Correlation Wizard
This wizard is used to correlate a Z-Stack image from the Light Microscope (LM) with the Z-Stack image from the Scanning Electron Microscope (SEM). The wizard consists of 4 steps which are described in the following chapters:
Import Z-Stacks
In this step you can import the aligned Z-Stack images from the LM and the SEM, e.g. the Z-Stack image from the LM in the left container and the Z-Stack image from the SEM in the right container.
If you click on the Left Container button, the image is opened in the left image container.
If you click on the Right Container button, the image is opened in the right image container.
See also
Correlation
In this step you correlate the images.
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Parameter |
Description |
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Transform |
Here you select which Z-Stack will be transformed. During transformation, a pixel in the overlay image of the Z-Stack is calculated by using pixels of the two original images that shall be overlaid/merged. |
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Interpolation |
Here you can select one of the following interpolation methods: |
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Nearest Neighbor |
The gray value of the resulting pixel in the overlay image is made of a pixel which is located next. This interpolation method is very fast. |
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Linear |
The resulting or calculated pixel in the overlay image is assigned to a gray value, which is the result of a linear combination of gray values derive from pixels located nearby (in the original image). |
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Cubic |
The calculated pixel in the overlay image is assigned to a gray value, which is calculated by means of a polynomial function using gray values of pixels in the original images; these pixels are located nearby the calculated pixel. |
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Mode |
Here you can choose an algorithm mode: |
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3-Points |
If selected, this mode enables you to set 6 correlation points after clicking on the Set Points button (3 points in each Z-Stack in each container). |
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4-Points |
If selected, this mode enables you to set 8 correlation points after clicking on the Set Points button (4 points in each Z-Stack), 3 points in the first z-section, the last point in the last section. |
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Correlation Points |
If you click on the Set Points buttons, you can set the correlation points. The number of correlation points is according to the selected algorithm. The cursor will change to a pipette symbol. Simply click in the image to set the points. Start with setting the first three points in the left container then set the corresponding correlation points in the right container. If a correlation point is set, a check mark icon will appear in front of the corresponding point. When you select the 4-Points-Algorithm, the display will move automatically to the last image of the Z-Stack. Set the fourth correlation point in both containers. Make sure that the positions in both Z-Stacks are identical. After you have set all correlation points, the cursor will be changed backwards from the pipette to the arrow. Reset deletes all correlation points in the image. |
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Create correlated Z-Stack |
If you click on this button, the correlated Z-Stack will be generated and opened in a new image container. |
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See also
Manual Correction
In this step you can correct the correlation manually by moving and rotating the transformed image.
Therefore simply click on the Start button. Then you can interactively move the image by dragging and dropping it with the mouse or rotate the image by clicking on the circle button attached on top of the green image frame or using the Rotation slider. You can also change the image opacity by adjusting the corresponding slider.
If you click on the Accept button the manual correction, will be adopted to the correlated image.
See also
Create Final Correlation Image
In this step create the final correlation image. Therefore simply click on the Create final Z-Stack button. Click Finish to exit the wizard.