Preview calibration procedure; SMD_II

For technicians!

 

 

 The newly developed scanners and components of SMD_II requiring enhancements in the service program also.

While these developments, the preview calibration procedure was also modified and this results in the new preview calibration program.

 

 

Requirements

 

Before starting the preview calibration program following requirements and setups should be fulfilled and should be finished:

 

General

·               Scanner type and options defined (MicroscopeConfiguration.ini).    Link S_II; M_II, D_II

·               Implemented hardware units adjusted and defined.                             Link S_II; M_II, D_II

·               Preview camera defined (MicroscopeConfiguration.ini).                     Link S_II; M_II, D_II

·               Hardware limits defined (MicroscopeConfiguration.ini).                      Link S_II; M_II, D_II

·               Scan camera defined in (Microscope settings dialogue).                    Link S_II; M_II, D_II

·               Implemented objectives defined (Microscope settings dialogue).       Link S_II; M_II, D_II

 

Scan BF image path adjusted

·               Condenser position adjusted                                                                    Link S_II; M_II, D_II

·               Chromatic aberration adjusted                                                                  Link S_II; M_II, D_II

·               Stitching adjusted                                                                                        Link S_II; M_II, D_II

·               Camera rotation angle adjusted                                                                Link S_II; M_II, D_II

 

The scanner is able to scan tissues in a high quality, only the preview quality is wrong.

 

 

 

 

               Start the service program

The software asks the service password:          seristen

 

Select the option: Preview calibration

 

Execute following adjustments next

 

·         Preview objective aperture set                                                                Link S_II; M_II, D_II

·         Preview objective focus adjusted                                                           Link S_II; M_II, D_II

·         Preview camera position and rotation angle adjusted.                      Link S_II; M_II, D_II

 

 

 

 

 

 

 

 

 

 

 

 

 

 

            Structure of the screen

 

1    Upper adjustment window

 

·        Commands for the adjustments are shown here

 

 

6   Camera window

 

The camera window contains the image of the

·        Preview camera  or

·        the scan camera

depending on the step in progress.

 

 

3   Collected adjustment parameters

 

·        As the steps are finished, defined parameters and values are shown and collected here.

 

 

4   Bottom adjustment window

 

·        Mainly common commands for the adjustments.

 

 

5   Instruction window

 

·        Instructs the operator (technician) what to do.

 

 

 

 

 

 

 

2   Stage movement and focus tools

 

·        Move the X-Y-stage to desired positions.

·        Set the focus of the scan image during adjustments.

 

 

 

Steps: Type in a step number. The value is true for the focus motor as well as the X-Y-movements.

 

 

If a known position should be reached, you may type in a desired step number into the fields X: and Y:; then press GotoXY

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Steps of calibration

 

 

 

 

 

 

 

 

           Step 1  Camera and objective

 

Task

Please select camera and objective.

 

Objective:      Select one of the installed objectives (20x recommended).

 

Camera:        Select the installed BF scan camera (recommended).

 

1.     Set and select the installed and used objective magnification. The image path of the scanner will be set to the selected magnification. With this magnification the preview calibration will be executed.

2.     Select the installed scan camera.

 

·       If the settings are correct, press “Activate camera”.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

·       If there is any trouble with the camera, press “Redo”.

 

 

 

 

 

 

 

 

 

 

 

 

           Step 2  Insert the preview calibration slide

Task

In the numerical field select or type in the slide position of the Tray or the Magazine, in which the single width calibration slide is found.

 

 

·       If the settings are correct, press “SlideIn”.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

           Step 3  Set Top X- and Y-position

 

Task

Move the stage to the position where the top of the slide can be seen.

This will set the first preview Y-position and the preview X-position!

Then cut the part which covers the top of the slide with crop from top track bar and press Calibrate all!

 

 

 

 

Cut the part above the slide. For this, move the bar.

Set the exposure time o the camera.

 

·       Type in a value and press “PWExp”.

