Biological Imaging:
Why Slices?
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.
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.
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.