This function allows you to automatically align the individual planes of a z-stack image if they are not positioned precisely above each other.

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 which is used to align the images.

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Translation

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

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Rotation

The neighboring sections of the z-stack are rotated in relation to each other.

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Translation + Rotation

The neighboring sections of the z-stack are translated and rotated in relation to each other.

Interpolation

Selects how the interpolation is 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.

Region

Selects which parts of the image should be considered for the calculation of the transformation matrix.

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Full

Considers the entire image for alignment.

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Rectangle Region

Allows you to draw a region of interest into the image. Only the image information of this region is then considered for the calculation of the transformation matrix for alignment. The resulting transformation matrix will be applied to the full image.
After you have drawn a rectangle region into the image, you can see and change its coordinates with the X/Y/W/H input fields.

Crop Output

Not visible if the Third Dimension (if available) is set to a particular dimension instead of 2D Slices.
Activated: The image is cropped and only keeps the section which is covered by the entire dimension, i.e. by all z-slices. 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

Activated: Displays the image channels. Selects one of the image channels which will be used to calculate the alignment transformation matrix, which then is also applied to the other channel(s).
Deactivated: Calculates an alignment transformation matrix for each individual channel.