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Taking Measurements

To access the measurement mode of the program click on the measurement tool located in the tool panel Measure Tool or select Edit >> Mode >> Measure from the main menu.

TIP: Pressing the M key will switch to this mode as well.

While in this mode you may click on a structure in the 2D or 3D window to compute its width. You may also click and drag in the 2D window to measure a length as well. The values of the measurements are displayed on the status bar at the bottom of the main window. NeuronStudio will try to determine the optimal 3D position within the data from the mouse position. The width measurement is always taken in the XY direction (perpendicular to the optical (Z) axis of the microscope). In addition, the measurement is re-centered after the width is calculated.

  • Hold down the Ctrl key while clicking to over-write the last measurement.
  • Use the Up and Down (arrow) keys to change the position of a measurement.
  • Use the Left and Right (arrow) keys to change the angle of a measurement.

TIP: Only measurements that have a length greater than zero (by clicking and dragging) can be repositioned and/or rotated.

If the slice viewer is active, creating a measurement while viewing from the forward (along the optical axis) direction will force the Z coordinate of the measurement to be placed at the Z position of the current slice.

Note that if the location of your mouse click falls outside the boundaries of the region of interest, then no new measurement will be created.

Example: (no length)

1) Identify a structure to be measured.

Measure Example 1 Image 1

2) Left click over the structure to take a measurement (width). Note how the measurement has been re-centered.

Measure Example 1 Image 2

Look at the status bar at the bottom of the main window to view or record the measurement(s). Note that these values can later be saved to a file.

TIP: You should try to aim for the center of the structure when clicking.

Example: (with length)

1) Identify a structure to be measured. Click and drag along the apparent length of the structure. A line will be drawn as you drag to help visualize the length.

Measure Example 2 Image 1

2) Release the mouse button. A width will be calculated by default at the midpoint of the length line.

Measure Example 2 Image 2

3) If necessary the position of the measurement can be moved along the length line by using the Up and Down (arrow) keys. Note that the width is recalculated after each press of a key.

Measure Example 2 Image 3

4) Again if necessary, the angle of the width calculation can be rotated by using the Left and Right (arrow) keys. As with moving the measurement, the width is recalculated after every key press.

Measure Example 2 Image 4

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Send questions or comments to: alfredo.rodriguez@mssm.edu