Geometric

Transformation File

Enables you to select the file on which the alignment calculation is based. The transformation file ideally matches the zoom and resolution settings used for the image to be aligned.

Adjust per Channel

Activated: Opens a list with the channels to allow an individual adjustment of each channel. For every channel you have the following options:

–

Process Channel

Processes this channel according to the input.

–

Skip Channel

Skips this channel when processing. This channel will not be in the output image.

–

Copy Channel

This channel is copied into the output image without processing.

Orientation

-

Flip Horizontally

Flips the image horizontally.

-

Flip Vertically

Flips the image vertically.

-

Rotate 90 CW

Rotates the image by 45 degrees clockwise (CW).

-

Rotate 90 CCW

Rotates the image by 45 degrees counterclockwise (CCW).

-

Rotate 180

Rotates the image by 180 degrees.

-

Mirror at +45 Diagonal

Mirrors the image at +45 degrees diagonal.

-

Mirror at -45 Diagonal

Mirrors the image at -45 degrees diagonal.

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.

–

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.

–

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.

–

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.

–

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.

-

Translation

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

-

Rotation

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

-

Iso Scaling

The magnification is adjusted from section to section.

-

Skew Scaling

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

-

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.

-

Nearest Neighbor

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

-

Linear

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

-

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.

Reference Channel

Selects the channel that serves as reference for the alignment.

Target Channel

Selects the channel that is targeted for alignment.

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).

–

Scene Component

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

–

Phase Component

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

–

Z Slice Component

Only visible for z-stack images.
Selects the z-slice that is used to calculate the alignment transformation matrix.

–

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.

–

Tile Component

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

Load Transformation

Activated: Allows you to load the result of a previous transformation.

–

Transformation file

Allows you to select the respective *.xml file with the previously used transformation.

Save Transformation

Only visible if Load Transformation is deactivated.
Activated: Saves the result of the transformation process in an *.xml file for later use.

Preprocessing

Selects which method should be used for preprocessing.

–

No Preprocessing

Uses no preprocessing.

–

Sobel

Uses the Sobel method for preprocessing, see Sobel.

–

Laplace

Uses the Laplace method for preprocessing, see Laplace.

–

Roberts

Uses the Roberts method for preprocessing, see Roberts.

–

Enhance Contour

Uses the Enhance Contour method for preprocessing, see Enhance Contour.

–

Maximum Gradient

Uses the Maximum Gradient method for preprocessing, see Gradient Max.

–

Delineation

Uses the Delineation method for preprocessing, see Delineate.

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.

–

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.

–

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.

–

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.

–

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.

-

Translation

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

-

Rotation

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

-

Iso Scaling

The magnification is adjusted from section to section.

-

Skew Scaling

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

-

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.

-

Nearest Neighbor

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

-

Linear

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

-

Cubic

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

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).

–

Scene Component

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

–

Phase Component

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

–

Z Slice Component

Only visible for z-stack images.
Selects the z-slice that is used to calculate the alignment transformation matrix.

–

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.

–

Tile Component

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

Palette

Sets the color-pattern for the projection.

ROI

Specifies the range of the dimension (chosen below) which will be used for the projection.

Dimension

Selects whether to perform the projection along the time (T) or along the z-axis (Z). Only dimensions which are available in your data set are shown.

Quantitative

Activated: Uses a quantitative method which first creates a maximum intensity projection and then determines at which plane a pixel was located. After that it attributes a color of the LUT to the pixel. This method can sometimes produce abrupt transitions, but the pixel color representing depth or time corresponds correctly to the colors in the annotation.

Deactivated: This method attributes a color of the LUT to each plane and then separates the result into RGB channels. Subsequently, it creates a maximum intensity projection of each RGB channel and then combines the results into one image. Note that while this might result in a more pleasantly looking image, the method can produce colors which do not correspond to colors in the annotation!

Output File

Defines the name and path of the output xml file.

Alignment Quality

Selects the alignment quality. The higher the selected quality, the slower but more robust and accurate the alignment will be. This is mostly relevant for large z-stacks. For 2D images the function should be fast enough even with the highest quality setting.

–

Low

Uses the fastest setting, which can be especially useful for large images containing dense biological structures.

