FOV and Preview Area

For experienced technicians and beginners

 

 

 

The following chapter shows the preview image path, captured with the preview camera and the image path of the Field Of View, captured by the scan camera. Mainly the construction, proportions and relations of the optical paths to each other are discussed and calculations are performed in relation to different sensor and pixel sizes of the preview and the scan camera. These calculations are performed by the preview calibration program and resulting values are used during the preview creation process of “SlideScanner.exe”.

 

 

             Contents

General

Theory

Creation of preview

Sample scan process

Relations and calculations

Preview camera’s view

PreviewAndBarcodeScanning

Optical path and Field Of View

            Influence of the camera adapter

            Sensor characteristics

 

Pixel position and corrections

            Calculate the offset value

 

·      The following procedures are done by software, automatically, but in some situations the shown information may help to understand processes.

 

The slide dimensions are defined as:

 

Width (X):        25.00 to 26.00mm

Length (Y):      75.00 to 76.00mm

 

 

 

 

 

 

                   General

 

Pannoramic scanners including always a preview unit and a scanner unit to create a virtual tissue from the sample, situated on the slide.

 

·      The entire slide is principally divided into 2 areas, the scan area where the sample is expected to be and the barcode area, containing information about the tissue.

 

The made preview is shown in the preview window of Slide Scanner and it shows the entire content of the scan area, so the user is able to select the tissue, parts of the tissue (if the tissue is large) or only small areas of interest.

 

·      The preview camera captures the barcode area also during the preview creation process and the taken image is transferred to the barcode analyzing and decoding software module.

·      In aspects of hardware, the main difference between both areas is that any part of the scan area may be seen by the scan camera also while the barcode area can only be seen by the preview camera.

 

 

 

The scan area (shown for SCAN and P250), defined by the values of “Scan area” X-min, X-max, Y-min and Y-max differ in each scanner type and in scanners of the same type also, but the parameters are named in each scanner type as shown.

 

·      The scan area on the slide is ~24.5mm (X) x ~54.5mm (Y) (SCAN and P250); it depends highly on the scanner type and the slide holding mechanics.

 

·      In the file “MicroscopeConfiguration.ini” the parameters of “Scan area” are named as “ScannableArea” and found in the section [HardwareLimits].

 

More information can be found in the chapter “Specimen holder” of “P250”, “SCAN”, “MIDI” and “DESK”.

 

See also:       “Areas of slide”        S_M_D” and “P250

 

 

 

 

 

 

In DESK and MIDI type scanners, the area of the slide stud (as a part of the slide holding mechanics) will be excluded from the stage movement range and so, from the scan area also to avoid collision with the focus pin or the objective.

 

More information can be found in the chapter “Slide stud area” “MIDI” and “DESK

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                   Theory

 

 

·      The task of the preview image path is done with the preview camera and its own preview objective; while the path of the scan image is handled by the scan objective, the camera adapter and the scan (main) camera.

·      Both optical paths are separated from each other and are in physical distance to each other.

·      The arrangement of the preview camera’s optical path works correctly like a common known digital camera.

·      The preview camera creates a view of a slide part by reducing the seen area to the size of the preview camera’s sensor.

·      The arrangement of the scan camera’s optical path works inversely in relation to a common known digital camera.

·      The image path of the scan camera will enlarge a very small area on the slide, the Field Of View (FOV) to the size of the sensor.

 

·      This means, the construction of the image path of both cameras is inverse to each other!

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

By moving the slide over the scan objective’s pupil, the tissue, situated on the scan area of the slide, will be scanned.

The scanned fields of view are rotated, cut and stitched by the “SlideScanner.exe” and then, the virtual tissue or “Virtual Slide” can be analyzed by the help of the Slide Viewer.

 

 

Remark

 

To avoid confusion,

·      we are not using the term FOV (Field Of View) for the preview camera, use the term “Preview camera view” instead!

