Preview unit; S_II
For technicians and
partly for sales managers!
To find the
position of the entire tissue to be scanned or parts of it, a preview of the
slide is made. The tissue is defined as a darker part of the slide in relation
to its surrounding. Because dust, grease or fingerprints (specks) fulfills
often the same requirement as the tissue itself; specks may be viewed as tissue
also. Therefore, the surface of the slide and the cover slip should be as clean
as possible.
The following description is based on the Software
version 1.21 and the scanner “Pannoramic SCAN_II”, the components, procedures and
adjustments are nearly the same in the MIDI_II and the DESK_II.
The entire preview unit is a part of the scanner unit
and designed to fulfill the following 2 tasks:
Contents
The
version numbers of the service program “SlideScannerService.exe” and the scan
program “SlideScanner.exe” are important, because the preview calibration
program uses program parts (.dll-files) of the program “SlideScanner.exe”.
Attention: Do not mix the versions of SlideScanner.exe and SlideScannerService.exe!
Always use these programs with the same version number; otherwise the
SlideScannerService.exe program could produce unwanted results and
SlideScanner.exe does not work correctly or even freeze!
Since the software version
1.16 the units of the scanner are configured in the file
“MicroscopeConfiguration.ini”, section [Microscope].
The actual version of the preview unit in the scanner SCAN_II is defined
by the use of the following parameters and values:
[Microscope]; S_II
SerialNumber = SC150-21xxxx
MicroscopeType = 3DMic11
ScanCameraType = AVT Marlin F146C
PreviewCameraType
= CVrmc_m8_pPro
BarcodeReaderType
= PreviewCamera
LoaderType = SL_6Mag_25Slide_NoSensor_Vertical_2
CameraChangerType = CC_None
ReflectorTurretType = RT_3DH_10Pos_Belt
BrightfieldLightSourceType = RGBLedLight
ObjectiveChangerType = OC_2Pos
ObjectGuideXYZType = OGXYZ_1.2mm
FlashUnitType = NoFlashUnit
NDFilterType = ND_None
PreviewLightType = PreviewLightUnitType_Type4
PowerSwitchBoardType = PowerSwitchBoard_None
[HardwareLimits]
Principle
of brightfield preview
Brightfield illuminated
preview
“Scan
area” and “Barcode area”
The entire preview and barcode unit is situated on the
“horseshoe”; and this is a part of the
scanner unit.
Horseshoe
The horseshoe is a part of the scanner unit, and
contains the following components:
The preview mirror reflects
the image of the preview in an angle of 90 degrees; the mirror does not need
adjustments.
Construction,
Preview camera Scanner plate and horseshoe
The preview illumination illuminates the background of
the slide in the size of the preview camera’s field of view.
The
barcode illumination consists of four LED’s and these are situated on a small
PCB.
To reach an evenly and bright illuminated barcode
area, the position of the LED’s can be modified by positioning the entire PCB
if the mounting bolts are loosened or by bending the LED’s carefully,
separately.
“Barcode adjustments”, “Barcode illumination”.
The entire preview
unit is situated on the edge of the scanner plate, parallel to the magazine
unit.
The
position is fixed with two fixing pins and hold by the mounting bolt.
“Scanner plate” and “Horseshoe mounting”
Remove the
preview unit
· Disconnect
the cables for the preview illumination, the barcode illumination and the
preview camera’s USB cable
· Remove
the mounting bolt and then the entire preview unit can be removed frontward.
Mount the preview
unit
· Fit
the fixing pins of the scanner unit into the position fixing holes of the
horseshoe and push the entire preview unit onto the edge of the scanner unit.
· Drive
in the mounting bolt.
· Connect
the cables for the preview illumination, the barcode illumination and the
preview camera’s FireWire cable
The preview objective and camera holder allows the adjustment
of the preview camera rotation angle in a limited range.
