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Scientific Visualization Project

Project Description

Marie Chapla from the Florida State University Oceanography department is researching how manatee's hear sound in water. To do this research she has taken CT and MRI scans of a manatee head. It is the purpose of this project to help her discover how a manatee hears sound by rendering the CT and MRI data into 3 dimensional images so that Marie can measure the distance between the bones in the manatee ear.

Many thanks go to Kevin Beason, Wilfredo Blanco, Yoshihito Yagi, and of course Marie Chapla for their help on this project.

Project Phase 1 - CT Data

We first had to identify the data and make sure it was usable. The following images show that we had good data once loaded into Amira. The next step is to make it usable.

Project Phase 2 - Raw Data

The CT data was broken up into seperate sets of data each with different voxel sizes. This made the data very hard to work with. We needed to merge the data into one dataset so that it would be easier to work with. To do this we exported the CT data as Amira Raw data. Once in a raw data format, the data could be arranged into a proper working set and loaded back into Amira as one set of data. The following images show the data as loaded into Amira as raw data and as two working sets. The 000 data set is the low resolution set and the 400 set is the high resolution data set.

Project Phase 3 - 3D Surfaces

Now that the data is loaded in the way we want it, it was time to start rending the Manatee tissue in the way we wanted it displayed. The fist issue was to properly identify the differnt tissue densities within the data set so that the isosurfaces could be rendered. We found that the soft tissue density ranged from -900 to 100 and the bone tissue density ranged from 100-1000. The first set of images show the two different density types.

You will notice that the colors don't exactly match the colors of Manatee skin and bone. Therefore, the next task was to create Amira colormaps to properly color the tissue which is shown in the second set of images.

Project Phase 4 - Decimate the Data

We wanted the data to be smoother and the be easier to work with. By resampling the data in Amira to a lower dimension we were and to make it quicker to work with the data. The following images show the result of resampling the data. The image of the Amira workspace shows the different Amira objects created to do this.

Project Phase 5 - Isolines

Marie suggested that it would be helpful to be able to identify the boundries between the different density materials. Adding isolines to the Manatee orthoslices, this would segment the different densities. The following images show the red isolines on a Manatee orthoslice.

Project Phase 6 - Surface Reconstruction

To be able to measure the ear bones of the Manatee, Marie needed to be able to isolate the different bones in the Manatee ear. Amira allows the user to isolate specific tissue densities on the orthoslices and then reconstruct those isolated surfaces into 3 dimensional rederings. The following images show the different bones of the Manatee ear that Marie was able to isolate on the orthoslices. Once this surfaces have been reconstructed, the different surfaces reconstructions can be turned on or off.

Project Phase 7 - Pane Renderings

Pane was used to create renderings of the Manatee data that include shadows and a lot of detail. The following images show the Pane renderings of the Manatee data. As well, a couple of mpeg movies are linked below that "fly" through the Manatee.

To be able to show the soft tissue and the bone tissue together a slice needed to be cut away from the Manatee soft tissue. To do this, the soft tissue iv code was clipped in the desired area before rendering with Pane. To clip the soft tissue, Yagi's iv clipping program was used.

Lastly, Pane was also used to create a rendered Open Inventor .iv file that contains shadows and more detail. A link is below to this .iv file that can be opened in Open Inventor's ivview program.

MPEG flying by the front of the Manatee.

MPEG flying by the side of the Manatee.

Open Inventor .iv file of Manatee Skull.