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:
- "Independent" Each non-registration axis is registered independently. For example, applying separate Z-registrations for each timepoint of a 4D stack.
- "Linked" All elements of the non-registration axis are registered with a single transform. For example, applying the same registration at a timepoint to all slices of a 4D stack.
Transformation mode (default = "Rigid") Controls the type of registration being applied:
- "Affine" Applies the full affine transformation, whereby the input image can undergo translation, rotation, reflection, scaling and shear.
- "Rigid" Applies only translation and rotation to the input image. As such, all features should remain the same size.
- "Similarity" Applies translation, rotating and linear scaling to the input image.
- "Translation" Applies only translation (motion within the 2D plane) to the input image.
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:
- "First frame" All images will be compared to the first frame (or slice when in Z-axis mode). For image sequences which continuously evolve over time (e.g. cells dividing) this can lead to reduced likelihood of successfully calculating the transform over time.
- "Previous N frames" Each image will be compared to the N frames (or slice when in Z-axis mode) immediately before it (number of frames specified by "Number of previous frames"). These reference frames are consolidated into a single reference image using a projection based on the statistic specified by "Previous frames statistic". This mode copes better with image sequences which continuously evolve over time, but can also lead to compounding errors over time (errors in registration get propagated to all remaining slices).
- "Specific image" All images will be compared to a separate 2D image from the workspace. The image to compare to is selected using the "Reference image" parameter.
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" The transform is calculated from a separate image from the workspace (specified using "External source"). This could be an image with enhanced contrast (to enable better feature extraction), but where the enhancements are not desired in the output registered image. When "Other axis mode" is set to "Linked", the external image must be the same length along the registration axis and have single-valued length along the non-registration axis. However, when set to "Independent", the external image must have the same axis lengths for both the registration and non-registration axes.
- "Internal" The transform is calculated from the input 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_ExtractionLocal region sigma (default = "65.0")
Maximal absolute local displacement (px) (default = "12.0")
Maximal relative local displacement (px) (default = "3.0")