·      The slide area, seen with the scan camera will always be named as “FOV”!

 

 

 

                   Create a preview

 

 

By moving the slide over the view of the preview camera, only a part of the slide will be seen (figure A).

The distance and orientation of the camera, as well as the preview objective magnification was chosen so, that the entire X-dimension can be seen, and a bit more, so stitching becomes possible.

 

 

Because the scan area in Y-direction is much larger than the vertical view of the preview camera, the entire preview image will be captured in 3 sections (3 images; figure B).

 

·      The overlapping of the images is required for stitching!

 

The 3rd capturing of the scan area is much more than required; so the not required part of the image will be cut at the end of the preview creation process.

 

 

 

 

·      The preview camera makes a fourth image also; its content is the entire barcode area.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The three images, made by the preview camera view will be rotated, stitched and finally cut to the dimensions of the Scan Area by software.

 

 

·      By correcting each preview image by the preview camera rotation angle, the images are rotated exactly horizontal.

·      By fitting (stitching) the images exactly to each other, no gaps are visible or overlapping of the images will not occur.

·      By cutting the assembled images to the size of the Scan Area of the slide, the preview capturing process is finished and the content of the Scan Area is shown in the preview window of the program “SlideScanner.exe”.

 

 

 

The barcode area itself is captured by 1 image of the preview camera. 

 

·      The barcode area will be rotated by the camera rotation angle; the image is rotated exactly horizontal.

·      The X-dimension will be cut, but it is a bit larger than the X-dimension of the Scan Area (its limit is the widest possible slide dimension X).

·      The Y-dimension is cut only by the deviation from the horizontal direction (defined by the rotation angle of the camera), to keep the barcode area as large as possible.

·      The barcode image is not stitched to the Scan Area; it will be shown in a separate “Barcode window” instead!

 

 

 

·      During execution of the preview calibration procedure steps, required values for the position and size of the captured images, rotating angle of the preview camera view and stitching values are defined.

·      Accordingly parameters and values are collected and found in the section [PreviewAndBarcodeScanning] of the file ‘MicroscopeConfiguration.ini”.

 

 

 

 

 

 

 

 

 

 

Brightfield illuminated preview; double width slide

Because the slide is double in width, the preview images are also make twice.

The advantage of this is, that the mechanics and optics modifications are minimized.

The images are taken as shown with numbers.

 

·         In practice we can say, the image capturing process of the single width slide preview is done twice.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Define sample dilation

 

 

 

 

To be sure, the entire sample will be scanned, dilation can be defined.

 

·      Usually, the dilation’s size is between 300 and 1000μm, seldom above.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Sample scan process

 

 

 

The software divides the sample to be scanned, seen by the preview camera into fields of views; the size of the FOV depends on the resolution of the scan camera and the magnification of the camera adapter and of course, the magnification of the objective. Each field of view contains a small part of the neighbor FOV. In this way, stitching becomes possible. Because the capturing of the FOV’s is done on a meandering course, the Y-direction is often changed. If the hysteresis in Y-direction is too much, stitching will not work correctly; therefore, we have to check the hysteresis in Y-direction. The maximal allowed hysteresis is 4 μm (=4 motor steps).

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Relations and calculations

 

 

                   Preview camera’s view

 

 

First, we are discussing the preview image path related to the pixel size of the preview camera and then, we calculate the entire view of the preview camera. This algorithm is more precise in relation to other techniques, because all dimensions will be referenced to the slide surface and can be handled in [μm].

 

·      If we are doing the same procedure with the FOV of the scan camera (later in this chapter), differences between the position of the FOV in relation to the start point of the preview camera’s view can be eliminated and so, starting co-ordinates of both views can be fit to each other.

 

 

The distance of the preview objective to the slide may vary in a small range, because we adjusting the preview camera’s position and its rotation angle.

 

·      By adjusting the focus of the preview objective and / or the position of the preview camera, the magnification of the objective will be a bit affected.

