Biomedical Engineering Reference
In-Depth Information
A variety of atlas-based segmentation methods have been described in the
literature [3, 11, 12, 15, 16, 21, 23, 24, 38, 41]. The characterizing difference
between most of these methods is the registration algorithm that is used to
map the image coordinates onto those of the atlas. One important property,
however, is shared among all registration methods applied for segmentation: as
there are typically substantial shape differences between different individuals,
and therefore between an individual and an atlas, the registration must yield a
non-rigid transformation capable of describing those inter-subject deformations.
In this chapter we take a closer look at an often neglected aspect of atlas-
based segmentation, the selection of the atlas. We give an overview of the differ-
ent strategies for atlas selection, and demonstrate the influence of the selection
method on the accuracy of the final segmentation.
11.2
From Subject to Atlas: Image
Acquisition and Processing
We illustrate the methods and principles discussed in this chapter by segmenting
confocal microscopy images from 20 brains of adult, honeybee workers. Con-
focal laser scanning microscopy is a type of fluorescence microscopy, where a
focused laser beam deflected by a set of
xy
-scanning mirrors excites the fluores-
cently stained specimen (i.e., the dissected brain). The emitted fluorescence is
then recorded by inserting a so-called “confocal pinhole” into the microscope's
optical path. This pinhole ensures that only light from the focal plane reaches
the detector, thus enabling the formation of an image that can be considered
an optical section through the specimen. By moving the position of the speci-
men along the optical axis of the microscope a three-dimensional (3D) image is
generated [8, 69, 88]
The staining of the bee brains depicted in this chapter followed an adapted
immunohistological protocol. Dissected and fixated brains were incubated with
two primary antibodies (nc46, SYNORF1) that detect synapse proteins [28, 46].
Because cell bodies in insects reside separately from fibers and tracts, this stain-
ing ensures response from those regions in the tissue that exhibit high synap-
tic densities, i.e., neuropil, while somata regions remain mostly unstained. A
Cy3-conjugated secondary antibody sensitive to the constant part of the primary
