Preview unit; S_M_D

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 1.15 and the scanner “Pannoramic SCAN”, the components, procedures and adjustments are the same in the MIDI and the DESK..

 

The entire preview unit is a part of the scanner unit and designed to fulfill the following 2 tasks:

 

 

 

Contents

Configure the preview unit

Preview components

Areas of the slide

Mechanical adjustments

BF preview calibration

Barcode reading

 

 

 

 

 

 

 

 

 

 

 

 

 

Requirements

 

 

 

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!

 

 

 

 

 

 

 

 

 

 

 

 

 

Configure the preview unit

 

 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 250 is defined by the use of the following parameters and values:

 

[Microscope]

SerialNumber=xxxxx

MicroscopeType=3DMicX

ScanCameraType=

PreviewCameraType=CVrmc_m8_pPro

BarcodeReaderType=PreviewCamera

LoaderType=SL_6Mag_25Slide_NoSensor_Vertical

ReflectorTurretType=RT_3DH_10Pos_Gear

ObjectGuideXYZType=OGXYZ_1

PreviewLightType=PreviewLightUnitType_Type1

 

 

Remark

In earlier scanner versions this section may be very small, only the preview camera type may exist. If parameters and values are missed, these options are handled like usually for Pannoramic S_M_D.

 

MicroscopeType=3DMicX

·      The scanner type is defined here:         3DMic5 = DESK      3DMic6 = MIRAX SCAN          3DMic7 = MIDI       3DMic8 = SCAN 150 and Pannoramic SCAN

 

Depending on the presence of the darkfield preview illumination there are two parameter values possible in the section [Microscope].

 

PreviewLightType=PreviewLightUnitType_Type1;        The darkfield preview illumination is not present; only brifhtfield preview images are possible.

 

PreviewLightType=PreviewLightUnitType_Type2;        if the darkfield preview illumination unit is present; this enables the creation of the darkfield preview also.

 

PreviewCameraType=CVrmc_m8_pPro;          if the preview camera is “VRmagic”

PreviewCameraType=DFK_21F04;                 if the preview camera is “DFK 21F04”

 

 

 

 

 

 

 

Principle of brightfield preview

 

 

 

 

Brightfield illuminated preview

 

  • The preview illumination illuminates the background of the entire field of view of the preview camera, behind the slide.
  • Because the slide is much larger then the field of the preview camera’s view, the scan area of the slide is captured in 3 sections; the made 3 images are rotated, cut and assembled by software; the required parameters are defined during the preview calibration process and collected in the section [PreviewAndBarcodeScanning] of the file MicroscopeConfiguration.ini.
  • The assembled preview, the scan area of the slide, is shown in the preview window of the slide scanner program.
  • The barcode area is only a little bit smaller than the captured field of the preview camera’s view and is shown in the barcode window.

 

 

 

 

See also:      Scan area” and “Barcode area

 

                    Creation of preview

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Components and construction

 

 

 

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.

 

See also:      Construction, Preview camera DFK 21F04

                    Scanner plate and horseshoe

 

 

 

 

 Preview illumination

 

The preview illumination illuminates the background of the slide in the size of the preview camera’s field of view.

 

See also:      Preview illumination

 

 

 

 

 

Barcode illumination

 

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.

 

 

See also “Barcode adjustments” “Barcode illumination”.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Preview unit mounting

 

 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.

 

See also:      Scanner plate” and “Horseshoe mounting

 

 

Remove the preview unit

·      Disconnect the cables for the preview illumination, 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

 

 

 

 

 

 

 

 

 

 

Because the production of the preview camera “DFK 21F04” was discontinued, the scanners S_M_D are delivered since spring 2013 with the camera VR magic “VRmc-8+ PRO”.

 

·      The horseshoe is modified to the requirements of the camera and objective holder for the camera VR magic “VRmc-8+ PRO”.

·      The construction of the camera mounting is the same as in the P250.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Preview camera and objective holder

 

 

 Camera DFK 21F04

 

To make the preview camera position adjustable, a mounting plate is used. The mounting plate is mounted to the horseshoe at three positions, so a three-point-adjustment is realized.

 

 

 

 

 

 

 

 

·      With the “Adjustment bolts” the plane of the preview camera will be defined and this position is fixed by the “Mounting bolts”.