 

·      To avoid confusion, we are not using the term FOV (Field Of View) for the preview camera, we using the term “Preview camera view” instead!

 

The seen area on the slide can be calculated as follows:

 

Seen preview camera area pro pixel = (Preview camera pixel size) * (Preview objective magnification)

 

 

 

 

 

 

 

 

Example calculations

 

Camera

Effective pixel array size

Active pixel size

(H) pixels

(V) pixels

(H) µm

(V) µm

VRmagic

2056

1544

3.2

3.2

Used:

2048

1536

3.2

3.2

DFK 21F04

640

480

5.6

5.6

 

Preview objective magnification DFK 21F04                ~ 8.2

Preview objective magnification Tamron (VRmagic)   ~ 4.7

 

Seen slide area / pixel X [µm] = (Preview camera pixel size X) * (Preview objective magnification)

 

Seen slide area / pixel Y [µm] = (Preview camera pixel size Y) * (Preview objective magnification)

 

So we can say:

 

x’ = 5.6 x 8.2             Seen preview camera area pro pixel x’ (DFK 21F04 (H)) =               ~46 µm

y’ = 5.6 x 8.2             Seen preview camera area pro pixel y’ (DFK 21F04 (V)) =                ~46 µm

 

 

x’ = 3.2 x 4.7             Seen preview camera area pro pixel x’ (VRmagic (H)) = 15.04 or    ~15µm

y’ = 3.2 x 4.7             Seen preview camera area pro pixel y’ (VRmagic (V)) = 15.04 or    ~15µm

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The CCD size of the preview camera DFK 21F04 is

 

                                   640 (H) x 480 (V) pixels.

 

 

 If we are multiplying the value of the seen area on the slide with the number of pixels (H) the result is

 

                                                                                                          ~29.5mm

 

and multiplied with the number of pixels (V) the result is      ~22mm.

 

·      The preview camera’s view (DFK 21F04) has a size of 29.5mm x 22mm.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Because the preview camera’s view is stitched and cut to the Scan Area on the slide, a width of approximately 24.5mm is used.

 

 

By dividing this value by the width of the preview camera pixel width on the slide (46μm), the used pixel number is approximately 532 preview camera pixels horizontal.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The same calculations can be executed with the preview camera VRmagic; the principle is the same.

 

The used sensor size of the preview camera VRmagic is

 

                                                                                              2048 (H) x 1536 (V) pixels.

 

 

 

 If we are multiplying the value of the seen area on the slide 15µm with the number of pixels (H) 2048 the result is

 

                                                                                              30.72mm and

 

multiplied with the number of pixels (V) the result is  23.04mm.

 

·      The preview camera’s view (VRmagic) has a size of 30.7mm x 23.0mm.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

  One pixel of the preview camera VRmagic sees an area of 15 x 15µm on the slide.

 

 

·      This area (FOV size: see the example FOV size) is seen by the scan camera on the slide within ~ 24 x 18 pixels of the preview camera (VRmagic).

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                   [PreviewAndBarcodeScanning]

 

The following parameters (and others) are influenced during the preview calibration process.

 

·      Parameters used for the pixel position adjustment are shown only!

·      See also:       Handling the *.ini files” and “PreviewAndBarcodeScanning

 

[HardwareLimits]

 

These values are defined before the preview calibration process starts!

 

1 =  ScannableAreaXMin

2 = ScannableAreaYMin

3 = ScannableAreaXMax

4 = ScannableAreaYMax

 

 

Following parameter values are defined during the preview calibration process!

 

 [PreviewAndBarcodeScanning]

 

11 = PreviewCropLeft

12 = PreviewCropTop; often zero, its value is included in “Crop from Top”

12a = Crop From Top;

13 = PreviewCropRight

14 = PreviewCropBottom

 

 

 

 

 

 

 

 

 

 

FOV size: see the example FOV size

6 = umX/Pixel

7 = umY/Pixel

 

 

These values are defined by the used optics in the image path of the scan camera!

