Image adjustments for 3D tracing

The 3D tracing algorithms use information from the image data. For this reason, it is important to make adjustments using the Image Adjustment tool prior to tracing if the image doesn't display as expected (too dark, not clear enough, etc.). The adjustments you make will be dynamically reflected in both the main (2D) and 3D Environment windows.

Selecting a single color channel in multichannel images, directs Neurolucida 360 software to associate that color channel with any structures traced while the selection is active. You can select color channel(s) using the Channel panel on the left side of the 3D environment window or in the Image Adjustment window as described below; the result is identical.

Adjustments for fluorescence images

These instructions are pertinent for both multichannel and single-channel fluorescence images.

  1. Click the Adjustment button on the Image or Workspace ribbon in the 2D window to open the Image Adjustment panel.
  2. With Ungroup color channels checked, check or uncheck individual channels to turn their display on or off.
  3. Check Apply changes to stack then adjust brightness and contrast by adjusting gamma, black point and white point in the histogram: Drag the white square, black triangle and white triangle respectively.

    4. The changes are reflected dynamically in the 3D Environment.

  4. Verify your changes:
    • Navigate within the image:  Open the Image Organizer by going to Image > Tool panels > Organizer, right-click over the name of the image, select Go to plane and enter the desired z position.

      OR

      Use the maximum projection view: Click Image > View > Max projection.

Adjustments for brightfield images

  1. Click the Adjustment button on the Image or Workspace ribbon in the 2D window to open the Image Adjustment panel.
  2. Check Apply changes to stack then adjust brightness and contrast by adjusting gamma, black point and white point in the histogram: Drag the white square, black triangle and white triangle respectively.

    3. The changes are reflected dynamically in the 3D environment.

  3. Verify your changes:
    • Navigate within the image:  Open the Image Organizer by going to Image > Tool panels > Organizer, right-click over the name of the image, select Go to plane and enter the desired z position.

      OR

    • Use the minimum projection view: Click Image > View > Min projection.