·      By adjusting the plane of the preview camera, the camera rotation angle will be adjusted also!

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 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:

  • Hold the camera from beneath (the rear of the camera) and loosen the position fixing bolt a little bit until the camera becomes barely moveable.
  • By loosening one of the “Rotation angle” bolts and tightening the opposite bolt, the rotation angle will be modified.
  • If the correct camera rotation angle is found, tighten the “Position fixing” bolt; further information can be found in the chapter “Adjust the preview camera rotation angle”.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Preview camera and objective

 

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.

 

  • The distance ring has a thickness of 1.5 mm nominal.
  • The shown focus value is for information only, the real value will be found during the preview calibration process.
  • Set the value of the aperture iris to 3.0.

 

 See also:     Preview camera VRmc-8+ PRO

                    Preview objectiveTAMRON 23FM16SP

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Areas of the slide

 

 

 

Scan area

 

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.

 

See also:      Define the scan area”.

 

 

 

 

 

 

 

 

 

 

 

 

Barcode area

 

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”.

 

See also:      Barcode illumination”; “Adjust the barcode illumination”, “Step 16 of the preview calibration procedure and “Barcodes in practice

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

When shall I check or define the scan area?

 

  • If the X-Y-stage was exchanged
  • If the parallelogram was adjusted
  • If any modifications on the specimen holder or its mounting was taken
  • If the scan area of the slide is too small or too much.

 

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.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Scan area and specimen holder

 

 

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.

 

 

 

 

PSCAN

 

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.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

PMIDI

 

The slide is held in the specimen holder with the help of three slide studs, situated on the longer edges as shown.

The surrounding of the slide stud is left out automatically from the scan process since the software version 1.14 and needs not more to be excluded manually from the scan area (until software version 1.16).

 

 

·      During movements with the service program, please do never touch the slide stud with the focus pin or the objective!

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 Since the software version 1.16

 

To avoid, that the objective may touch the slide stud, the area of the slide studs is defined explicitly; new parameters are implemented in the section [HardwareLimits] of the file “MicroscopeConfiguration.ini”.

·      Move the stage to the positions “Knot#Left”, “Knot#Right”, “Knot#Top” and “Knot#Bottom” 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.

·      Because the objective will never reach the slide stud “MidiKnot3”, these values should be left unchanged.

 

·      Please take this into account, if software is upgraded from an earlier version to the version 1.16 or higher!

 

 

 

 

 

 

 

 

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 areas are excluded from the scan area!

·       Because the objective will never reach the slide stud “MidiKnot3”, these values should be left unchanged.

 

·      The path of the file “MicroscopeConfiguration.ini”, since the version 1.15 is:

 

                    C:\ProgramData\3DHISTECH\SlideScanner\MicroscopeConfiguration.ini

 

 

Remark

Because the values are always checked before executing the number of steps to go in the scan program, the value of “-2000 steps” will be cut to the value of the hardware limit!

 

 

The stud has a size of about

 

Top to bottom:        12mm

Left to right:            8mm

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

PDESK

 

The slide is hold in the specimen holder by the help of one slide stud on the shorter, inner edge and by the lock handle on the outer, shorter edge. Furthermore, along the longer edges of the slide there are leading rails situated to lead the slide during slide insertion. All this facts should be taken into account if the scan area is defined. The surrounding of the slide stud is left out automatically from the scan process since the software version 1.14 and needs not to be excluded manually from the scan area (until software version 1.16). If you are working with the service program take care of the focus pin and the objective. 

 

·      During movements with the service program, please do never touch the slide stud with the focus pin or the objective!

 

 

 

 

 

 

 

 

 

Since the software version 1.16

 

To avoid, that the objective may touch the slide stud, the area of the slide stud is defined explicitly; new parameters are implemented in the section [HardwareLimits] of the file “MicroscopeConfiguration.ini”.

·      Move the stage to the positions “KnotLeft”, “KnotRight”, “KnotTop” and “KnotBottom” 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.

·      Please take this into account, if software is upgraded from an earlier version to the version 1.16!