To adjust the camera rotation angle:
In the
scanners S_M_D the preview camera VRmc-8+ PRO can be used to create
the brightfield preview and also to capture the barcode since the
software version 1.16.
Because the camera has 2 different tasks, each kind of
image is illuminated from another illumination source and these are of a
different kind also, the adjustment of the aperture iris size and the focus
position of the objective are important.
Preview objective, TAMRON
23FM16SP
The scan area
defines the part of the slide on which the tissue, scanned by the scan camera,
is expected to be. The entire scan area is captured by the preview
camera in three sections and is shown in the preview area of the program
SlideScanner.exe.
The scan area is limited by the mechanical
construction of the specimen holder and should be defined as large as possible;
it is not defined in relation to the cover slip.
In all cases, the specimen holder should never be
touched by the focus pin or the objective! In other words, the scan area
is that area of the slide, on which the focus pin and the objective can be
moved seemingly during scanning the tissues, without touching the specimen
holder.
The barcode area is situated beside the scan area and contains
stickers or labels with information about the tissue.
If the label contains a barcode, the analyzed and
decoded barcode can be used as file name for the scanned tissue.
· The
entire barcode area is captured by one field of view of the preview camera.
· To see
the information of the barcode area, it is illuminated by the barcode
illumination.
· An
evenly illuminated barcode area and a well adjusted focus of the preview
objective increase the readability of the barcode.
· The
correct position of the barcode area will be defined in the step 16 of the
preview calibration procedure.
Important
Stickers and labels should be placed only beside the
cover slip; the opposite surface from beneath is glass only. If labels are
placed on the opposite side also, the slide will not be hold correctly in the
specimen holder and “slant fields of view” are produced during the scan
process; see also: “Stage skew check”.
“Barcode illumination”; “Adjust the barcode
illumination”, “Step of the
preview calibration procedure” and
“Barcodes in practice”
When shall I check or define the scan area?
The scan area is defined during the system integration
procedure.
If the scan area was modified, the steps and checks,
described under “Adjust the
pixel of the preview camera to the field of view of the scan camera” must be executed.
The scan area values may vary from scanner to
scanner (depending on the specimen holder and parallelogram adjustment and
mechanical tolerances); so the scan area has to be defined for each
scanner separately.
In all cases, the scan area values of X-min,
X-max, Y-min and Y-max are set just before the focus pin or the objective
touches the specimen holder; the accuracy of the limits is 100 steps.
The slide is hold by the specimen holder on the
longer, lower edge and with a slide clamp on its upper edge, on the barcode
area; see the red lines on the right. As you can see, the definition of the
limits X-min and Y-max are critical.
X-max and Y-min are given by the maximal usable slide
size and are not critical; they could be the slide edge of the largest, allowed
slide dimensions.
Because
there is a rounded corner on the specimen holder as shown on the right (X-min
and Y-max corner), there are two possibilities to define
the scan area, shown with the red and green lines.
The Y-max value
can be more decreased (the scan area will be shortened in
Y-direction) and the value of X-min can be decreased (the scan area
will be larger in X-direction). Technically, both solutions can be accepted,
but in practice, the users prefer the solution as shown with the green lines.
The difference between both solutions is more hundred steps in each direction.
Please take this into account if you are defining the scan area.
The following “flow chart” describes the steps for
Pannoramic SCAN_II especially. The steps for MIDI_II and DESK_II are similar, but named
values and actions, given by the construction of the specimen holder can
differ.
· This
procedure assumes that the hardware limits of the X-Y-stage unit are already
defined.
· The
path of the file “MicroscopeConfiguration.ini”, in the version 1.14 is:
C:\ Documents and Settings\All Users\Application
Data\3DHISTECH\SlideScanner\ MicroscopeConfiguration.ini
· The
path of the file “MicroscopeConfiguration.ini”, since the version 1.15 is:
C:\ProgramData\3DHISTECH\SlideScanner\MicroscopeConfiguration.ini
·
The scan area values to
be used are set just before the focus pin or the objective touches the specimen
holder mechanics. The accuracy of the limits is 100 steps.
