Registration

Modules performing alignment of images within a stack to account for sample drift or other motion.

Apply offset correction

Best focus stack

Extract a Z-substack from an input stack based on either manually-selected slices, or an automatically-calculated best-focus slice.

Concatenate stacks

Combine two or more image stacks into a single stack.

Convert 3D stack (switch Z and T)

Emsures 3D stacks (or 4D with multiple channels) are of the expected type (timeseries or Z-stack).

Crop image

Crop an input image in X and Y using pre-defined limits.

Extract substack

Extract a substack from the specified input image in terms of channels, slices and frames.

Flip stack

Flips the order of slices in stack.

Focus stack

Channels will be focused individually.

Image type converter

Change the bit-depth of an image stack.

Interpolate Z axis

Interpolates Z-axis of image to match XY spatial calibration

Remove image

Removes the specified image(s) from the workspace.

Replace image

This module duplicates an image into another, existing, image.

Unwarp images

Unwarp images (manual)

Uses the bUnwarpJ_ plugin by Ignacio Arganda-Carreras.