 

umX/pixel [µm] = (CCD X pixel size (H)) / (objective magnification * camera adapter magnification)

umY/pixel [µm] = (CCD Y pixel size (V)) / (objective magnification * camera adapter magnification)

 

 

 

 

 

 

 

 

 

 

 

 

PreviewImageTopLeftCornerPositionX

 

PreviewImageTopLeftCornerPositionX = ScannableAreaXMin

 

·      The values of PreviewImageTopLeftCornerPositionX and ScannableAreaXMin are identical.

 

 

 

 

 

 

 

 

 

CornerPositionY = PreviewImageTopLeftCornerPositionY

CornerPositionX = PreviewImageTopLeftCornerPositionX

 

·      The value of the parameter “PreviewImageTopLeftCornerPositionY” defines the starting FOV’s position in Y-direction. The value of the parameter “ScannableAreaYmin” will be set to the calculated value of “PreviewImageTopLeftCornerPositionY” after the preview calibration procedure is finished.

 

·      The X-value for the start position of the first FOV is defined by the value of  “PreviewImageTopLeftCornerPositionX” and the value of “PreviewCropLeft”

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                   Optical path and Field Of View

 

The pupil of the scan objective is very close to the tissue, so, the small area on the tissue will be enlarged by the objective and the camera adapter.

 

The seen area on the slide is always defined by the size of the camera’s CCD; more precise, the effective number of pixels horizontal and vertical and the optical means in the image path.

 

 

 

The objective type “Plan-Apochromat” requires a tube lens to create the image. In opposite to other objective types, an infinite space exists between the objective and the tube lens, in which the light rays are parallel.

 

So, optical means, like the filter block in fluorescent scan sessions can be inserted (by the help of the turret unit)

 

·      The filter block’s components do not affect the magnification of the image path!

 

Remark

Links refer to P250!

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                   Calculate the FOV pixel size

 

 

Example

 

If we assume that the scan camera has the named values (see below), we can easily calculate the area for 1 pixel, seen on the slide; this is also the maximal resolution in the optical path for the example construction. If the calculation is done with an objective magnification of 20x and the camera adapter magnification should be 1x, the result will be:

 

 

CIS- VCC-F52U25CL

Effective Pixel Number:     1624 (H) × 1224 (V)

Unit Cell Size:                     4.40μm (H) × 4.40μm (V)

 

            x’ [μm] = 4.40 (H) divided by 20 = 0.22μm or 220nm

 

            y’[μm]  = 4.40(V) divided by 20 = 0.22μm or 220nm

 

The value of x’ is also named as                         umX/pixel [µm] and

The value of y’ is also named as             umY/pixel [µm]

 

 

If the values are multiplied with the effective number of pixels (H) and (V) the result will be:

 

0.22 x 1624 =                       357.28 [μm] (H) and

 

0.22 x 1224 =                       269.28 [μm] (V)

 

So the dimension of the FOV for this example image path will be

 

Example FOV size:            Slide X-direction 357.28µm (H) x Slide Y-direction 269.28µm (V)!

 

 

·      The real dimension of the FOV depends highly on the optical means, used in the image path!

 

 

 

 

 

 

 

 

 

 

 

 

 

                   Influence of the camera adapter

 

The useable magnification of the camera adapter depends on the size of the sensor (useable geometry x and y in pixels), the used objective magnification and the construction of the image path (Length of the camera tube).

 

·      The resulting magnification of the image path is defined by the product of Objective Magnification multiplied by the Camera Adapter Magnification.

 

Example

If the Objective Magnification is 20x and the camera adapter magnification is 0.63x the resulting magnification of the image path will be 12.6x.

 

Image magnification = 20 x 0.63 = 12.6

 

Advantage

By reducing the image magnification, the dimension of the FOV will be increased; the scan speed increases because the number of FOVs to be scanned is reduced.

