Biomedical Engineering Reference
In-Depth Information
The many faces of ImageJ. The open source nature of
ImageJ (native version shown top running on Windows
Vista) allows for the main window to be fully
customised to a particular function as has been done
in the case of NeuronJ [7] (middle running on
Windows XP) and for biological imaging Fiji (bottom
running on Windows Vista)
Figure 5.1
5.2.2 Workfl ow
￿ ￿ ￿ ￿ ￿
Before getting to grips to write a solution to an imaging problem in
ImageJ, a clear workfl ow must be conceived incorporating any
preprocessing of the images, the functions required, combining the
functions into the programmable elements of ImageJ, internal calculations
and fi nally the outputs. Once this has been clearly stated, a workfl ow
within imageJ can be transcribed onto the plan and coding can begin.
Customer input is invaluable to understand the exact nature of the input
images and what the output should contain. Input images can be discrete
image documents, such as lossless formats such as TIFFs, or more
commonly the lossy formats such as JPGs, which are typical outputs
from digital capture equipment. Alternatively, images can be in the form
of an image sequence as in an AVI movie fi le, which can be read into
ImageJ as a sequence of images. ImageJ can display multiple spatially or
 
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