Imaris Learning: Measurement Points | Tutorial

Measurement Points

Tutorial

featured

November 2013

 

This how-to section describes how to measure distances and angles between arbitrary locations within your image using Imaris Measurement Points

Within the MeasurementPro module, Imaris offers tools for making quick manual measurements directly on your 3D image. The distance and angles between arbitrary locations can be easily obtained by interactively specifying the measurement point’s positions. Measurement points can be placed anywhere within your 3D volume data, either on Surpass objects (Spots, Surfaces, Cell, Filaments, Ortho and Oblique Slicers) or in the volume rendered image structures of interest.

Even without creating an object, you can start measurement in the volume rendered image. Start a new set of measurements by adding a Measurement Points object to your current Surpass Scene.

Under the Edit tab, four options enable you interactively to place measurement points at the required locations.

To start inserting measurement points the pointer must be in the Select mode. The size of the 3D curser box can be adjusted with the mouse wheel.

The first two options, All visible channels and Specific channel, are relevant if you want to perform measurements in a volume rendered image.

The All-visible channel option places a point at the cursor position while the depth through the volume is determined by the most intense voxel of all the channels. Add a new point by holding down the Shift key and clicking the left mouse button at the location of your choice. After placing a second point, a line connecting the two points is created and the measured distance between two non segmented structures of interest is displayed. Add another point and for each pair of adjacent points, the angle between their common point is computed and displayed next to the angle arc.

For multichannel images placing points at the correct depth within a 3D image could be a challenging task. You can either control which channels are visible in the viewing area by selecting or de-selecting channels in the Display Adjustments window or select the Specific channel option. By selecting the Specific channel option, a new measurement point is placed at the most intense voxel of the selected channel, even if that channel is overlaid with other channels of higher intensity.

When measuring previously segmented objects, you can choose between two options: Surface of Object or at Center of Object.

If the Center of Object option is selected, the point placement depends on the type of created object. Points are set at the center of the sphere for Spots and Vesicles, or at the center of the homogeneous mass for Surfaces Cells and Nuclei. For Dendrites and Spines objects, points are placed at the dendrite/spine center axis.


Once measurement points are placed, you can modify their position. To do so change the position of the point, you should first select the point and then move it using Shift + left mouse click. Alternatively, the point’s position can be interactively adjusted by entering a numerical value in the X, Y, or Z field. Under the Edit tab, you can also alter the name of a point or delete a single point.

To change how points are displayed and to customize the given information, use the options found under the Settings tab.

The Line Mode defines how inserted points are connected. There are two options: Polygon and Pairs. The Polygon option connects all points in succession. Select the Pairs option to connect only two consecutive points and the angle measurements are disabled.

You can choose between three different shapes of points: Tetrahedron, Cube or Sphere. In addition, you can adjust points’ diameter, line width, font and colour of labels.

By selecting the Intensity box, intensity values for all channels are displayed at each point. More information about intensity can be found under the Intensity tab.

For all connected points, the intensity profiles of each voxel along the measurement line are displayed in the Histogram. The x-axis of the histogram represents the length of the line while the channels intensity is displayed on the left-hand side. Below the histogram, you can find the channels and lines selection. Select the channels and lines to be displayed and the histogram updates accordingly.

Select the Statistics tab and the summarized numerical information is shown. The Overall table lists the total number of points. Under the Detailed tab, the pull down list displays the available statistical variables. You can select to display angle, distance, position or intensity data. As for other statistic values in Imaris, all values can be exported to Excel

If you have questions about these or any other features found in Imaris, please contact our Sales or Support team.

Sign up for the Bitplane Newsletter!

Receive articles like this one, release notes, product launches, press releases and more with our regular newsletter. It's free to subscribe, will be sent every 6 weeks, and you can opt out at any time.

NAME
EMAIL


Try Imaris FREE for 10 days?