Biomedical Engineering Reference
In-Depth Information
the right question coupled with a programmer who can translate
that question into code does the computer become useful rather than
useless!
In fact the computer becomes invaluable when performing imaging
tasks in a non-subjective manner and at a speed that might take a
human operator a lifetime to complete. Microprocessor performance
has increased according to the predictions of Moore's law [1]. Around
20 years ago the desktop PC would have been stretched to perform image
analysis on a 20 megapixel, 24 bit image, having just 32 MB RAM and a
25 MHz CPU. Today's PCs can cope with this high demand, having
increased data-handling speeds, multicore processors in combination
with GBs of RAM and clock speeds in the GHz range.
The aim of this chapter is to provide users with an introduction to the
capabilities and potential applications of open source image processing
tools, and to help fi nd solutions to problems. The predecessor of
ImageJ fi rst appeared in the 1990s, when it was known as NIH image
and was available to run under the Macintosh operating system. The
author and collaborator Iain Couzin created a custom imaging suite of
bespoke tools to address the challenging visual research questions, the
software produced was known as ICBiovision [2]. Such a bespoke piece
of software had some advantages in that it fully met the requirements
for which it was designed. However, when an analysis outside the
defi ned scope was required, there was no way to achieve this goal without
the further effort of low-level coding - the software was not easily
extensible.
In the 1990s, desktop PCs increased in power and digital camera
specifi cation followed a similar upwards curve. The need for, and utility
of, image analysis as a way to non-subjectively and quantitatively
assess many different biological questions therefore increased. The utility
of ICbiovision made clear the potential for image analysis in many
different scientifi c arenas and a new tool box was needed to provide
imaging solutions. Another imaging software package utilised was
Aphelion [3]. This piece of software provides the user with access to a
large number of tools that could be threaded together into macros. One
downside with Aphelion is that it is a commercial piece of software, with
a restrictive licence. Also, the application was dependent on a particular
operating system. As the company upgraded its operating system then
Aphelion was left behind. There were many other pieces of commercial
image analysis software available but these came shackled with licence
fees. It was at this point that ImageJ was rediscovered, after its
metamorphosis from NIH image, to an open source Java language
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