–

Medium

This is the default setting for bead measurements with normal density.

–

High

This setting is for bead measurements if higher accuracy is required.

–

Highest

This is the most accurate setting. It is recommended if High does not deliver a good result and if there is a large z-mismatch of channels.

Reference Channel

Selects the reference channel to which other channels will be aligned. If alignment proves difficult, select the channel with the best signal to noise ratio or the one that has the most overlap with the other channels.

Adjust per Channel

Activated: Opens a list with the channels to allow an individual adjustment of each channel. For every channel you have the following options:

–

Process Channel

Aligns this channel according to the parameters.

–

Skip Channel

Skips this channel when processing. This channel will not be in the output image.

–

Copy Channel

This channel is copied into the output image without alignment.

Input Pixel 1 - 3

If you click on the corresponding buttons, you can define the 3 input pixel points.

The selected point is shown in the graphics plane. This serves as an aid to orientation when you are clicking on the reference points.

Reference Pixel 1 - 3

If you click on the corresponding buttons, you can define the 3 reference pixel points.

Interpolation

Here you can specify how the rotation influences the neighboring pixels.

-

Linear

The rotated pixel is given the gray value calculated from the linear combination of the gray values of the pixel closest to it and this pixel’s nearest neighbor.

-

Cubic

The rotated pixel is given the gray value resulting from a polynomial function of the pixel that is closest to it.

Display Mode

-

Horizontal

Flips the image horizontal.

-

Vertical

Flips the image vertical.

-

T/Z

Only visible if input image is a multichannel image.
Reverses sequence of the sections (Z) or time points (T).

Projection Plane

Here you choose the type of the projection plane (Frontal (X/Y), Transverse (X/Z), Sagittal (Y/Z)).

Method

-

Maximum

Uses the brightest pixel along the projection beam.

-

Minimum

Uses the darkest pixel along the projection beam.

-

Average

Calculates the average of all pixels along the projection beam.

-

Weighted Average

This method is related to the calculation of the extended depth of focus. It prefers structures with more lateral sharpness along the projection beam. The output image contains more significant details.

-

Standard Deviation

Calculates the standard deviation of pixel grey values along the projection beam.

Start Position

Here you adjust the starting position of the project plane (in pixel units or z-stack positions depending on the chosen projection plane). The maximum range results automatically of the size of the input image.

Thickness

Here you adjust the thickness of the cutting plane (in pixel or z-stacks depending on the chosen projection plane). The maximum range results automatically of the size of the input image.

Scaling in X

Adjusts the desired scaling for X using the slider or input field.

Scaling in Y

Adjusts the desired scaling for Y using the slider or input field.

Scaling in Z

Adjusts the desired scaling for Z using the slider or input field.

The following parameters are only visible if Adapt Sizes is deactivated:

Shift in X

Sets the shift in the X direction using the slider or input field.

Shift in Y

Sets the shift in the Y direction using the slider or input field.

Shift in Z

Sets the shift in the Z direction using the slider or input field.

Angle

Enter the angle by which you want the input image to be rotated around using the slider or input field. Positive angles rotate the images clockwise.

Angle X

Enter the angle by which you want the input image to be rotated on the X axis using the slider or input field.

Angle Y

Enter the angle by which you want the input image to be rotated on the Y axis using the slider or input field.

Angle Z

Enter the angle by which you want the input image to be rotated on the Z axis using the slider or input field.

The following parameters are only visible if Adapt Sizes is deactivated:

Center X

Enter the X coordinate of the center of the rotation using the slider or spin box/input field.

The value 0 means that the image is rotated around its center point. Negative values mean that the center of the rotation in the image is shifted to the left in relation to the image's center point. Positive values shift the center to the right.

Center Y

Enter the Y coordinate of the center of the rotation using the slider or spin box/input field.

The value 0 means that the image is rotated around its center point. Negative values mean that the center of the rotation in the image is shifted downwards in relation to the image's center point. Positive values shift the center upwards.

Center Z

Enter the Z coordinate of the center of the rotation using the slider or spin box/input field.

The value 0 means that the image is rotated around its center point. Negative values mean that the center of the rotation in the image is shifted forwards in relation to the image's center point. Positive values shift the center backwards.

