This method allows you to bring the individual planes of a z-stack image into line if these are not positioned precisely one above the other. This is the case, for example, when you acquire z-stacks at an oblique angle using a stereo microscope.

Parameter

Description

Quality

Selects the quality level that you want the function to work with. The calculation of the alignment is based on a so-called image pyramid. The higher the selected quality, the more levels of the image pyramid are used to calculate the alignment and the more precise the alignment will be. However, the higher the selected quality is, the slower the calculation of the alignment will get.

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Low

This is the most imprecise but also the fastest calculation of the alignment. It uses a low number of levels (2) of the image pyramid for the alignment calculation.

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Medium

This is a more precise but also a slower calculation of the alignment than the one before. It uses a medium number of levels (3) of the image pyramid for the alignment calculation.

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High

This is a more precise but also a slower calculation of the alignment than the two before. It uses a high number of levels (4) of the image pyramid for the alignment calculation.

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Highest

This is the most precise but also the slowest calculation of the alignment. It uses the highest number of levels of the image pyramid for the alignment calculation.

Registration Method

Selects the method or a combination of methods which is used to align the images.

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Translation

The neighboring sections of the image are shifted in relation to each other in the X and Y direction.

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Rotation

The neighboring sections of the image are rotated in relation to each other.

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Iso Scaling

The magnification is adjusted from section to section.

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Skew Scaling

The neighboring sections of the image are corrected for skewness/shearing.

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Affine

The neighboring sections of the image are shifted in X and Y direction, rotated and the magnification is adjusted from section to section.

Interpolation

Only visible if Show All is activated.
Selects how the interpolation should be performed if a pixel is calculated from several individual pixels.

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Nearest Neighbor

The output pixel is given the gray value of the input pixel that is closest to it.

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Linear

The output pixel is given the gray value resulting from the linear combination of the input pixels closest to it.

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Cubic

The output pixel is given the gray value resulting from a polynomial function of the input pixels closest to it.

Crop Output

Only visible if your image does not contain multiple tiles or scenes.
Activated: The image is cropped and only keeps the section which is covered by the entire dimension (e.g. by all z-slices or time points). The output image can be of different size than the input image.
Deactivated: The output image is not cropped and keeps the size of the input image. The image borders might get filled with a default pixel value.

Single Component

Only visible if you have selected an input image which contains dimensional components (e.g. scenes, z-planes, time points) and if this component is not selected as Third Dimension.

Activated: Displays a control to select the dimensional component that is used to calculate the alignment transformation matrix.
Deactivated: Calculates an alignment transformation matrix for each individual component (e.g. for each individual scene).

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Scene Component

Only visible for images with multiple scenes.
Selects the scene that is used to calculate the alignment transformation matrix.

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Phase Component

Only visible for images with multiple phases.
Selects the phase that is used to calculate the alignment transformation matrix.

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Channel Component

Only visible for images with multiple channels.
Selects the channel that is used to calculate the alignment transformation matrix.

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Time Component

Only visible for time series images.
Selects the time point that is used to calculate the alignment transformation matrix.

Single Tile

Only visible for images with multiple tiles and if Single Component is activated.
Activated: Displays the Tile Component control.

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Tile Component

Selects the tile component that is used to calculate the alignment transformation matrix.