1.
Insert a medium large slide or the Test slide #2.
2.
Start the SlideScannerService.exe program, Low level
service part.
3.
Go forward to 26000 steps in +X direction.
4.
Press Home1 then Home2 for the Y-stepper motor.
5.
Press Home1 then Home2 for the X-stepper motor.
6.
Go to position X=4000 steps.
7.
To find the “rounded” corner of the specimen holder,
go to the position Y-max. This position is nearly 74000 steps or somewhat
below. The real value can be found in the section [HardwareLimits]. If the
specimen holder is touched by the focus pin, move the Y-stepper backward by 100
steps until the specimen holder is not touched and memorize this number of
steps in Y-direction. If necessary, go to Y-Home1,2 for the Y-stepper motor and
forward again to the memorized position (if steps where lost).
8.
To find the lower edge of the “rounded” corner of the
specimen holder, decrease the number of steps by
9.
After each movement of the specimen holder (either in
X- or Y-direction) check the limit as described in the paragraph above “To
check the found limit position”.
10. Decrease /
increase the number of steps in the X-direction and the Y-direction until the
correct corner point is found (see also “The physical construction of the
specimen holders”).
11. If the corner
point is found without touching the specimen holder and without lost steps
update the parameter “ScannableAreaPositionXmin” with the found value of steps in
X-direction and the value of the parameter “ScannableAreaPositionYmax” with the
found value of steps in Y-direction in the file “MicroscopeConfiguration.ini”
section [HardwareLimits] and save the file.
12. With the 3200
steps button go backward in -Y-direction (along the specimen holder side,
defined by the parameter X-min) until the inner edge of the slide is reached
and check after each click the correctness of the value for the parameter
“ScannableAreaPositionXmin” as described in the paragraph above “To check the
found limit position”. Collision with the specimen holder must not occur! Do
the step 12 logically on each already defined edge.
13. To define the
values for the parameters “ScannableAreaPositionXmax” and
“ScannableAreaPositionYmin”, move the specimen holder into the opposite corner
and repeat the flow chart from step 3 logically. In
step 6 start with the position X = 24000 and in step 7 use the value of Y=23000
steps as a starting point.
14. If the corner point is found
without touching the specimen holder and without lost steps update the
parameter “ScannableAreaPositionXmax” with the found value of steps in
X-direction and the value of the parameter “ScannableAreaPositionYmin” with the
found value of steps in Y-direction in the file “MicroscopeConfiguration.ini”
section [HardwareLimits] and save the file.
15. Repeat step 12
logically with all four edges of the defined scan area. If anywhere collision
occurs, define the appropriate parameter value again and actualize it in the file
“MicroscopeConfiguration.ini” section [HardwareLimits] and save the file.
“Scan area and
specimen holders”, “PMIDI”
and “PDESK”
Adjustments of the preview unit
The
adjustment of the preview unit includes:
Prerequisites
for the BF preview calibration
The success of the preview calibration procedure is
bound to the following components and parameter values:
When shall I do a preview
calibration?
Steps of the preview
calibration procedure
Remark: To
adjust the aperture of the preview objective the focus unit should be removed
or the horseshoe can be dismounted.
Remark: To
adjust the aperture of the preview objective the focus unit should be removed
or the horseshoe can be dismounted.
Adjust
the focus position; Tamron
Start the service program and select the option
“Preview calibration”.
Load the preview slide in “Manual” mode.
“Insert or
remove a slide manually”
After inserting the single width preview calibration
slide, the live view of the preview camera is shown in the camera window.
Use the
components of the calibration slide to adjust the focus of the preview camera
objective.
After tightening the mounting
bolts and adjustment bolts, any kind of shadow should be eliminated and the top
of the slide should not be cut.
