Physical Fractionator workflow >

9. Match tissue sections

In this step, you can align the contour of the region previously traced to the corresponding region on the lookup section image. The high-power images of the reference section acquired previously (step 8: Acquire alignment images) are associated with the contour and will be aligned along with the contour.

The lookup image is now displayed along with the contour that was traced over the reference image.

Align the contour with the appropriate region on the lookup section:

  1. Re-size the image using the zoom tools so you can see the region.
  2. Under Align the tracing, specify the number of points you will use to align the contour with the image of the lookup section.
  3. Click the Align tracing button and start aligning.
    1. Click a point on the contour then click the corresponding pint in the reference image.
    2. Click the next point on the contour then its corresponding point in the reference image.
    3. Repeat for the number of points specified in step 2.
    4. Click Stop Alignment.
  4. Re-do the alignment as many times as necessary to obtain an acceptable alignment.

Align to Lookup Section:

  1. Choose a low power objective where you can see a substantial portion of your region of interest.
  2. Select the corresponding lens from the Select Lens Drop drop-down menu.
  3. If the lookup section is on a different slide from the reference section, place the lookup section slide on the stage.
  4. Use the joystick to align the contours on the screen to the tissue in the lookup section as closely as you can.

Align the Tracing:

Once the tracing is aligned as closely to the tissue as possible, use the Align Tracing matching function to refine the alignment between the tracing and the tissue.

  1. Under Align the tracing, specify the number of points you will use to align the contour with the image of the lookup section.
  2. Click Align Tracing and start aligning.
    1. Click a point on the contour then click the corresponding pint in the reference image.
    2. Click the next point on the contour then its corresponding point in the reference image.
    3. Repeat for the number of points specified in step 2.
    4. Click Stop Alignment.
  3. Re-do the alignment as many times as necessary to obtain an acceptable alignment.

 

The contours will never line up perfectly with the Lookup section.