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Masking Properties of Imaris

In this How to section, you will learn how to segment and analyse an arbitrarily shaped region of interest (ROI). You will learn how to define such a ROI by generating a surface object from manually created contours. This method can be helpful in visualization and measurement of structures, which cannot be easily segmented from the background or neighbouring structures.

Creation of Arbitrarily Shaped ROI

To start the creation of arbitrarily shaped ROI, you have to cancel the automatic Surface creation wizard. You can do that either by clicking on the Cancel button or by selecting the Skip automatic creation, go to manual editing button.

The creation wizard is halted and the Draw Tab is automatically opened. In the viewing area, a drawing plane is displayed. To provide an unobstructed slice view, switch off the Volume rendering.

Under the Board tabs, adjust the Orientation and Visibility and select the initial ROI Slice position. Under the Mode tab, several drawing mode tools are provided.

Select the Click mode 

Starts the process of creating a arbitrarily shaped ROI, click within the image and insert the first point. Each new click creates a connected line to the previous point. To finish, move the cursor to the initial point and click.

On the plane where ROI ends, either you can draw an individual contour adjusted to your sample or you can copy the contour from the previous slice. If you want to copy the same shape to the selected plane switch to the Board tab and click on the Copy button. Change to the required plane and click on the Paste button.

When you are satisfied with the ROI defining contours, click on the Create Surface button  to create a surface between the previously drawn regions.

Mask Channel

To apply a certain function not on the entire image but only in a region of interest (ROI) you will use the Mask Channel option. In the Surpass tree, select the Surfaces object and click on the Edit tab  and under the Mask Properties select Mask button.

A new mask window appears and there you can select the channel that you want to mask.

Select the channel you want to mask. Before applying mask, check the Duplicate Channel box and an additional masking channel is automatically displayed in the Display Adjustments window. Select Constant inside/outside option and check the box Set voxels outside surface to zero. As a result, voxels outside the ROI are not displayed. Click on the button OK to apply the mask.

In the Display Adjustment Window a new channel is created. To see the result, turn off all original channels and in the viewing area only newly created channel is displayed that only shows signal within the created ROI.

Volume and other relevant statistical information about random shape ROI could be found under the Statistical tab  of the Surfaces object.

ROI Segmentation and Analysis

Now you can start segmentation and focus your analysis on a specific ROI within your image. Select the object type you want to create and follow the creation wizard paying attention to the following: the source channels is not the original channel but newly created masked channel

Once the signal in the masked channel is segmented, various biologically relevant statistical data obtained from the arbitrarily shaped ROI can be found in the Statistics tab where advanced filtering and further data extraction can be performed.

For more information about manual surface creation, please visit our web site at

Date: October 2013

Category: How-to Guides


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