Biomedical Engineering Reference
In-Depth Information
These can be particularly useful to apply to processed images to provide
the user with a visual check of the numerical results.
In addition to opening and closing of images, the ImageJ macro
language offers a good deal of fi le and folder handling to smooth your
workfl ow. For example, result images, plots and data can be saved to
particular locations and temporary images stored and then deleted at the
end of the workfl ow. Making a plan of what you intend to do in terms of
image processing on your images is the next important step in the
workfl ow. It is a good working knowledge of all the ImageJ functions that
allows the user to describe in his or her own words what they want to do
and then translate this into the ImageJ commands. The macro language of
ImageJ is focused in its functionality towards its core function of analysing
images and is constantly being added to in new versions. Generally,
macros containing these latest commands are not back compatible with
older versions of ImageJ so using the ImageJ updater regularly is a good
habit to get into. This command simply checks the web for a newer
version and if found can download the update automatically and after a
restart of ImageJ it will be running the latest release. To prevent older
versions running macros that include functionality only available in later
versions, a function call such as 'requires (“1.45e”) can be added to the
macro to prevent trying to run a macro using an outdated version. There
are excellent guides available that give a full account of the ImageJ
functions, some of these have links to examples of macros which use them
and are included when downloading ImageJ. Further macro examples can
be found on the ImageJ website [10] where, 300+ macros, 500+ plug-ins
and 20+ scripts are available.
5.2.3 ImageJ community
ImageJ has a large following in academia and beyond due to its open source
nature, being freely available for download and use without restriction.
This has led to actual and virtual meetings of ImageJ users to share
experience and, of course, knowhow, macros, scripts and more. Indeed,
posting a request on how to do a task on the ImageJ forum often meets
with a quick and successful response from within the community. Users can
also search the archives to see if a question has already been answered [11].
This global network of ImageJ users is a great source of knowhow and
advice to help get a novice user up and running. In addition to the ImageJ
forum, the ImageJ web site hosts a large selection of macros that not only
provide useful functionality but also demonstrate how the different ImageJ
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