 

 

 

 

 

 

 

 

 

 

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

 

 

 

 

 

 

 

 

 

 

 


 

 

Check the found limit position

 

 To decide, the focus pin is whether on glass or metal is touched, the following actions can help.

 

·      Move the focus pin to the focus position of 800steps.

·      Move the specimen holder with the finger nail carefully to the left by about 0.5 mm maximal so, that the mechanical preload of the specimen holder is overridden; the slide is even disconnected from the focus pin.

·      Release the specimen holder abruptly.

·      The behavior and the sound can be used to decide the focus pin is whether on glass or on metal.

·      To use this method effectively, try this some times on different, non critical and critical positions on the slide; listening and memorize the sound for glass.

 

 

 

 

 

 

 

 

 

 

 

 

Define the scan area

 

 

The following “flow chart” describes the steps for Pannoramic SCAN especially. The steps for MIDI and DESK 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 Mservice.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 100 in X-direction until the specimen holder is reached.

 

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.

 

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.

·      See also “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:

  • Driver of the preview camera is installed.
  • Hardware limits of the X-, Y- and focus unit are defined.
  • Home position of the turret unit is already adjusted; the first filter position is defined.
  • Brightfield preview illumination was checked with the service program and can be switched on / off.

 

 

 When shall I do a preview calibration?

  • If the focus position of the preview objective was altered.
  • If the preview camera was loosened, dismounted, changed.
  • If adjustments are done on the parallelogram or the specimen holder or the X-Y-stage was exchanged.
  • If the scanned area of the tissue is different from the selected area in the preview window. 

 

 

 

 

 

 

 

Steps of the preview calibration procedure

 

  1. Set the aperture of the preview objective (Tamron objective only).
  2. Start the preview calibration procedure

3.               Adjust the focus of the preview objective.

4.               Adjust the rotation angle of the preview camera.

  1. Adjust the objective position of the 20x scanner objective (if not adjusted previously).
  2. Define the barcode area

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Preview camera position; DFK

 

Attention: If you adjusted the mechanical mounting of preview camera or you adjusted the focus of preview camera, a preview calibration should be done again. Otherwise, the scanned area of tissue will be different from the shown area in the preview window.

 

To adjust the preview camera you need a 1,5 mm hex wrench.

 

Start the service program “SlideScannerService.exe” and the option “Preview calibration”.

 

 

Adjust the preview camera position

 

Bring the Y-stepper in the position of -800 steps if the hardware limit of the Y-min position allows it. This value is suggested for all three scanner types. Set the X-stepper value to 28000.

The preview camera mounting is realized with three bolt pairs. The adjustment bolts define the distance of the camera holding plate from the base. The mounting bolts fix this distance.

 

·      By loosening the mounting and the adjustment bolts the preview camera becomes movable.

 

 

 

 

 

 

 

 

 

 

 

 

  • Adjust the top slide edge parallel to the edge of the live view preview camera window (in reality, the preview camera image will be rotated). The camera rotation angle is acceptable if the top of the slide edge is parallel to the top edge of the preview camera window; an acceptable deviation is often less then 0.5 degrees.

 

 After tightening the mounting bolts and adjustment bolts, any kind of shadow should be minimized and the top of the slide should not be cut too much.

 

 

 

 

 

 

 

 

 

 

 

Remark: The shadow on the top edge of the preview will be cut later, during the preview calibration procedure; “Step 2”.

 

·      On the slide bottom any kind of shadow must be eliminated!

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Adjust the preview focus; DFK

After inserting the calibration slide the live view of preview camera is shown in the camera window.

Use the crosses of the calibration slide to adjust the focus of the preview camera objective. After starting the preview procedure this focus position should never be changed, otherwise, the preview calibration procedure has to be done again.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Use the crosses of the calibration slide to adjust the focus of the preview camera objective.

  • Loosen the fixing bolt of the focus part of the preview objective, adjust the focus position so, that the centers of the circles are in focus and then tighten the fixing bolt.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Set aperture; Tamron

 

  • Loosen the aperture fixing bolt, set the aperture to a value of 3.0 and tighten the fixing bolt.

 

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.

  • The manual mode should be selected if the magazine unit is removed.
  • The automatic mode should be used if the magazine and slide loading procedure is done by the magazine unit and the slide loader.