Adjust the camera position; VRm
Bring the Y-stepper motor in the position where the
edge of the slide is near to the top edge of the preview window. Set the
X-stepper value to 28800.
Remark: This
adjustment is done only to see the top edge of the slide as sharp as possible;
so the camera rotation angle can be adjusted properly.
To loosen the camera and
objective holder you need a 1.5 mm hex wrench.
By loosening one of the “Rotation angle” bolts and
tightening the opposite bolt, the rotation angle will be modified; see also
“Preview objective and camera holder” above.
After tightening the mounting
bolts and adjustment bolts, any kind of shadow should be eliminated and the top
of the slide should not be cut.
The preview calibration part of
the SlideScannerService program adjusts the pixel view of the preview
camera to the FOV (Field of view) of the scan camera, because both cameras are
physically in distance to each other.
The preview calibration includes:
1. Defining
the position of the preview camera’s pixel and the scan camera’s FOV.
2. Adjusts
the pixel position of the preview camera to the FOV position of the scan
camera.
3. The
preview camera takes three images from the slide. The parameters for assembling
the three parts are defined in the preview calibration process.
4. Defining
the barcode area.
The calibration slide (Calibration slide single width)
defines positions inside the scan area with circles containing a
cross. The centers of the circles are marker positions for the preview camera
and the scan camera also.
To executing the steps, please
Barcode
reading and adjustments
For
technicians and sales managers!
These
instructions describe the procedure to define the barcode area and the
adjustments necessary for reading barcodes with Pannoramic S_M_D_II
scanners, equipped with
If the barcode reading is not allowed in the dongle for
the SlideScanner software, barcodes can not
be read; nevertheless the Matrox barcode dongle is connected
(important for DESK_II).
Check the barcode reader unit for
necessary adjustments:
· If the barcode print quality on
the barcode area is high or acceptable and barcodes can be read, but some
barcode types are unreadable (with also a high print quality), then adjustments
may be needed.
Before
you start adjusting the components of the barcode reader, try to read barcodes of different
kind and codes and do the following checks; see also barcodes in practice:
1. If there is no
barcode readable or available:
· Check
the Matrox
driver installation
· Check
the presence of the dongle
for barcode reading
· Check
the validity of the license file or dongle
· Check
the focus position
of the preview camera
· Check
the size of the preview
objective aperture
· Check
the selected barcode type in the dialogue “Barcode settings”
2. If several barcodes are
unreadable:
· Check the barcode print quality on
the slide’s barcode area
· Check
the uniformity of
illumination on the barcode area
· Check the size of the barcode area
· Check
the focus position
of the preview camera
· Check
the size of the preview
objective aperture
· Check
the selected barcode type in the dialogue “Barcode settings”
Define the barcode area
We assume that the preview calibration procedure is
already done and the barcode area is defined properly. For details to define
the barcode area please refer to the “Step
16: Fit the barcode area into the red square”.
Attention:
·
Do not copy the
MIL Runtime folder to your desktop! Instead copy the folder to C:\. Because
there are a lot of long file- and folder names inside
the MIL Runtime folder, the maximal path length will exceed the limit, and
the install procedure can not be executed successfully. Never install the MIL
Runtime via network!
·
For further
information please refer to “Setup the
Matrox Imaging Library”.
Start the
Pannoramic scan software and check the barcode
readability.
Adjust the
preview camera parameters and barcode illumination for barcode reading and preview capturing
For a successful
barcode reading the adjustment of the barcode illumination, the correct setting of the focus position of
the preview camera is essential. For this adjustment a slide with a white label
area and a barcode test set is required.
Attention
If you adjusted the focus position
of the preview camera objective you have to do the preview calibration process
again. For details to execute the preview calibration please refer to the “Preview calibration above”.
A fully white
barcode area can be created easily by sticking a blank adhesive label onto the
slide and the edges are cut around with a utility knife. The white barcode area
is required to check the uniformity of illumination.
