Sean Lauber:AMIRA - Creating Label Fields by Lung Segmentation

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In order to evaluate changing densities in the lung of an affected animal, you need to separate the lung portion of the CT scan from the rest of the CT scan. This is done by creating a lung "label field". One method of generated a lung label is by a process called "thoracic segmentation". The idea is to color in sections of the lungs, using the ribs as a guide, and interpolate the label between sections. This will generate a 3D segmentation of the lung which can subsequently be analyzed for density values by histogram analysis.

1. Open the relevant .raw file

2. Adjust the parameters accordingly. For data from the MCPTI I use the following parameters:

Amira-lung label00.png

3. Then open the Segmentation Editor (see the cursor):

Amira-lung label01.png

4. In the Segmentation Editor, open a New Label Data file (see the cursor), and the lung CT data will load:

Amira-lung label02.png

5. Add a New Material (see cursor, in this case Material2) so you can add label data to a material file.

Amira-lung label03.png

6. I like to adjust the Data Window to better show the CT data

Amira-lung label04.png

7. Select the Paint tool so you can begin coloring in the lung label. I like to use a point size of 60 to begin, and as I move on increase the size to 100.

Amira-lung label05.png

8. Bring up the position of the CT scan towards the head (either scroll up/down over the CT image or adjust the bar directly below the CT image). Position the image to show the first set of ribs (see figure) and color in the area (shown in red in the figure, this should take a single click of the mouse).

Amira-lung label06.png

9. To clean up the image, hold down ctrl and click the mouse to delete label, use this feature to exclude the region surrounding the spinal cord.

Amira-lung label07.png

10. Scroll down approximately 3 ribs (watch the ribs emerge from the spinal cord area), then color in this lung section. Delete the label surrounding the spinal cord (as shown in the figure).

Amira-lung label08.png

11. Next we want to interpolate the label that you made at the first set of ribs to the label you just made at this 4th set of ribs. To do this go to Selection/Interpolate or press ctrl-I. Scroll up and down to verify that the interpolation worked.

12. From the 4th set of ribs, go down another 3 sets. Color in this area (I like to use paint brush size 100 from here on), remove spine label, and interpolate.

Amira-lung label09.png

13. From this 7th set of ribs, go down until you see the diaphragm begin to appear. This is located just below the heart. Color in this area, remove spine, and interpolate.

Amira-lung label10.png

14. From the region of the diaphragm, scroll down until you don't see any lung left. Color in this region as indicated, remove spine and interpolate. You don't want to color the whole of this region because much of it is not lung, and you want to color it in in the indicated shape so when it interpolates upwards it forms the desired shape.

Amira-lung label11.png

15. Remove as much of the diaphragm as you can, then ensure that the segmentation looks okay. You shouldn't have very much or any bone in the segmentation and you want to avoid the fatty layer around just outside of the ribs. The lung segmentation is now complete!

16. To save the label, add the label to the material (Material2) by clicking the + sign (see cursor). At this point the red coloring should be exchanged by a thin line (in this example it's a purple line). Make sure you have Material2 highlighted, if you have nothing highlighted, then the label you've just created will be lost.

Amira-lung label12.png

17. Return back to the Object Pool (the section you were in at the beginning of this lesson - its the first symbol on the top left, 2 symbols back from the Segmentation Editor symbol)

18. Right click on the label (now below the .raw file) and save the file. Make sure to save the file as .am

Amira-lung label13.png