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NEXT UNIT NEXT PAGE UP CATEGORY PREVIOUS PAGE PREVIOUS UNIT Biological Imaging:
Why Slices?
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Why are Magnetic Resonance Images taken in slices? Isn't it difficult to imagine the whole image if you can only see one slice at a time? Why not just do an xray, so that you can see the whole image at once?

The type of imaging done - xray, MRI, CAT scan - is usually chosen according to what the radiologist wants to see and what method will be safest for patient. Simple xrays and CAT scans tend to show us hard tissues such as bone. MRI can be weighted (T1 or T2) to show different types of soft tissues like muscle, liver, brain, etc. Simple xrays take a picture of the whole subject; MRI's and CAT's focus their magnetic field and xrays onto a thin layer of the subject and collect a series of pictures in slices. Is there an advantage to taking these pictures in slices as opposed whole images? You decide.

The images used in this exercise are of a 48-hour chick embryo. The embryo was fixed and sliced in very thin sections (each slice is 10 microns or .01 mm thick). Pictures were taken of each slice under a light microscope and scanned into the computer. Special software was then used to stack the slices back into a 3-dimensional chick embryo.

An x-ray

This figure shows the chick embryo rendered by the computer to mimic an xray or a light microscope. When light (xray or visible depending on the wavelength) shines through the embryo, the denser areas appear lighter creating a 2-dimensional ghostlike image. The eyes of this embryo have been labeled. On the top edge of one of the eyes we have placed a red dot. Can you tell which eye (left or right) has the red dot? Radiologist use many different clues to read xrays, but it is still difficult to determine exact positions on an xray.

Below is the same 48-hour chick embryo rendered to mimic the stacked slices of an MRI or CAT scan.

A whole 3D model

A 2D view

The slices of the stack are composed of rows of square units called pixels. When you stack the slices, they collectively become a volume and the individual pixels extrude from squares to become cubes or voxels. If we know how many voxels represent a cubic micron, we can create a 3-dimensional grid over the volume. We can then use this grid to locate and measure the volumes of different embryonic structures. For this image, each square of the grid represents a 100 square microns.

Below is the same volume rotated forward 45 degrees. In each successive image below, a 100 micron slice will be removed. We continue to remove slices until we find the red dot. Which eye contains the red dot? Can you determine the exact position of the red dot using the 3-dimensional grid? Discuss why determining exact positions of structures on MRI's or CT's might be advantageous to a surgeon.

Slice (Z=000 microns)


Slice (Z=100 microns) Slice (Z=200 microns)
Slice (Z=300 microns) Slice (Z=400 microns)



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EGG BIOLOGICAL IMAGING DATABASE EGG MATH EMBRYOLOGY NIH Image HOME Copyright (C) 1998 University of Illinois at Urbana-Champaign