 See also:     Insert or remove a slide manually

After inserting the preview calibration slide (Test slide #2) the live view of the preview camera is shown in the camera window.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Use the crosses of the calibration slide to adjust the focus of the preview camera objective.

  • Loosen the fixing bolt of the focus part of the preview objective, adjust the focus position so, that the centers of the circles are in focus and then tighten the fixing bolt.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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.

 

  • Loosen the brightfield preview illumination adjustment and fixing bolts a little bit and remove the shadow from the top edge of the live view window, then tighten the bolts carefully; they are driven into plastic!

 

 

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.

  • Hold the camera from beneath (the rear of the camera) and loosen the camera holder fixing bolt a little bit until the camera becomes barely moveable.

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.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

  • Adjust the top slide edge parallel to the edge of the live view preview camera window (in reality, the preview camera image will be rotated). The camera rotation angle is acceptable if the top of the slide edge is parallel to the top edge of the preview camera window; an acceptable deviation is often less then 0.5 degrees.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Remark: The shadow on the top edge of the preview will be cut later, during the preview calibration procedure; “Step 2”.

 

·      On the slide bottom any kind of shadow must be eliminated!

·      Modify the preview illumination position, until the requirement is fulfilled; check also the correct preview camera position!

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Preview calibration procedure

 

 

 

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 (Test slide #2) defines positions inside the scan area with circles containing a cross. The centers of the crosses are marker positions for the preview camera and the scan camera also.

 

 

 

 

 

 

 

Calibration program tools

 

 

 

 

X- Y- Stage area

 

X: steps        Actual position of the X-stepper motor

 

Y: steps        Actual position of the Y-stepper motor

 

X-Y step:      5000   Step range for the blue arrow buttons

 

 

 

Scale 1, 10, 100

The step number of the numbered buttons can be varied between at least 2 steps (Scale=1) and 2000 steps (Scale=100). This way, you can find desired positions quicker.

 

·      With a right click on a numbered or arrow button the original direction will be inverted. The stepper motor is moved with the number of steps written in the button but the movement occurs in opposite direction.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Focus

Auto: Finds the focus position via the auto focus function, realized in the program SlideScanner.exe.

 

1600: Actual focus position field

 

Step rate:    Step rate for the blue arrows. By right clicking on an arrow button (or a numbered button also), the original direction will be inverted by the actual number of steps, given in the field “Step rate”.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Each step of the preview calibration procedure is finished by pressing the NEXT button.

With the Previous Step button you can go backward step by step. At some steps this option is not available. 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The command and status window tells you the instructions, what to do and results of calculations.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                                 Steps of preview calibration

 

 

 

 

Step 1:   Automatic slide handling:     uses the slide insert and remove options offered by the SlideScanner.exe program.

 

Manual:   moves the specimen holder to a position where a slide can be easily inserted or removed. The insert or remove procedure is done by the user, manually (e.g. if the magazine unit is removed).  

 

See also:      Insert or remove a slide manually

 

 

 

 

 

 

 

 

 

 

 

 

Step 2:   Cut from top:

Go to the position Y= 14000 with the Y-Stage tool, so that the top of the slide is visible. If the preview camera is already adjusted and there is a shadow visible on the top part, it has to be cut off with this option. Because the entire preview is assembled from three preview camera images, this shadow have to be fully cut. See also „Adjust the preview camera position”.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Step 3:   Position the central circles between the red lines:

 

 

                With the tools in the “X- Y-Stage area” the desired result will be reached. An accuracy of 200 steps is enough.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Step 4:     Adjust the threshold until only the circles are visible:

 

Remark: This step is done only one time, if the three circles are in the middle of the preview window.

 

Before threshold adjustment

  

 

 

 

 

 

 

 

 

 

 

 

 

Adjust threshold until the inside of the circles is empty, without dots or lines, but the circles are fully visible.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The desired result after the threshold adjustment

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Step 5:     Place the red squares over the circles:

 

The cross in the middle of the red squares should be inside of the circle, but an exact match with the center of the circle is not required. The squares are numbered; please place the squares in the right order: 1, 2, and 3 from left to right.

 

  • By dragging one of the red squares with the left mouse button all three squares are moved at the same time, by dragging with the right button, you can move each square separately.

