This method allows you to automatically align the individual tiles of a tile image with one another. When acquiring a tile image, the stage movement is not precise down to the pixel level of the camera sensor. To bypass this technical limitation and to have a margin to compensate for this inaccuracy, tiles are usually overlapped by a few percent. To align them, the overlaps between neighboring tiles are analyzed. The tiles are then shifted and rotated against each other to make the transitions between them as seamless as possible. Multi-position images as opposed to tile images cannot be stitched.

Direct Processing

When you use Stitching in Direct Processing, not all the parameters are available (e.g. Fuse Tiles or Correct Shading). Some functionality is not available because there is no image available yet during the setup of Direct Processing. This means that taking reference settings from the 2D view or processing dimensions Reference only is not possible. For experiments containing multiple scenes, each scene is thus processed separately. Direct Processing also always keeps both the acquired and processed image, so an inplace stitching is not available.

Parameter

Description

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.