3-D Magnetic Resonance Microscopy Raw Data Example

  This image shows a partial data set obtained by MR microscopy in the specialized facility at Duke University. The specimen is an isolated, fixed cochlea from the guinea pig. The cochlea is represented as a series of slices which are being shown sequentially here. Each slice consists of 256 x 256 points (called voxels). Each voxel represents a cube with sides of 25 microns in length. Typically, a cochlea is represented by approximately 200 slices, which means that the gray level is defined for more than 13 million voxels. The image above shows only half of a data set, from the modiolus to the round window, with only every 5th slice shown. Thus, the resolution we have available is higher than this image would indicate. The major value of this data is that the true 3-D geometry of the specimen is maintained in a non-destructive technique. This contrasts with conventional histology where distorted or missing sections can result inaccuracies of the 3-D representation.

Resolution of the Inner Ear by Different Imaging Techniques

This illustration shows the inner ear resolved by a variety of techniques:
A) Conventional MR Imaging as used for clinical evaluation. The cochlear spiral and semi-circular canals are resolved (white) in the middle of the image, but there is insufficient resolution to make out detail of the internal structures of the inner ear. Image courtesy of Tanioka et al.,(1991) Head and Neck Radiology 178:141-144.
B) Computerized Tomography (CT scan) in which the inner ear spiral is well resolved. In this figure a thin bony partition between two cochlear turns can be seen within the cochlea (the white structure) in the middle of the frame. However, the membranous boundaries between fluid spaces are not resolved by CT. Image courtesy of Brodie, H. et al, Interactive Temporal Bone Anatomy Program, University of California at Davis.
C) Cochlea as seen by conventional histology. Note the internal boundaries between the three fluid compartments, scala tympani perilymph, endolymph and scala vestibuli perilymph. However, reconstucting histological sections into 3-D images is extremely time consuming and labor intensive. Accuracy may be impaired by distorted or missing sections.
D) Cochlea as seen by high-resolution MR. Note that the resolution is high enough to detect membranous boundaries, but does not approach the detail available by conventional histology. This degree of resolution can only be achieved with fixed, isolated specimens as displayed here.

MR microscopy is therefore the techniques of choice for quantitative analysis of the complex 3-D fluid spaces of the inner ear.

Analysis of the Images

The above illustration shows a single section of an MR image in which different structures have been "tagged". The abbreviations and corresponding colors are:
SV : Scala Vestibuli - cyan
ST : Scala Tympani - green
ELS : Endolymphatic Space - magenta
OC : Organ of Corti - red
SL : Spiral Ligament - blue
After each structure has been tagged in each of the approximately 200 slices of the specimen (which is a time-consuming procedure), the structure represented by an individual color can be "extracted" for further analysis. Volume can be measured by counting up the number of voxels in the structure (each 25 x 25 x 25 micron voxel represents a volume of 15.6 picoliters). Area and distance measurements are made by customized routines programmed for the NIH Image analysis program.

All Stuctures of the Cochlea

 

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