 

·      The squares are numbered; please place the squares in the right order: 1, 2, 3 from left to right.

 

 

 

 

 

 

 

 

 

 

 

 

Step 6:     If the calculated circle centers are correct...

 

 

The correct result is shown on the right.

The blue crosses meeting the center of the circles.

 

Step 7, 8 and 9:

Repeat the steps 3, 5 and 6 on the top of the camera window logically.

 

Step 10, 11 and 12:

Repeat the steps 3, 5 and 6 on the bottom of the camera window logically.

 

 

 

 

 

 

Step 13:   Move the stage to the most homogenous background illumination

 

Some times on the left edge of the camera window illumination differences are visible. By moving the stage to the right by several hundreds of steps the uneven illumination can be eliminated or minimized.

 

·      If the stage is moved too much in the direction X-min of the scan area, the unevenly part of the illumination may be visible.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                                                                                                                Without uneven illumination   

 

 

 

 

 

 

 

 

 

 

 

 

 

Step 14:   Find the centre of the spots

 

Fit the center of the black cross with the centre of the red cross by using the X- Y- stage control buttons.

Before you press the NEXT button for the first time, you can correct the scan camera position / rotation angle and the 20x objective focus position.

After starting this step the auto focus option adjusts the focus position for the scan camera. Now you can adjust the focus position of the objective for the scan camera manually, if required.

 

After pressing the button “TEST Backlash” check the position of the crosses to each other again and correct this if necessary. After pressing the TEST button the X-Y-stage is moved to the next circle by pressing the NEXT button (the same button with double task).

 

 

 

 

 

 

 

 

 

 

 

 

 

Repeat this procedure with all 9 circles.

·      Since the software version 1.15 only the 4 corner circles are used.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Step 15:   Place the red squares onto the corner circles

 

The cross in the middle of the red squares should be inside of the circle, but an exact match with the center of the circle is not required.

By dragging one of the red squares with the left mouse button all four squares are moved at the same time, by dragging with the right button you can move each square separately.

 

·      The squares are numbered! Please place the squares in the right order: 1, 2, 3 and 4 from top left to bottom right.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 



 

Step 16:  Fit the barcode area into the red square

 

With the X-Y-stage control buttons bring the barcode area of the slide into the red rectangle. The border, given by the red rectangle should be a little bit away from the left slide edge. Because the slide width tolerances of the allowed slide size are growing up or reduces the right side of the slide, the right edge should be fully inside the red rectangle if we are not using the widest possibke slide.

The lower edge of the slide should be equal with the lower edge of the preview camera window.

 

Furthermore, we adjust now the barcode illumination.

·      Bend the LEDs carefully so, that the barcode area is illuminated nearly homogenously.

·      Modify the exposure time of the preview camera to lower values, so the adjustment can be checked easier.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

After finishing step 16 a dialog appears on the screen and you can check the result of preview calibration visually, if you answering YES (Igen).

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Step 17:  Test the result

By selecting a higher resolution with the “Scale factor” the possibility to find the centre of the circle is higher. The goal of this option is that by clicking with the cursor in the middle of a circle on the preview window (right window), to see the center of the circle in the camera window.

This way, you can check the result of the calibration before exiting the calibration program.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 At the end of calibration, please do not forget to save the resulting parameter values to the file “MicroscopeConfiguration.ini” by pressing the ”Update Parameters” button.

 

Exit the preview calibration program by pressing the button DONE.

 

Next we scan the top left circle with the program “SlideScanner.exe”.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Adjust the pixel position of the preview camera

 

 

 

 

 

 Adjust the pixel position of the preview camera to the field of view of the scan camera.

 

The goal of this adjustment is, to see the same part of the tissue with the scan camera and the preview camera also.

This task is done by the preview calibration program, but the software is not able to find this position correctly. Therefore, we must adjust the position of the pixel of the preview camera more precise to the position of the field of view to the scan camera “manually” by modifying pre-calculated parameter values.

 

As shown on the right the scan program offers in the preview window the entire circle for scanning (dilation=0; the red-brown area).

By checking the scan result with the viewer, we can see, the circle is cut, so the offered area is incorrect.

 

·     The size of the cut part is variable.