 

Crop_From_top

 

 

 

 

 

 

 

 

 

·       If the settings are correct, press “Calibrate all”.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

           Step 4  Barcode settings

Task

Please set the barcode position and barcode area, then press “Set barcode params”.

 

4a Barcode area size

Adjust the size of the barcode area so, that the barcode area of the slide is inside the shown rectangle.

 

 

In the numerical fields “Left”, “Top”, “Right” and “Bottom” type in numerical values to modify the size of the rectangle.

 

·         If the size of the rectangle is correct, press “Set barcode crop rectangle”

 

 

 

 

Remark

Because the slide dimensions of the calibration slide are not the maximal allowed dimensions, the values for right and bottom should be defined a bit larger than the slide edge!

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

4b Barcode area position

Sett the position of the barcode area so, that the barcode area is in the center of the camera window.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

4c Barcode illumination

Adjust the position of the barcode LEDs so, that the barcode area is illuminated evenly (bend the LEDs carefully).

 

Type in a value for the exposure time, then press “PWExp”

 

·         Repeat the step until the brightness of the barcode rea is acceptable.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

           Step 5: Find circle centers

 

Task

Move the stage to the position, where the top left circle’s center can be seen on the scan camera image!

Then press Estimate BR!

 

 

 

 

Step_5a.gif5a  Set camera parameters

Because the scan camera is used first time in the preview calibration process, camera parameters should be set.

 

Exposure time

In the numerical field type in a value (e.g. 6) and press “Set Exp”.

·         Repeat the step until the brightness of the scan camera window is acceptable.

 

White Balance

·         Press the button “Calc WB”.

 

Remark

As often as you press the white balance, the color of the screen may be changed, because the RGB BF illumination unit is used.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

5a_5f_menus.gifSteps_5b_f.gif

 5b Find the top left circle

Move the stage in +X-direction first, and then use any movement button to see the circle center in the camera window.

 

·         If parts of the circle are visible, set a step size of 50steps and find the focus position of the scan objective.

 

5c  Refine top left circle center

The center of the circle is shown in the center of the screen; the circle center meets the screen cross.

 

5d  Estimate BR

The stage moves to the position of the Bottom right circle.

If the center of the circle is not visible on the screen, use the stage tools to find the circle center.

 

5e  Refine bottom right circle

The center of the bottom right center circle (4)  is shown in the center of the screen.

 

5f      Calculate

By pressing calculate, Required positions are calculated and the preview camera’s position is fit to the scan camera’s position.

If the calculation is finished, the program goes to the step 6.

 

 

 

 

 

 

 

 

 

 

 

 

           Step 6  Calculate circle centers

 

Task

Move the stage to the position, where the bottom right circles center can be seen on the scan camera image!

Then press calculate button.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

           Step 7  Check result and finish

Task

The preview calibration has been finished.

Now click on the full preview image on the right side, then compare it with the scan camera image!

If they match, then press Ini update button and remove slide!

 

 

 

 

Check the preview calibration result!

Remember, the preview image of the slide (the scan area) is made by 3 images of the preview camera and the three images are stitched to each other.

Now check the stitching quality; result is shown on the right.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

If the calibration result is acceptable,  save the ini parameters next

 

·       Press "Ini update"

 

 

To finishing the calibration procedure, Press

 

·       SlideOut and

 

·       Exit

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Calibration result check

 

 

 

Scan the corner circles of the calibration slide

 

Start SlideScanner.exe and load the calibration slide.

Deselect unwanted circles from scanning

Prepare the preview so, that only the corner circles are selected for scanning, as shown.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

By enlarging the preview to 600%, the stitching quality can be checked.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Prepare scan parameters

 

1 Routine work

 

2 Scan option

 

3 Set Preview options

 

4 Routine work

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Scan result

 

By opening the scanned calibration slide with the slide viewer, the scanned result can be checked.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Preview calibration finished

 

END