viewer
• Open the ROI tool

7.1.1 Creating ROIs

To create an ROI you can use the toolbar shown below to select what type of ROI is to be created.

• rectangle
• circle
• point
• line
• polygon
• text

To create an ROI, first click on the ROI type you wish to create such as the rectangle icon, then click on the image viewer and drag the shape to the desired size.
Once a ROI is created it can be manipulated by first clicking on the arrow icon. Depending on the shape it can be moved, resized or rotated. Double clicking on a line will split it into two segments creating a polyline, this can be repeated to create as many segments as needed. The nodes on the line can be moved around to the required shape. Double clicking inside a shape will allow you to enter a text label.

• Create a few ROIs in your image
• Move and resize an ROI
• Create a line and then split it into a polyline with several segments
• Add a text label to one of your shapes.

7.1.2 ROI Manager

Once ROIs are created, these appear in the ROI manager tab. The ROI manager tab is the default view of the ROI tool. Using the manager tab it is possible to select the individual ROIs. The visibility check box also allows you to toggle the visibility of the ROI in the image viewer.

• Create 3 different ROIs
• Select the first ROI using the list in manager tab
• Toggle the visibility of the second ROI

By right clicking on one of the ROIs in the manager tab it is possible to bring up the ROI manager options menu shown below:

This menu lets you duplicate, merge, split, propagate and delete individual ROIs.

Exercise 4

• Try to duplicate an ROI
• Try deleting an ROI
• One of the most useful options in the propagate option. Selecting this option will bring up the ROI assistant tool as shown below.

The ROI assistant is useful to propagate ROIs through the Z and T dimensions. To propagate the ROI a click, drag and release procedure is following. Click and hold the ROI drag it to the desired Z/T value, and release to apply the propagation.

• Select an ROI in the Manager.
• Right click on the ROI to bring up the manager options
• Click on Propagate to bring up the ROI assistant.
• Propagate the ROI over the whole Z stack.
• Propagating the ROI will result in an update in the ROI manager. The ROI manager will now display the propagated ROIs in the same tree branch as the original ROI, as shown below:

7.1.3 ROI Inspector

The ROI inspector is accessed by clicking on the inspector tab. Clicking on the tab will bring up the following panel:

The inspector panel allows you to edit various properties of the ROI.

• Disable the show text
• Enable the show measurements
• Change the fill colour for the ROI

7.1.4 ROI Results

The ROI results are accessed by clicking on the results tab. Clicking on the tab will bring up the following panel:

This panel contains the various geometrical properties for the ROI.

• Draw a rectangle ROI
• Find the area of the rectangle area in the results tab

7.1.5 ROI Graph Pane

The graph pane panel will display the histogram for the selected ROI.

• Select an ROI in the manager tab
• View the graph pane to see the histogram
• Disable a channel in the image viewer and view the histogram updated for a single channel

7.1.6 ROI Intensity View

The ROI intensity view is accessed by clicking on the intensity view tab. Clicking on the tab will bring up the following panel:

This panel displays various statistics about the intensity values contained in an ROI.

• Select an ROI in the manager tab
• Locate the mean and standard deviation of intensity values for channel 1.