 

This chapter describes which parameter values must be modified to fit both areas.

 

 

 

Important remark

·     The offered scan area, offered by the preview camera’s view, will be named as “Spot”

·     The really scanned area is represented by the “Circle”.

·     Of course, the entire area is scanned by the scan camera, but our reference position will be the center of the circle in relation to its surrounding.

·     In the picture above, the circle is cut, this means, the offered area for scanning (offered by the preview camera) will not met the real position of the circle on the slide.

·     Therefore, we have to shift the offered preview area (the spot) to the left and a bit downward; so we will see the circle in the center of the offered scan area.

·     All modifications, described below are done with the offered scan area, offered by the preview camera’s view!

 

 

 

See also:      Pixel position and corrections and  FOV and Preview

 

 

 

 

 

 

 

 

 

 

 

 

Scan the top left corner circle

 

Start the SlideScanner.exe, load a magazine with the calibration slide, insert the calibration slide and set the following options:

 

In the preview section check the box “Use selection box”.

 

Select the upper left corner circle of the calibration slide with the selection box as shown. Hereby it is important, that a small not scanned area is included inside the selection box (white area).

 

 

Select the options “Fill holes in scan area” and “Remove specks”.

 

Select the “Scan area dilation” to zero.

 

With “Manual threshold” checked, adjust the threshold of the preview so, that unwanted pixels are not disturbing the view.

 

Adjust the “Speck size” as needed.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Select “Live view” in the section “Focus”.

 

Find any edge or a part of the cross with the positioning tool (below the preview window) in the upper left corner circle in the preview window and bring it into focus.

 

Check the option “Limited focus range” and click “Set current”.

 

This way we are using the limited focus range for the upper left corner circle during the scan process.

 

 

 

 

 

 

In the dialog “Scan options” uncheck the checkbox “stitching”.

 

The focus frequency values are shown for the marlin camera.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Define a destination path for the slide to be scanned.

 

If the directory already exists, you can select it by using “Browse”, otherwise you can type in a path in the field “Slide directory path”.

 

Exit the dialogue “Scan options” with OK.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Type in a file name and start the scan process.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

With the viewer program we checking now the result, it can be somewhat like this.

 

As visible, the circle is situated in the bottom left corner of the spot, defined by the preview camera. Therefore, the circle should be moved to the right and upward in relation to the spot.

 

·   In practice, we are shifting the spot (the tissue area, offered by the preview camera) downward and to the left, so, the circle position moves center-ward!

 

 

 

·      The spot represents the scan area, offered by the preview camera.

·      The circle represents the actual position of the scan camera in relation to the preview camera (the spot).

·      The goal is now to move the circle into the center of the spot.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

  

 Use this calculation table to correct the position of the circle

 

 

This table is available as an Excel file and by setting the desired input parameters (In the green pull down menus) the configuration in front of you can be selected. The result is shown in the yellow fields; this value should be added or subtracted respectively from the named parameter value. The parameters are found in the file MicroscopeConfiguration.ini section [PreviewAndBarcodeScanning].

 

The “Status” line shows mistakes, if the selected parameters can not be used in conjunction with the defined scan camera, but the calculated result is always correct for actually set options! 

 

·     The status informs you, that the selected combination is incorrect, it is a warning only!

 

See also:    FOV and Preview”; “Calculate offset value” and “Sensor characteristics

 

 

Load the EXCEL table

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Preview corrections and pixel position

 

Scan the 4 corner circles of “Test slide #2”. To achieve a good scan quality it is necessary to define a focus limit range in the option “Focus” of the scan program. With the Pannoramic viewer program we are checking the relation between tissue (the circle with cross) and the spot (visible surrounding of the sample) of the scanned test slide #2. The goal is to fit the image, offered by the preview camera (the spots) with the circles, the real position of the tissue. Use the table above to calculate the values for fitting the tissue nearly to the center of the spot.

