This method allows you to align the channels of your image. The alignment is done based on a transformation file created with another function, see Create Channel Alignment Transformation. Note that the channel number and names have to match exactly with the ones used to create the transformation file. The alignment is applied on all 2D images/z-stacks along all other dimensions. If you have tiled images, for example, the same channel transformation is applied to all tiles individually. You can also align SIM (Structured Illumination Microscopy) raw images.

Parameter

Description

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:

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Process Channel

Processes this channel according to the input.

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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.