Registration

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

Best focus stack

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

Channel extractor

DEPRECATED: Please use ExtractSubstack module.

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 image in X and Y using pre-defined limits or limits based on the extents of objects in a collection.

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

Focuses a Z-stack into a single plane using the StackFocuser Fiji plugin.

Image type converter

Change the bit-depth of an image stack.

Interpolate Z axis

Interpolates Z-axis of image to match XY spatial calibration

Merge channels

DEPRECATED: This Module has been superseeded by the more generalised "Concatenate stacks" Module.

Register images

DEPRECATED: Please use separate automatic and manual modules instead.

Remove image

Removes the specified image(s) from the workspace.

Replace image

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