Description

Apply slice-by-slice (2D) affine-based image registration to a multi-dimensional stack. Images can be aligned relative to the first frame in the stack, the previous frame or a separate image in the workspace. The registration transform can also be calculated from a separate stack to the one that it will be applied to. Registration can be performed along either the time or Z axes. The non-registered axis (e.g. time axis when registering in Z) can be "linked" (all frames given the same registration) or "independent" (each stack registered separately).

This module uses the Block Matching plugin and associated MPICBG tools to detect matching regions from the input images and calculate and apply the necessary 2D affine transforms.

Parameters

Input image (default = "") Image from workspace to apply registration to.

Apply to input image (default = "true") When selected, the post-operation image will overwrite the input image in the workspace. Otherwise, the image will be saved to the workspace with the name specified by the "Output image" parameter.

Output image (default = "") If "Apply to input image" is not selected, the post-operation image will be saved to the workspace with this name.

Registration axis (default = "Time") Controls which stack axis the registration will be applied in. For example, when "Time" is selected, all images along the time axis will be aligned. Choices are: Time, Z.
Other axis mode (default = "Independent") For stacks with non-registration axis lengths longer than 1 (e.g. the "Z" axis when registering in time) the behaviour of this other axis is controlled by this parameter:

Transformation mode (default = "Rigid") Controls the type of registration being applied:

Fill mode (default = "Black") Controls what intensity any border pixels will have. "Borders" in this case correspond to strips/wedges at the image edge corresponding to regions outside the initial image (e.g. the right-side of an output image when the input was translated to the left). Choices are: Black, White.
Enable multithreading (default = "true") When selected, certain parts of the registration process will be run on multiple threads of the CPU. This can provide a speed improvement when working on a computer with a multi-core CPU.

Relative mode (default = "First frame") Controls what reference image each image will be compared to:

Number of previous frames (default = "1") Number of previous frames (or slices) to use as reference image when "Relative mode" is set to "Previous N frames". If there are insufficient previous frames (e.g. towards the beginning of the stack) the maximum available frames will be used. Irrespective of the number of frames used, the images will be projected into a single reference image using the statistic specified by "Previous frames statistic".

Previous frames statistic (default = "Maximum") Statistic to use when combining multiple previous frames as a reference ("Relative mode" set to "Previous N frames").
Reference image (default = "") If "Relative mode" is set to "Specific image" mode, all input images will be registered relative to this image. This image must only have a single channel, slice and timepoint.

Calculation source (default = "Internal") Controls whether the input image will be used to calculate the registration transform or whether it will be determined from a separate image:

External source (default = "") If "Calculation source" is set to "External", registration transforms will be calculated using this image from the workspace. This image will be unaffected by the process.

Calculation channel (default = "1") If calculating the registration transform from a multi-channel image stack, the transform will be determined from this channel only. Irrespectively, for multi-channel image stacks, the calculated transform will be applied equally to all channels.

Layer scale (default = "1.0")

Search radius (px) (default = "50")

Block radius (px) (default = "50")

Resolution (default = "24")

Minimal PMCC r (default = "0.1")

Maximal curvature ratio (default = "1000.0")

Closest/next closest ratio (default = "1.0") "Correspondence candidates from local descriptor matching are accepted only if the Euclidean distance to the nearest neighbour is significantly smaller than that to the next nearest neighbour. Lowe (2004) suggests a ratio of r=0.8 which requires some increase when matching things that appear significantly distorted.". Description taken from https://imagej.net/Feature_Extraction

Local region sigma (default = "65.0")

Maximal absolute local displacement (px) (default = "12.0")

Maximal relative local displacement (px) (default = "3.0")