Transform
Image processing operations leading to changes in the whole stack layout. For example, substack extraction, cropping or drift correction.
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.
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.
Project image
Project an image along the z-axis into the xy-plane.
Replace image
This module duplicates an image into another, existing, image.