 

Disadvantage

The resolution of the virtual tissue is reduced.

 

 

 

 

Conclusion

·      The camera adapter fits the image, seen by the objective in the focus of the camera sensor and influences the resulting magnification of the image path and the size of the FOV.

 

·      If the camera adapter magnification is 1x, then no lenses are inserted, and the sensor is in the focus of the tube lens; the optical magnification is defined by the objective magnification.

·      If the camera adapter magnification is 0,63x, then the lens of the camera adapter enlarges the FOV; the resolution of the scanned tissue is decreased.

·      If the camera adapter magnification is 1,6x, then the optics of the camera adapter makes the FOV smaller, and the resolution of the scanned tissue is increased!

 

 

 

 

 

 

 

 

 

 

Sensor characteristics

 

 

 

Preview cameras

Camera

Effective pixel array size

Active pixel size

(H) pixels

(V) pixels

(H) µm

(V) µm

VRmagic

2056

1544

3.2

3.2

Used:

2048

1536

3.2

3.2

DFK 21F04

640

480

5.6

5.6

 

Preview camera pixel view = (Preview camera pixel size) * (Preview objective magnification)

 

Preview objective magnification DFK 21F04                   ~ 8.2x

Preview objective magnification VRmagic                       ~ 4.7x

 

·      Preview camera pixel view DFK 21F04 =   46µm

·      Preview camera pixel view VRmagic =        15µm

 

 

Useable magnifications and resulting resolutions of scan (main) cameras

Camera

Pixel array size

used ; [Pixels]

Pixel size [µm]

Useable Magnification; Resolution [µm]

Active

Valid

0.63x

1.0x

1.6x

(H)

(V)

(H)

(V)

(H or V)

20x

40x

20x

40x

20x

40x

Grasshopper3; color­* 3)

2448

2048

3.45

3.45

4.87*

0.39

0.19

0,24

0.12

X

X

Stingray*

1380

1030

4.65

4.65

6.58*

0.52

0.26

0.33

0.16

X

X

Marlin* 1)

1368

1024

4.65

4.65

6.58*

0.52

0.26

0.33

0.16

X

X

Adimec Q-12A180* 2)

4096

3072

5.5

5.5

7.78*

X

X

X

X

0.24

0.12

CIS-VCC F52U25CL

1624

1224

4.40

4.40

4.40

0.35

0.18

0.22

0.11

X

X

CIS-VCC FC60FR19CL*

2048

2048

5.5

5.5

7.78*

X

X

0.39

0.19

0.24

0.12

Hitachi HV-F22CL

1360

1024

4.65

4.65

4.65

0.37

0.18

0.23

0.12

X

X

Sony DFW-X710* 1)

1024

768

4.65

4.65

6.58*

0.52

0.26

0.33

0.16

X

X

 

Monochrome scan cameras (FL or RGB illuminated)

Grasshopper3; mono3)

2448

2048

3.45

3.45

3.45

0.27

0.14

0,17

0.08

X

X

AxioCam MRm R3

1388

1040

6.45

6.45

6.45

X

X

0.32

0.16

X

X

PCO-edge 4.2

2048

2048

6.5

6.5

6.5

X

X

0.32

0.16

X

X

PCO-edge 5.5_@ 2.5Mp

1600

1600

6.5

6.5

6.5

X

X

0.32

0.16

X

X

PCO-edge 5.5_@ 4.0Mp

1920

1920

6.5

6.5

6.5

X

X

0.32

0.16

X

X

PCO-edge 5.5_PCON

2560

2160

6.5

6.5

6.5

X

X

0.32

0.16

X

X

 

X)          Not defined, can not be used

* Calculations for these cameras are done by using the factor sqrt(2)

                        Resolution [µm] = (Active camera pixel size * sqrt(2) ) / (objective magnification * camera adapter magnification); used if single chip camera with Bayer method

·      sqrt(2)= required, because debayering (creation of color information in single chip cameras with Bayer method); and generation of JPEG file

                        If real color camera or monochrome (FL) camera:

                        Resolution [µm] = (Active camera pixel size) / (objective magnification * camera adapter magnification)

 

            1) No longer delivered

            2) Useable since SW version 1.20 only!

