Importing Organ Atlas

Import Organ Atlas to co-register with Optical 3D imaging (DLIT or FLIT):

1. Select Import -> Organ Atlas in the File menu

2. Click on Add Organ Files

Importing Organ Atlas

Importing Organ Atlas

3. Select ALL organ files from the list you want to import and click on Open. The list MUST include a file named skin.iv

4. The file skin.iv should appear in the Select Skin Mesh field. Click on “Generate Mesh Coefficients”

Importing Organ Atlas

5. A message should appear that the mesh was generated successfully.

6. Type in the Organ Atlas Name the name you’d like to define for your atlas and click on Save Organ Atlas

Importing Organ Atlas

7. A message will appear saying that the atlas database was saved and should be available for loading.

8. The Atlas newly created is now available in the list of Organ Atlas in the 3D Tools Organs tab.

Importing Organ Atlas

9. Note that the atlas includes all components corresponding to the Open Inventor files included when importing the atlas (see step 3 above). In this example, it includes “bone”, “pillow”, “skin” and “traser”.

10. Then the user can select in the “Fit organs to the mouse” menu the rigid registration option (1st option from top), and click to launch the fitting algorithm.

Importing Organ Atlas

11. The fit generally runs for about 1 minute – see the result below.

12. By de-selecting the skin from the list of organs, one can uncover the anatomy of the mouse and the organs of interest (in this example, the skeleton)

Importing Organ Atlas

13. Below is the same result after rotating the mouse and zooming in to look at the detailed 3D reconstruction co-registered with the CT data.

Saving CT data as segmented surfaces in Open Inventor (*.iv) format

Using Amira 5.2.1 1. Open data by selecting the 2D image slices comprising the 3D data set.

Importing Organ Atlas

2. Enter in the relevant information for voxel sizes and Channel type. Voxel size units are in mm. Please see the Amira Help manual for an explanation of the inputs for the ‘Channel Conversion Dialog’.

3. The Object will appear in the Pool window

Importing Organ Atlas

4. Right click the Object in the Pool window and drag-click to the Orthoslice view. The orthogonal slices will appear in the display window.

a. Alternatively, after selecting the Object in the Pool, an button titled ‘Orthoslice’ will appear in the Pool window.

5. Right-click the Object again in the Pool window and drag down to Display->Isosurface.

a. Alternatively, when selecting the Object in the Pool, a button title ‘Isosurface’ will appear in the Pool.

Importing Organ Atlas

6. The Isosurface module will appear in the Properties window where you can set the voxel intensity Threshold to segment the relevant surface. For the CT dataset in the example, an intensity Threshold set at ~43 segments the mouse skin. We advise setting the Downsample Option and set the downsampling to 4 or 8 to reduce the number of vertices describing the surface.

7. The surface will appear in the view window when the ‘Isosurface’ object is selected.

Importing Organ Atlas

8. For the skeletal surface, a higher intensity threshold can be set, such as values close to ‘100’ in this example.

9. The skeletal surface for the intensity threshold set in step 8.

Importing Organ Atlas

10. Once each surface is computed, create the surface as an Amira SURF format in the Isosurface module in the Properties window by the drag-down menu under ‘more options’.

This must be done for each separate organ surface.

11. An Amira SURF format object now appears in the Pool window.

Importing Organ Atlas

12. Deselect the ‘Isosurface’ Object connected to the original data, and select to display the Isosurface associated with the Amira SURF format object.

13. If the number of vertices is too high (>10,000), then simplify the mesh by doing the following: while the Amira SURF format object is selected, select the ‘Mesh’ icon tool in the Properties window, and then change the number of faces to a value <10,000. Click on ‘Simplify Now.’

Importing Organ Atlas

14. Transform the surface. Small animal imaging instruments tend to read out the data with the z-axis defined as running longitudinally along the animal body. The x-axis tends to be defined as running left-right on the animal, and the y-axis runs anterior-posterior. In the IVIS Spectrum, the y-axis usually runs longitudinally along the animal body, and the z-axis runs in the anterior-posterior direction. Therefore, the surfaces segmented from small animal imaging instruments should be rotated in order for efficient and optimal registration of CT or MR data to IVIS Spectrum data.

a. Click on the ‘Transform Editor’ icon in the Properties window when the Amira SURF format object is selected. Click on the ‘Dialog’ button.

Importing Organ Atlas

15. Select the ‘Relative Global’ tab, and make the following changes highlighted in yellow. Hit the ‘Apply’ button when finished.

Importing Organ Atlas

16. Once the transform as been performed for viewing, the transform must be applied directly to the data by hitting the ‘Apply Transform’ button in the Properties window (when ‘Transform Editor’ icon is selected. Allow the action to Proceed if desired.

17. Saving the new surface as an Open Inventor file: Once one is satisfied with the surface, save the surface by first selecting the surface object and then drag-down to ‘Save Data As…’ in the File menu.

Importing Organ Atlas

18. Save the surface as an Open Inventor (*.iv) format for importing the surfaces to be listed with a particular dataset as a Living Image Organ Atlas file. Each organ needs to be under a separate surface and filename. For Living Image Organ Atlas importing, one file must be the mouse skin surface and be named “skin.iv” .

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Reference Guide 14