Preview unit; D_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 DESK_II”, the components, procedures
and adjustments are the same as in the MIDI_II and the SCAN_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 Pannoramic DESK_II
is true since the software version 1.23 and uses the following parameters and
values:
[Microscope]
SerialNumber = PDESK-024xxx
MicroscopeType = 3DMic12
ScanCameraType =
PreviewCameraType = CVrmc_m8_pPro_Double
BarcodeReaderType = PreviewCamera
LoaderType = SL_1Slide_DoubleWide
CameraChangerType = CC_None
ReflectorTurretType = RT_None
BrightfieldLightSourceType =
RGBLedLight
ObjectiveChangerType = OC_None
ObjectGuideXYZType =
OGXYZ_TypeDouble
FlashUnitType = NoFlashUnit
NDFilterType = ND_None
PreviewLightType =
PreviewLightUnitType_Type3
PowerSwitchBoardType = PowerSwitchBoard_None
[HardwareLimits]
Principle
of brightfield preview
The principle of creating the preview has not
changed in relation to the DESK, but, because now the preview has to be done
for double width slides also, the procedure is modified.
Brightfield illuminated
preview; single width slide
“Scan
area” and “Barcode area”
Brightfield illuminated
preview; double width slide
Because the slide is double in width, the preview
images are also made twice.
The advantage of this is, that the mechanics and
optics modifications are minimized.
The images are taken as shown with numbers.
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 DFK
21F04
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 door switch, the slide width
sensor, the barcode illumination and the preview camera’s FireWire 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
Horseshoe,
mountings
· The
horseshoe contains the mountings and drillings for the units as shown.
Preview camera and objective holder
Camera VR magic
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:
Since autumn 2016 with the camera VR magic
“VRmc-8+ C”.
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
Preview
camera Vrmc 8+/C with objective
Since autumn of
Adjust the real focus position with the focusing part of the objective
during the preview calibration procedure.
For camera and objective values, cabling, driver setup and others,
please refer to the camera VRmC-8+ PRO, above.
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 4 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 4 of the
preview calibration procedure” and
“Barcodes in practice”
Barcode
area of double width slide
As discussed above, the barcode area of the double
width slide is realized by capturing 2 images.
Because the images 7 and 8 are stitched together,
pixels of the barcode may be lost during
stitching and so, the barcode may be unreadable.
Therefore, please do not place barcode in the stitched
area.
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.
D_II
The slide is hold by the specimen holder on the
longer, left edge and with a slide clamp on its right side, on the barcode
area. 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.
To avoid, that the objective may touch the slide stud,
the area of the slide stud is defined explicitly; parameters are implemented in
the section [HardwareLimits] of the file “MicroscopeConfiguration.ini”.
· With the
service program, move the stage to the positions “DeskKnotLeft”,
“DeskKnotRight”, “DeskKnotTop” and “DeskKnotBottom” just before the objective
would touch the slide stud and actualize the value of the appropriate
parameter; the accuracy should be 100 steps.
· If the
objective was changed from 20x to 40x the slide stud area has to be defined
again.
The values are found at the end of the section
[HardwareLimits] in the file “MicroscopeConfiguration.ini”.
· The values, shown on the right are for
demonstration only and should not be used!
· The defined area is excluded from the scan area!
· The path of the file
“MicroscopeConfiguration.ini”, since the version 1.15 is:
C:\ProgramData\3DHISTECH\SlideScanner\MicroscopeConfiguration.ini
Define
the slide stud area
· The values of the
slide stud area are defined just before the objective would touch the slide
stud; please use an accuracy of 100 steps.
·
To define the values, please use the same technique as
described above, in the chapter “Define the scan area”.
· The defined areas are excluded from the scan area!
· Because
the objective will never reach the slide stud “MidiKnot3”, these values should
be left unchanged.
“Scan
area and specimen holders”, “PMIDI” and “PDESK”
The following “flow chart” describes the steps for Pannoramic
SCAN especially. The steps for
· 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 'Calibration slide
single width'.
2.
Start the Service 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.
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
3.
Adjust the focus
of the preview objective.
4.
Adjust the
rotation angle of the preview camera.
Set
PV objective aperture
Remark: To adjust
the aperture of the preview objective the focus unit should be removed or the
horseshoe can be dismounted.
Use the
components of the calibration slide to adjust the focus of the preview camera
objective.
Set
aperture; Tamron
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” or “Automatic” mode; select the
appropriate option.
After inserting the single width preview calibration
slide, the live view of the preview camera is shown in the camera window.
“Insert or
remove a slide manually”
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 refer to
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 scanners,
equipped with
If the barcode reading is not allowed in the dongle for
the SlideScanner software, barcodes can not
be read; nevertheless the barcode dongle is connected.
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.
Requirements
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”.
Driver
installation
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; also if the label is stacked on slanted.