Adjust the barcode
illumination
Start the program
“SlideScanner.exe” with the service password. Insert a slide with white label
area and select the tab “Service” and “Microscope control”. In the pull down
menu “Video source” select the “Preview camera”. After click on “live view”
check the checkbox “Barcode area illumination” and set the “Backlight
illumination intensity” to zero.
To reach a
uniform barcode area illumination, please bend the LED’s carefully and observe
the live view. By modifying the PCB position, the uniform illumination of the
barcode area can be also reached.
1.
Adjust the position of the PCB.
2.
Bend the LEDs carefully until a uniform
barcode area illumination is reached.
The following
dialog is implemented since the version 1.11 in the program
“SlideScanner.exe” and can be found in “Options”, “Barcode settings”.
1D
Barcode Types, 2D Barcode Types
Check the
appropriate radio button for the barcode type you are expected to read. In
the file “Barcode print check.pdf” you will find enclosed the barcode set
and you can compare the view of barcode to the samples.
1D
Barcodes with check digit
This barcodes
including a check of correct reading the barcode and this is added as a digit
of the barcode (always the last character position). With checked checkbox
“Exclude check digit” this check digit is not displayed and is also not a part
of the read barcode. For test possibilities you can uncheck this checkbox, the
check digit will be displayed and is a part of the read barcode.
Fore
ground color
The foreground
color is black. If the barcode is reverse printed (white barcode on black
background) select the foreground color as white.
Preprocess
Barcode Image
Sharpen
The sharpness is
calculated meanwhile the barcode image is taken.
Gamma
modification
A slider will be
opened and you can adjust a value for gamma in the range of
Contrast
modification
A slider will be
opened and you can adjust a value for contrast in the range of
Special
Barcode Settings
Barcode
string length
You can define a
string length, coded in the barcode. This way, the barcode detection will be quicker. If
the number of coded characters in the barcode and the number of characters to
be read defined here is not identical, an error message occurs, “There is no
barcode”. If zero is selected (default) any string length can be read.
Maxi code
dot spacing
The dot spacing
for the dots in the maxi code can be defined. Maxi code barcode can be created
with dot spacing different from the default value (0). For successful barcode
decoding this dot spacing value must be defined here.
Other
Use
barcode compensation Image
This is one of
two possibilities to increase the readability of barcodes. The compensation
image, taken with the “Grab New” option is used to compensate the barcode image
for best barcode decoding results. The image is stored and will be used until
this checkbox is checked.
Grab
New
A new
compensation image is taken of the barcode area and will be stored; the
previously took compensation image will be overwritten. It is important, that
an exact white (not light gray) area is inserted and the surface should be very
smooth. An only white paper surface is too rough.
Barcode
exposure time increase
This is another
possibility to increase the readability of barcodes. Because the automatically
calculated exposure time often produces a too dark view of the barcode area,
you can increase the brightness of the view; and so you increase the
readability of barcodes. The calculated exposure time reflects to the value of
100 percent. To find a well usable value for the exposure time, the start value
of 100 percent should be increased by a step rate of 10 percent until the
optimum was found.
Check
barcode reading with different barcodes and types
Now we are
checking the readability of defined barcodes. For this purpose a set of
barcodes is required that fulfill the requirements in pixel size and mechanical
dimensions for the smallest, readable barcodes. In the appendix you find a set
of barcodes for testing. If this page is printed onto an adhesive label sheet
and each label is stuck on a slide, you created your own barcode test set. For
further details see the appendix. After all these barcodes are recognized
successfully by the Matrox Imaging Library, check some samples of the
user’s unreadable barcodes. See also chapter “7 Barcodes in practice”.
1. Start the program “SlideScanner.exe” and
in the tab “options” of the first selector screen select the option “Barcode
Settings”.