Angle

Enter the angle by which you want the input image to be rotated around using the slider or input field. Positive angles rotate the images clockwise.

Interpolation

-

Nearest Neighbor

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

-

Linear

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

-

Cubic

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

Edge Smoothing

Activated: Performs edge smoothing.

PaveWholePlane

Activated: Paves the whole resulting plane with tiles; there might be empty tiles.

Inactivated: Creates only tiles which contain also parts of the image.

ProcessMask

Activated: Rotates also the mask of valid/invalid pixels.

Inactivated: Ignores the mask of valid/invalid pixels. Pixels previously marked as invalid will have an intensity of zero after rotation but are not marked as invalid.

IncludeGraphic Elements

Activated: Rotates also the graphical elements together with the image.

Inactivated: Rotates only the image, but not the graphical elements.

Average Pixels X

Adjusts how many pixels are averaged in the lateral X dimension to calculate the output image. The size of the output will be smaller by this factor.

Average Pixels Y

Adjusts how many pixels are averaged in the lateral Y dimension to calculate the output image. The size of the output will be smaller by this factor.

Average Pix. 3rd Dimension

Only visible, if a third dimension other than 2D Slices is selected below.
Adjusts how many pixels are averaged in the lateral third dimension selected below. The size of the output will be smaller by this factor.

Third Dimension

If your input image has a third dimension you can select it here for re-sampling.

• Z (sections of a Z-Stack)
• C (Channels)
• If 2D Slices is selected, the third dimension will not be re-sampled.

Third Dimension

Only available if Show All is activated and if the acquired image is three dimensional.

Selects the third dimensional shift.

–

2D Slices

The third dimension is shifted by 0 which means the image is only shifted in X/Y direction.

–

Z

The shift is in z-direction.

–

C

Shifts the channel.

If you have a 32 channel image, the first 30 channels are copied and/or interpolated into the last ones (for an 32 channel lambda image this would result in a shift to the red spectrum).

When selected, the checkbox Adjust per channel is not available.

Adjust per Channel

Only available for images with multiple channels.

Opens a list with the channels to allow an individual adjustment of each channel.

–

Process Channel

Shifts this channel according to the input.

–

Skip Channel

Skips this channel when processing. This channel will not be in the output image.

–

Copy Channel

This channel is copied into the output image without a shift.

Shift in X

Selects the shift of the content in X direction.

Shift in Y

Selects the shift of the content in Y direction.

Shift in Z

Selects the shift of the content in Z direction.

Shift in Z

Selects the shift of the content in z direction.

Interpolation

Here you can select how you want interpolation to be performed.

-

Nearest Neighbor

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

-

Linear

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

-

Cubic

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

Inplace

The stitching is directly applied to the original image.

New Output

A new image is generated as a result of the stitching process. The original image is not modified.

Fuse Tiles

Only visible if New Output is selected.
Activated: Blends all adjacent tiles into each other to compensate for shading and other continuity errors. The image remains a tile image, this option does not generate an image without tiles. The tiles created after stitching are of a different size and serve as basis for building an image pyramid. Note that this can cause problems if you want to open the stitched image in another application (e.g. Fiji).

Correct Shading

Only visible if New Output is selected.
Activated: Applies a shading correction to each image prior to stitching to correct uneven exposure. The dropdown list selects the reference that should be used for shading correction.

-

Automatic

The function automatically calculates a reference image from the input image.

-

Reference

The function uses an existing reference image. This must be selected in addition to the input image in the Input tool of the image parameters section.

Select Reference Image

Only visible in Batch mode and if Reference is selected as shading correction.

Selects a reference image for the shading correction.

Select dimension references for stitching

Only visible for multidimensional input images.
Selects a reference dimension (one channel, z-position, time point or scene) from your multidimensional data set. This reference dimension is either stitched exclusively (no other planes of the dimensions are stitched) or serves as reference when stitching all planes of the dimensions.

-

Get all dimensions from 2d view

Selects the reference dimensions based on the current planes from the 2D view by clicking .

-

All by reference

Uses only the reference image plane for calculating the stitching of this dimension. All other planes are stitched accordingly and appear in the output image.

-

Reference only

Uses only the selected reference image plane of this dimension. No other planes appear in the output image, e.g. the result of stitching a z-stack with Reference only would be a normal 2D image.

