Biomedical Engineering Reference
In-Depth Information
The starting point to achieve accurate measurement of parameters is
capturing consistent images in terms of lighting, focus, exposure and
quality. Setting a digital SLR camera to full manual settings ensures a
consistent focus, exposure and quality. The lighting is crucial, and
consistency in this department is made by the use of grey cards and colour
checking cards, such as those made by xrite (
http://www.xrite.com
).
During imaging, inclusion of a QR code could be made to automatically
assign the results in the image against a treatment identifi er.
As with the seed images, automation is key within industry and in this
case a semi-automatic approach is taken as the image scale was undefi ned.
The user must fi rst ascribe this to the images either by using a calibration
object in the image of a known size, to allow a fully automatic solution
(it could be the QR code for example), or by drawing a line of a known
length just once if all images are to the same scale. Once this has been
completed, the ImageJ macro is pointed at a folder hosting all the images,
which are then automatically processed into false colour images and a
results table produced. Importantly, false colour images can be used to
allow the user to check that the parameters have been measured correctly,
and to check whether any erroneous results may have been recorded. A
key advantage of image analysis is that the original images are stored and
can be reprocessed should novel parameters be identifi ed that need to be
subsequently measured. In this example, plants could also be imaged at
different wavelengths, for example using infrared to examine water
content, or using a laser scanner to generate 3D information. This
information can be used in conjunction to allow a multiparameterisation
of plant features to measure phenotype.
5.6 Summary
ImageJ is a freely distributed, open source solution for image analysis,
which affords the user many different levels of interaction ranging from
performing simple tasks from the menus through to high levels of
automation by its in-built macro language, plug-ins and Javascripts. It
benefi ts greatly from the large number of users in a global community
that comes together virtually online in forums and in reality at conferences,
which leads to its continual development, support and new version
releases.
From a user and company perspective, ImageJ offers some unique
characteristics associated with open source software. First, its free
distribution means that everyone in a 20 000+ organisation can
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