6. LSServer, Scanner Shell and Download
6-32
Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5
2004-11
Geometry
Geometry
group box
The
Geometry
group box contains the following elements:
•
The
static text
,
which appears after “
Geometry:”,
displays the name of
the currently loaded *.saf file.
•
Scan area
option button:
Select the
Scan area
option button to set the appropriate scan area either by
dragging the four red borderlines by mouse or by typing in the distances,
measured from the lower left corner.
Units are given in mm.
Minimum Scan area: 1mm x 1mm
See Scan Area on page 6-34 and Scan Area option button on page 6-14, for
more information.
•
Autofocus
option button:
Select the
Autofocus
option button to specify the position of autofocus scan
lines.
The Autofocus is a scan in vertical direction (= z-scan) measuring the
reflection light of the 633 nm laser in order to bring the sample exactly into
the right focal plane. For this purpose z-scans are performed along the
autofocus scan lines that can be positioned either by dragging green lines by
mouse or by typing in the distances (units in mm), measured from the lower
margin.
The width of the autofocus scan lines is given by the
Amplitude
(unit in mm).
For more information, see Autofocus on page 6-35.
Select
Autofocus
to make the
Advanced Autofocus…
button available and
to change autofocus parameters or to select a different autofocus and/or
autofocus mode. For more information, see Advanced Autofocus.
Minimum Autofocus: 3mm x 3mm
•
Barcode
option button:
Select the
Barcode
option button to specify the reading position of the
barcode by dragging the blue line by mouse or by typing in the distance in
mm from the lower margin.
The total slide area must be at least 37.5 x 15.0 mm,
otherwise there is no
room for a barcode. The barcode area is from 37.5 mm to the total slide
length.
This option is not available if your instrument is equipped with a
barcode bottom reader. The reading area is fixed in that case.
See Barcode on page 6-36 and Barcode Area option button on page 6-16, for
more information.
•
AGC
option button
Select the
AGC Scan Area
option button to start automatic gain control scan
area selection.
AGC is only available in:
•
Single Scan Mode
•
Dual Sequential Scan Mode
It is not possible in Dual Parallel Scan Mode because the Cross Talk
phenomenon with special dye combinations (e.g. Cy3 and Cy5), where signal
from one channel will be detected in the other channel and can therefore lead
to incorrectly calculated gain values.
See AGC (Automatic Gain Control) on page 6-37 and AGC Scan Area option
button on page 6-16, for more information.