 

The appropriate parameters are found in the file “MicroscopeConfiguration.ini” section [PreviewAndBarcodeScanning]. In reality, we are moving the spot (the area, seen from the preview camera), not the tissue (position of the scan camera). All corrections described here are made with the preview image. The calculated values are added to or subtracted from the actual values. For correction you can use integer values only (except “PreviewImageMicrometerPerPixelX” and “PreviewImageMicrometerPerPixelY”), fractions should be rounded.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Shift the spots up or down

 

With this correction the entire tissue (all four corner circles) are moved seemingly up or down respectively and only the circles connected with line “1” should be observed after correction and scanning, in relation to the spots of the previous scan result. In reality the position of the scan area, seen by the preview camera is modified (the position of the spot). This way, the pixels, seen by the preview camera are adjusted to the FOV of the scan camera. In some cases, you are unable to fit the circles exactly; then you should use an optimum value. The parameter value to be modified for this adjustment is “PreviewImageTopLeftCornerPositionY” and is situated in the file “MicroscopeConfiguration.ini” section [PreviewAndBarcodeScanning].

To shift the spots downward, increase the value of the parameter “PreviewImageTopLeftCornerPositionY”.

 

 

  

·      In the example on the right, increase the value of the parameter PreviewImageTopLeftCornerPositionY”.

 

 

See also:      Pixel position and corrections and  FOV and Preview

 

 Load the EXCEL table

 

 

 

 

 

 

 

 

 

 

 

 

 

Shift the spots left or right

 

With this correction the entire tissue (all four corner circles) are seemingly moved left or right respectively and only the circles, connected with line “2”, should be observed after correction and scanning in relation to the previous scan result. In reality the position of the scan area, offered by the preview camera is modified (the position of the spot). This way, the pixels, seen by the preview camera are adjusted to the FOV position of the scan camera. In some cases, you are unable to fit the circles exactly; then you should use an optimum value. The parameter value to be modified for this adjustment is “PreviewCropLeft” and is situated in the file “MicroscopeConfiguration.ini” section [PreviewAndBarcodeScanning].

To shift the spots to the right, increase the value of the parameter “PreviewCropLeft”.

 

 

 

·      In the example on the right, increase the value of the parameter PreviewCropLeft”.

 

 

 

See also:      Pixel position and corrections and  FOV and Preview

 

Load the EXCEL table

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Shift the right hand spots

 

The pixel size of the preview will be corrected or modified in X-direction of the entire sample. Because the influence of this parameter to the left hand part of the sample (circles) is very small, you can really use it to correct the position of the right hand circles, connected with line “3”.  To correct the position shown on the right, you should increase the value of the parameter “PreviewImageMicrometerPerPixelX by 0.1 to move the spot to the right (the tissue seemingly moves to the left in relation to the spot). If you adding to or subtracting from the parameter value 0.1 the spots are moving nearly by one FOV.  In some cases, you are unable to fit the circles exactly, then you should use an optimum value.

 

 

 

 

 

·       In the example on the right, increase the value of the parameter “PreviewImageMicrometerPerPixelX”.

 

 

See also:      Pixel position and corrections and  FOV and Preview

 

 

 

 

 

 

 

  

 

 

 

 

 

 

 

 

 

 

Shift the bottom spots

 

The pixel size of the preview will be corrected or modified in Y-direction of the entire preview image. Because the influence of this parameter to the upper circles is very small, you can really use it to correct the position of the lower circles, connected with line “4”.  To correct the position shown in the right hand picture, you should decrease the value of the parameter “PreviewImageMicrometerPer PixelY by 0.1 to move the spot upward (the tissue seemingly moves downward). If you are adding to or subtracting from the parameter value 0.1 the spots are moving nearly by one FOV. In some cases, you are unable to fit the circles exactly; then you should use an optimum value.

 

 

 

 

·      In the example on the right, decrease the value of the parameter “PreviewImageMicrometerPerPixelY”.

 

 

See also:      Pixel position and corrections and  FOV and Preview

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Prepare the preview for scanning

 

Start the Pannoramic SCAN software, load a magazine with the calibration slide, insert the calibration slide and prepare the preview of the test slide #2 as described above in the chapter “To scan the upper left corner circle”.

 

In the preview tools select the tools:

 

·   “Square or Rectangle” (a)

·   “Not scanned” (b) and

·   “Zoom 200%” (c).

