(This poster was presented by Gordon Kindlmann at the NIH Symposium on Biocomputation & Bioinformation Digital Biology: The Emerging Paradigm on November 7, 2003 in Bethesda, Maryland.)

Imaging of Utah Electrode Array, Implanted in Cochlear Nerve

Gordon Kindlmann3, Richard A. Normann1, Arun Badi1, James Bigler3, Charles Keller2, Richard Coffey3, Greg M. Jones3, Christopher R. Johnson3

1Department of Bioengineering
2Division of Pediatric Hematology-Oncology, School of Medicine
3Scientific Computing and Imaging Institute (SCI)
University of Utah, Salt Lake City, Utah 84112


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Figure 1: Utah Electrode Arrays developed by the Center for Neural Interfaces. The 4-by-4 array (a), photographed on a penny for scale, was implanted in the feline skull for this study. Arrays with more electrodes have also been created (b), including a slanted array (c) for varying the depth of focal stimulation.

Background

In spite of its outstanding success in some profoundly deaf individuals, cochlear implants are not effective in all implanted subjects. Problems of limited low frequency restoration, limited numbers of channels, and high stimulation threshold currents are a result of the stimulating electrodes being located some distance away from the cochlear nerve, with the modiolar bone intervening between the electrodes and the nerve. An array of penetrating electrodes, inserted directly into the auditory nerve may mitigate some of these problems. The active tips of the implanted electrodes abutting the cochlear nerve fibers should allow much more focal stimulation than can be achieved via present cochlear electrode arrays. The Utah Electrode Array (Figure 1), has been surgically implanted into the cochlear nerve of felines for periods of over six months. Non-invasively verifying the accuracy of the electrode array's placement within the cochlear nerve, in an anatomical region completely encased in thick temporal bone, requires a combination of high-resolution scanning, volumetric image processing, and visualization techniques.

Figure 2: University of Utah Small Animal and Microscopic Computed Tomography Core Facility. Gantry of the instrument is 98 mm and field of view is 88x88x45 mm. Specimens receive a radiation dose of 18-797R for scan resolutions of 21-93 μm.


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Figure 3: Sample slices of CT data. Slices (a), (b), (c) cut through the spiral turns of the cochlea while showing the approach of the electrode array leads, which pass through a hole in the modiolar bone (d), (e), ending with the array itself. Slices (f), (g) and final close-up (h) show the electrode shanks and tips as faint segments extending up and right from the electrode lead contacts (white spots). Streaking around electrode leads and contacts is a tomography artifact.

Imaging

Volumetric imaging was performed with a GE EVS-RS9 computed tomography scanner at the University of Utah Small Animal Imaging Facility (Figure 2), producing a 131 MB 16-bit volume of 425x420x385 samples, with resolution of 21x21x21 microns. Slices of the volume are shown in Figure 3. The resolution of the scan allows definition of the shanks and tips of the implanted electrode array. Figure 4 outlines the volumetric image processing for isolating the electrode array from the surrounding tissue so as to better highlight the structural relationship between the implant and the bone. There are distinct CT values for air, soft tissue, bone, and the electrode array, enabling the use of a combination of ray-tracing and volume rendering to visualize the array in the context of the surrounding structures, specifically the bone surface.


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Figure 4: Volumetric image processing of CT data. Fuzzy thresholding of the original data, shown with projection (a) and slice (b), isolates the voxels corresponding to the electrode array and leads (c), while a combination of edge-preserving and Gaussian filtering of the remaining voxels helps smooth bone surfaces (d). The results are combined into a new volume (e, f).
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Figure 5: Volume renderings of electrode array implanted in feline skull. The volume is rotated gradually upwards in columns (a), (b), and (c), from seeing the side of the cochlea exterior in (a), to looking down the path of the cochlear nerve in (c). From top to bottom, each row uses different rendering styles; (1): summation projections of CT values (green) and gradients (magenta); (2): volume renderings with opaque bone; (3): volume renderings with translucent bone, showing the electrode leads in magenta.

Visualization

Visualizations of the data were created with a parallel ray-tracing volume renderer. Ray-tracing is a method commonly used in computer graphics that supports highly efficient implementations on multiple processors for interactive visualization. Volume rendering permits direct inspection of internal structures, without a pre-computed segmentation or surface extraction step, through the use of multi-dimensional transfer functions. As seen in the visualizations in Figure 5, the resolution of the CT scan allows definition of the cochlea, the modiolus, the implanted electrode array, and the lead wires that connect the array to a head mounted connector. The co-linear alignment of the path of the cochlear nerve with the location of the electrode shanks and tips (Figure 5, column c) is the necessary visual confirmation of the correct surgical placement of the electrode array.

Ongoing and Future Work

Drs. Keller and Capecchi are investigating the birth defects caused by a mutation in a gene, Pax3, that controls the normal musculoskeletal development of mammalian embryos. In their model, they have activated a dominantly-acting mutant Pax3 gene, and have uncovered two of its effects. First is abnormal formation of the bones of the thoraco-lumbar spine and cartilaginous ribcage. Second is cranioschisis, a more drastic effect in which the dermal and skeletal covering of the brain is missing. Imaging of mutant and normal mouse embryos was performed at the University of Utah Small Animal Imaging Facility, producing two 1.2 GB 16-bit volumes of 769x689x1173 samples, with resolution of 21x21x21 microns. The two mutation effects can be seen with volume visualization; Figure 6 shows some recent results. Future work will focus on better ways to algorithmically extract fine structure of sparsely calcified embryonic skeletons from low signal-to-noise CT data, as well as quantifying and visualizing the morphological differences between mutant and normal embryos.

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Figure 6: Visualizations of mutant (left) and normal (right) mice embryos. CT values are inspected by maximum intensity projection in (a), and with standard isosurface rendering in (b). Volume renderings from various viewpoints (c, d, e, f) use multi-dimensional opacity functions for more accurate bone emphasis, depth cueing, and curvature-based transfer functions to enhance bone contours in image-space.

Conclusion

In both of the above studies, determination of three-dimensional structure and configuration played a central role in biological inquiry. Volume visualization provided visual confirmation of the precise location of an electrode array implanted in the feline skull, and it created detailed renderings of changes in bone morphology due to a Pax3 mutation in mice. The scientific utility of volume visualization will benefit from further improvements in its interactivity and flexibility, as well as simultaneous advances in high-resolution image acquisition, and the development of volumetric image processing techniques for better feature extraction and enhancement.

Funding

This work was supported by the National Heart Lung and Blood Institute P20 HL68566 (CRJ); the National Center for Research Resources P41 RR012553 (CRJ); and NINDS/NIDCD NO1-DC-1-2108 (RAN). The University of Utah Small Animal and Microscopic Computed Tomography Core Facility is supported by a University of Utah Research Instrumentation Grant.

Software

The software which produced all these images has been developed within the Scientific Computing and Imaging Institute, and is distributed as open source. It is available from Sourceforge.