Biology Reference
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Fig. 3 Detailed snapshot from a virtual slide obtained by imaging of a slide spat-
tered with glycerol on the cover slip. This is an example of how incorrectly prepared
slides can negatively infl uence automatic sample recognition. This is problematic
especially in case of low-contrast samples, such as cleared Arabidopsis seedlings
points is shown by green rectangles. During slide scanning, the
focus plane is determined by an imaginary line that connects the
neighboring focusing points.
29. In our case, we use a data server equipped with disk array of
raw capacity 6.0 TB.
30. The maximum number of samples that can be loaded depends
upon the size of the slide loader. Our system is designed for a
maximum 50 slides.
31. The proper setting of the shade avoidance and white balance
individually for each scan ensures the highest possible quality
and helps in recognizing the transparent objects, thereby
ensuring the specimen is optimally in focus.
32. This setting ensures that whole Arabidopsis seedlings—includ-
ing their most transparent portions (in particular, the tiny root
parts)—will be scanned. Avoid scanning of untidy slides,
which leads to poor recognition of samples and ultimately to
images that are not sharp (Fig. 3 ). According to our experi-
ence, scanning with a 10× objective is suffi cient for reliable
signal detection in the tiny structures of young developing
Arabidopsis seedlings.
33. Usually we allow the scanning of slides to run overnight.
34. Automated image analysis also can be applied, but an applica-
tion suitable for that purposes is not a part of the software
package delivered by Olympus.
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