 

 

 

By drawing rectangles, exclude the horizontal and vertical center circles from the scan process as shown with 1 and 2 of “The prepared preview”.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

  

 

Set the limited focus

 

With the limited focus the scan process of the test slide is done quicker and the circles are scanned sharpen. To ensure, that all four circles are scanned sharpen, the focus position must be checked for each of the circles, and depending on the focus position of each circle the limited focus range must be defined.

 

1.     With the positioning tool selected, find the center or any edge of the circle (1).

 

2.     Press the button “Auto focus” (2).

 

3.     Select a step rate of 5 or 10 focus steps and check the found focus position of sharpness (2a, 2b).

 

4.     If the sharp life view is found (3), check the checkbox “Limited focus range” (4) and press the button “Set current” (5). The software defines the limited focus range by the upper limit = actual focus position + 32 focus steps and the lower focus limit = actual focus position -32 focus steps.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Check or set the focus limit for the other 3 circles

 

5.     Repeat steps 1 to 3 with the next circle.

 

6.     Check the found focus position in relation to the existing focus range. If the found focus position is inside the existing focus limits, check the next circle.

 

7.     If the found focus position is outside the existing focus limit, type a new value for the upper or lower focus limit respectively as required (6). In the example on the right a value of 1560 for the lower limit would be acceptable. If the scanned circles are partly not sharp, might be the focus range must be defined larger.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Correct the preview and adjust the pixel position

 

1.     Insert test slide #2 and prepare the preview so, that only the four corner circles will be scanned. Check the focus position of all four corner circles as described above and define a limited focus range.  Use always a different file name for each scanned slide.

 

2.     Scan test slide #2.

 

3.     Switch to SlideViewer.exe and load the just scanned test slide.

 

4.     Check the position of the upper two circles in relation to their spots. For better visibility use the “color panel” “correction” option and shift the contrast slider downward and the gamma slider fully up. So you get better contrast for the spot and it will be more visible.

 

5.     Calculate the number of FOV for shifting the sample up or down respectively and modify the appropriate parameters (PreviewImageTopLeftCornerPositionY and PreviewCropBottom) in “MicroscopeConfiguration.ini” and save the file.

 

6.     Exit the entire SlideScanner.exe program and start it again to reload the .ini files with the new parameter values. Repeat steps 1 to 6 until the tissue fits their spots in Y-direction, see also above “Shift sample up / down. If this adjustment is finished, go to step 7.

 

7.     Repeat Steps 1 to 6 logically, but now we adjust the spots by shifting them left /right.  See also above “Shift sample left / right. Repeat this sequence until the position of the circles, connected with line “2” are in the centre of their spots, so the X-position is defined.  If this adjustment is finished, go to step 8.

 

8.     Repeat Steps 1 to 6 logically, but now we are adjust the spots connected with line “3”by shifting them left /right. This we achieve by modifying the parameter value of Preview ImageMicrometerPerPixelX. See also above “Shift the right hand spots”.

 

9.     Repeat Steps 1 to 6 logically, but now we are adjust the spots connected with line “4” by shifting them up / down. This we achieve by modifying the parameter value of PreviewImage MicrometerPerPixelY. See also above “Shift the lower spots.

 

 

 

 

 

 

Result of scanning the corner circles of the calibration slide and finishing the preview calibration adjustment

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

·      Please do not forget to uncheck the option “Limited focus range” and to check the option “Stitching”.

 

 

 

 


 

Finally

 

If the preview calibration and the pixel size adjustment was done and the program SlideScanner.exe is running, load a slide, increase the preview area size if necessary and check the correctness of the scan area adjustment as follows:

 

·    After the positioning tool is selected click on the edges and outside of the slide (in the preview area window) and check after each click the correctness of the position as described in the paragraph above “Check the found limit position”. The limit of specimen holder movement is always the scan area.  If the focus pin is jamming or the check sounds like metal, the scan area is too large and must be decreased at the appropriate edge.

 

·    Check the corners also, especially the “rounded” corner.

 

 

 

 

 

Save the file “MicroscopeConfiguration.ini” to the EEPROM of your scanner.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

  

 

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 adjustments

 

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 thePreview 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.

 

 

 

 

 

 

 

 

 

 

 

 

Barcode Settings dialog

 

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.

 

 

 

 

 

 

 

 

 

                                 Barcodes in practice

 

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.