2. Insert a slide with barcode.
3. In the selector guide “Barcode
settings” select the barcode type to be decoded. The type, shown on the slide
label and selected in the “Barcode settings” must be equal.
4. Press the button “Read barcode”.
5. The software starts the barcode reading
and decoding, the result is written in the field below the button “Read
barcode”. If the barcode can not be decoded in 5 attempts the error message
“There is no barcode” is displayed.
Attention:
Some 1D barcodes can be read
with different types and the contents of the barcode is different also. To
achieve the correct barcode content select always the appropriate barcode type
in “barcode settings”!
1. Repeat steps 2 to 4 with all slides of the
barcode check set.
2. Read barcodes from the users “Hard to
read” collection.
The following
examples show barcodes, coded with Data-matrix. The left hand column shows
the original barcode area of the slides and on the right hand
column you find the same slide as it is seen by the preview camera for barcode
analyzing and decoding. In the following we analyze the barcode print. Slides
with visible faults in the barcode should be excluded from the tissue creation
process. All the following barcode prints was read with the same illumination
setup. Unreadable barcode prints could also not be read after illumination
modifying. To ensure a high print quality and to increase the readability of
the barcode the slide’s barcode area should be clean and dry, free of moisture,
before printing. The printers, even ink jet printers should be maintained in
the defined time interval and the ink cartridge should be changed if the “ink
low” message occurs. Ink jet printers have often an integrated service part
with a “Clean” option in their drivers. Run the “clean” and “Test print”
options if the print quality is reduced.
Figure
1: The slide has a LASER printed barcode
paper label. A good solution, the barcode print is rich in contrast and
therefore easily and safely readable.
Figure
2: The barcode was printed with an ink
jet printer direct onto the surface of the slide. May be there was too much
ink, the slide was moved before the ink was dry or moisture is on the barcode
area meanwhile printing. Contrast poor, blurry or diffuse barcode print is
unreadable.
Figure
3: The barcode was printed with an ink
jet printer direct onto the surface of the slide. A nozzle does not work during
printing. A missed jet in the print may be readable or not, it depends on the
position, where the jet is lost. Maintain the printer.
Figure
4: The barcode was printed with an ink
jet printer direct onto the surface of the slide. Some jets have not enough
ink, so the contrast is partially reduced. A contrast reduced print may be
readable or not. Maintain the printer and / or change the ink patron earlier.
Figure
5: The barcode was printed with an ink
jet printer direct onto the surface of the slide. Some jets have not enough
ink, so the contrast is partially reduced. A contrast reduced print may be
readable or not. Maintain the printer and / or change the ink patron earlier.
Figure
6: The barcode is engraved by a LASER
beam. The contrast is reduced because a white surface (=background) is
“printed” (as a result of engraving) with glass, so the contrast cannot be
much. This barcode needs very uniform adjusted illumination, exact adjusted
white balance and shutter values.
Appendix
Create
your own barcode check set.
In the file
“Barcode print check.pdf” you will find enclosed the barcode set. The
content of this page generates a full, specified barcode
test set.
Please print the
file “Barcode print check.pdf” perhaps with a LASER printer onto an
adhesive label sheet with 27 labels organized as 3 columns with 9 lines of
labels, the upper border is 5 mm and the lower border is 3 mm,
with no border on the left and no border on the right.
The size of one
label is 70 mm x 32 mm without space to each other.
After printing,
stick each label onto a slide and cut it around with a utility knife.
Take into account
that the slide clamp lower part in Pannoramic SCAN cuts out a bit of
the barcode area. The shadow should not disturb the barcode print.
To prevent the barcode print from dust and
finger prints during use, stick a strip “tesa Film crystal clear” 19
mm in with or equivalent translucent strip over the barcode print; so it
becomes cleanable. If the adjustments are correct and no mistake occurred
meanwhile creation, all this barcodes are readable; even if the label is
stacked on slanted.