-

All individually

All planes of this dimension are stitched individually and appear in the output image.

-

Channels

Selects the channel that serves as reference. Clicking takes the current channels from the 2D view.

-

Z-Position

Selects the z-position that serves as reference. Clicking takes the current z-position from the 2D view.

-

Time

Selects the time point that serves as reference. Clicking takes the current time point from the 2D view.

-

Scene

Selects the scene that serves as reference. Clicking takes the current scene from the 2D view.

-

Illumination

Only visible for dual side illuminated images.
Selects an illumination side that serves as reference.

-

View

Only visible for multi view images.
Selects a view that serves as reference.

Edge Detector

-

Yes

Applies an edge detection algorithm to improve analysis of the overlaps between neighboring tiles. This can improve the alignment of the tiles and thus the stitching result.

-

No

No edge detector is applied.

Minimal Overlap

Sets the minimal amount of overlap between neighboring tiles that should be evaluated by the stitching function. The overlap is sets as % of the single tile dimensions (height and width).

Maximal Shift

Specifies the maximal extent of shift that can be applied to an individual tile during stitching. The shift is sets as % of the single tile dimensions (height and width).

Comparer

Selects a method for comparing the tile overlaps to find similarities for alignment.

-

Basic

Selects a basic (faster) comparison which uses phase correlation to find similarities.

-

Best

Selects an elaborate comparison which uses cross-correlation to find similarities.

-

Optimized

Selects an optimized comparison which uses cross-correlation implemented with the Intel Performance Primitives. This comparison is faster than the Best method.

Global Optimizer

Selects which tile overlaps are evaluated.

-

Basic

Only the overlaps (except diagonal overlaps) with the strongest contrasts in each tile are taken into account for stitching. The contrast is determined with a Sobel filter.

-

Best

All overlaps (except diagonal overlaps) of a tile are taken into account for stitching.

Defaults

Resets all parameters to their default values.

Undo

Resets the stitching changes done to the image.

Redo

Repeats the last undone change to the image.

Quality

Controls the computational effort which is spent to compensate shading artefacts of tiled images. You have the following options:

• Normal
• High
• Highest

Normal is the default and sufficient in most cases. For input images with pronounced shading artefacts and small overlaps, more computation effort can be selected with the High or Highest option.

Use Averaging

Activated: The blending information of all tiles is averaged and the same correction is applied to all tiles. This can be useful for tiled images with very low signal to noise ratio.

Deactivated: The blending between neighboring tiles is treated individually. This is the default and usually yields the best results.

Extended Blending

Only visible if Show All is activated.

Activated: Performs an additional spline-based correction to the pixels inside the overlap regions. This is the default setting.

Changing the setting is only needed in rare cases, for example when the blending result seems to overcompensate shading artefacts. In such cases, deactivate Extended Blending or Overlapping Region Blending.

Overlapping Region Blending

Only visible if Show All is activated.

Activated: Performs an additional linear blending only for the overlapping tile regions, which can correct residual blending errors that were not corrected by the blending function. This is the default setting.

Changing the setting is only needed in rare cases, for example when the blending result seems to overcompensate shading artefacts. In such cases, deactivate Extended Blending or Overlapping Region Blending.

Correction Factor Limit

Only visible if Show All is activated.

Defines an upper threshold for how strong the shading correction effect is applied. For each pixel a correction factor is calculated. For example, a value of 0.3 means the correction cannot deviate more than 30% from the original value. Larger values mean that stronger compensation is allowed, smaller values mean that the compensation is reduced.

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.

–

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.

–

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.

–

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.

–

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.

-

Translation

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

-

Rotation

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

-

Iso Scaling

The magnification is adjusted from section to section.

-

Skew Scaling

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

-

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.

-

Nearest Neighbor

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

-

Linear

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

-

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).

–

Scene Component

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

–

Phase Component

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

–

Channel Component

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

–

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.

–

Tile Component

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

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.

–

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.

–

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.

–

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.

–

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.

–

Translation

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

–

Rotation

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

–

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.

-

Nearest Neighbor

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

-

Linear

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

-

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.

-

Full

Considers the entire image for alignment.

-

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.