            3) Useable since SW version 1.21only!

 

 

 

 

 

 

 

Pixel position and corrections

 

 

If the preview calibration procedure is just finished and we scan one of the circles, the offered area to be scanned, offered by the preview window in the SlideScanner.exe, mostly will not fit the real position of the circle. Parts of the circle will be cut.

 

·      Check the FOV position of the scan camera in relation to 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 need to adjust the position of the pixel of the preview camera more precise to the position of the field of view of 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 position of the offered area is incorrect.

 

·      The size and position of the cut part is variable.

 

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

 

 

Important remarks

·      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!

 

 

 

 

                      Calculate required offset value

 

See also:       Preview_S_M_D” and Adjust the pixel position of the preview camera

 

                        P250_Preview” and “Adjust the pixel position of the preview camera

 

Load the EXCEL table

 

 

If the status message “OM or CAM invalid!” occurs, the camera adapter magnification or the objective magnification should be altered; the existing combination for the selected scan camera is not defined!

Nevertheless, the calculated result is always correct for all selected combinations!

·      See also the table above “Scan (main) cameras

·      The camera “PCO-edge 5.5_PCON” can not be used in conjunction with the DFK 21F04, but the result is even so correct!

 

 

 

  PreviewImageMicrometerPerPixelX

 

If the value of the Parameter "Shift sample" is Left or right,  the right hand circles are shifted to the left or to the right, as the selected value shows.

 

Because the value of PreviewImageMicrometerPerPixelX  affects mainly the right hand circles, these will be shifted to the left or to the right, by the calculation result.

 

 

PreviewImageMicrometerPerPixelY

 

If the value of the Parameter "Shift sample" is Up or Down,  the lower circles are shifted Up or Down, as the selected value shows.

 

Because the value of PreviewImageMicrometerPerPixelY  affects mainly the bottom circles, these will be shifted up or down, by the calculation result.

 

 

 

 

 

 

 

 

If we assume, the image on the right shows the scan result of the circle, we can say, the circle position fits not the center of the offered scan area (offered by the preview), the circle must be shifted to the right and upward a bit to meet the center of the spot.

·      In reality, we are always shifting the offered preview scan area of the circle, named as spot.

 

·      In the example on the right, the offered scan area have to be shifted to the left and a bit downward.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

If we are shifting the entire spot to the left by the size of 1 FOV, the FOV column, shown with “a” will be cut and the content of the FOV column, shown with “b” will be seen, the circle stays seemingly unchanged.

This way, because the offered area for 1 circle has not changed (only its position was moved) the circle can be fit to the center of the offered scan area for the circle.

 

Shift sample right

 

See:    Important

 

Load the EXCEL table

 

"PreviewCropLeft" = (Number of FOVs) x ((FOV X-dimension) / (PVcam µmX/pixel))

"PreviewCropRight" = (Number of FOVs) x ((FOV X-dimension) / (PVcam µmX/pixel))

 

·      Add the result to or subtract the result from the existing value of "PreviewCropLeft" and "PreviewCropRight".

 

The image on the right is conventionalized!

·      We know that the real FOV’s dimension depends on the optical means, used in the scan image path and the sensor dimensions!

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The result is shown on the right.

 

 

 

 

 

The image on the right is conventionalized!

·      We know that the real FOV’s dimension depends on the optical means, used in the scan image path and the sensor dimensions!

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

If we are shifting the spot by a half FOV size downward, the upper part, shown with “a” will be cut and the part, shown with “b” will be displayed. The circle moves seemingly upward.

