Module: Align

Align aligns images relative to each other, for example, to correct shifts in the optical path of a microscope in each channel of a multi-channel set of images.
For two or more input images, this module determines the optimal alignment among them. Aligning images is useful to obtain proper measurements of the intensities in one channel based on objects identified in another channel, for example. Alignment is often needed when the microscope is not perfectly calibrated. It can also be useful to align images in a time-lapse series of images. The module stores the amount of shift between images as a measurement, which can be useful for quality control purposes.

Note that the second image (and others following) is always aligned with respect to the first image. That is, the X/Y offsets indicate how much the second image needs to be shifted by to match the first.

Available measurements


Select the alignment method

Two options for the alignment method are available:


Crop mode

The crop mode determines how the output images are either cropped or padded after alignment. The alignment phase calculates the areas in each image that are found to be overlapping. In almost all cases, there will be portions of some or all of the images that don't overlap with any other aligned image. These portions have no counterpart and will be excluded from analysis. There are three choices for cropping:

Select the first input image

Specify the name of the first image to align.

Name the first output image

Enter the name of the first aligned image.

Select the second input image

Specify the name of the second image to align.

Name the second output image

Enter the name of the second aligned image.