 

Shift sample up

 

Load the EXCEL table

 

 

See:    Important

 

"PreviewImageTopLeftCornerPositionY" = (Number of FOVs) x (FOV Y-dimension)

"PreviewCropBottom" = - ("PreviewImageTopLeftCornerPositionY" / (PVcam µmY/pixel))

 

FOV Y-dimension [μm] = (Camera pixel size [μm] / (Objective magnification x Cam. Adapter magnification) * (Sensor (V) [pixels]))

 

 

 

The image on the right is conventionalized!

·      We know that the real FOV’s dimension depends on the optical means, used in the scan image path and the sensor dimensions!

 

 

 

 

 

 

 

 

 

 

 

 

Expected result

·      No parts of the circle are cut!

 

 

 

 

 

The image on the right is conventionalized!

·      We know that the real FOV’s dimension depends on the optical means, used in the scan image path and the sensor dimensions!

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                   Calculate required values

 

Scan camera

umX/pixel [µm] = (Sensor (H)  pixel size [µm]) / (objective magnification * camera adapter magnification)

umY/pixel [µm] = (Sensor (V)  pixel size [µm]) / (objective magnification * camera adapter magnification)

 

sqrt(2)= required, because debayering; (create color information in single chip cameras with Bayer method) and generation of JPEG file

FOV pixel size = (Scan camera pixel size) / (objective magnification * camera adapter magnification)

 

·      Add the result of the following calculations to or subtract the result from the existing value of the appropriate parameter value.

 

 

Important

 

Following formulas are prepared so, that the movement of the circle will be executed.

 

·      E.g.:    If we using the formula “Shift sample up”, the circle will be moved upward!

 

Load the EXCEL table

 

 

 

The image on the right is conventionalized!

·      We know that the real FOV’s dimension depends on the optical means, used in the scan image path and the sensor dimensions!

 

 

 

FOV Pixel size =Camera pixel size / (Objective magnification x Cam. Adapter magnification)

 

FOV size x = FOV pixel size x’ [μm] * Sensor (H) [pixels]

 

FOV size y = FOV pixel size y’ [[μm] * Sensor (V) [pixels]

 

 

 

umX/pixel [μm] = FOV Pixel size x' [μm]  = Camera pixel size (H) [μm]  / (Objective magnification x Cam. Adapter magnification)

 

umY/pixel [μm] = FOV Pixel size y' [μm]  = Camera pixel size (V) / (Objective magnification x Cam. Adapter magnification)

 

FOV X-dimension [μm] = ((Camera pixel size [μm]  / (Objective magnification x Cam. Adapter magnification)) * (Sensor (H) [pixels])

 

FOV Y-dimension [μm] = ((Camera pixel size [μm] / (Objective magnification x Cam. Adapter magnification)) * (Sensor (V) [pixels])

 

 

 

Shift sample up

 

"PreviewImageTopLeftCornerPositionY" = (Number of FOVs) x (Camera pixel size [μm]  / (Objective magnification x Cam. Adapter magnification)) * (Sensor (V) [pixels])

"PreviewCropBottom" = - ("PreviewImageTopLeftCornerPositionY" / (PVcam µmY/pixel))

 

 

Shift sample down

 

 "PreviewImageTopLeftCornerPositionY"= - ((Number of FOVs) x (FOV Y-dimension))

"PreviewCropBottom" = ("PreviewImageTopLeftCornerPositionY") / (PVcam µmY/pixel))

 

 

Shift sample right

 

"PreviewCropLeft" = +(((Number of FOVs) x (FOV X-dimension)) / (PVcam µmX/pixel))

"PreviewCropRight" = +(((Number of FOVs) x (FOV X-dimension)) / (PVcam µmX/pixel))

 

 

Shift sample left

 

"PreviewCropLeft" = - (((Number of FOVs) x (FOV X-dimension)) / (PVcam µmX/pixel))

"PreviewCropRight" = - (((Number of FOVs) x (FOV X-dimension)) / (PVcam µmXpixel))