Unwarp (manual)
Apply 2D B-spline unwarping transforms to align images from the workspace to other images from the workspace using manually-selected reference points.
Description
Apply 2D B-spline unwarping transforms to align images from the workspace to other images from the workspace using manually-selected reference points. When the module runs, the input and reference images are displayed. The user then selects matching points on each image and clicks "Add pair(s)". Points must be added in the same order on each image (ID numbers next to each point provide a reference). Points are shown in the control window and can be deleted by highlighting the relevant entry and clicking "Remove pair". Finally, the alignment is accepted by clicking "Finish adding pairs", at which point the images are closed and the transform is applied. If multiple slices/timepoints are to be aligned, the next image pair will immediately be displayed and the processes is repeated. The transformed input image can either overwrite the input image in the workspace, or be saved to the workspace with a new name.Alignments are calculated using the BUnwarpJ image transformation library.
Parameters
| Parameter | Description | ||||||||||||
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| Input image | Image from workspace to apply registration to. | ||||||||||||
| Apply to input image | 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 | If "Apply to input image" is not selected, the post-operation image will be saved to the workspace with this name. | ||||||||||||
| Registration axis | 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 | 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:
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| Fill mode | 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. | ||||||||||||
| Show detected points | When enabled, the points used for calculation of the registration will be added as an overlay to the input image and displayed. | ||||||||||||
| Enable multithreading | 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. | ||||||||||||
| Reference mode | Controls what reference image each image will be compared to:
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| Number of previous frames | Number of previous frames (or slices) to use as reference image when "Reference 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 | Statistic to use when combining multiple previous frames as a reference ("Reference mode" set to "Previous N frames"). | ||||||||||||
| Reference image | If "Reference 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 | Controls whether the input image will be used to calculate the registration transform or whether it will be determined from a separate image:
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| External source | 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 | 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. | ||||||||||||
| Registration mode | "The registration mode can be "Accurate", "Fast" and "Mono". The registration mode "Mono" makes the program to perform only unidirectional registration, i.e. from source to target. The two registration modes "Accurate" and "Fast" involve performing bidirectional registration and affect the stopping criteria internally used by the program." Description taken from https://imagej.net/BUnwarpJ | ||||||||||||
| Subsample factor | "The registration will be calculated using subsampled versions of the images but the results will be applied to the original ones. The image subsampling parameter can be chosen between 0 and 7, i.e. the image dimensions can be reduced by a factor of 2^0 = 1 to 2^7 = 128. This is very useful when registering large images." Description taken from https://imagej.net/BUnwarpJ | ||||||||||||
| Initial deformation mode | "Determines the level of detail of the initial deformation. In bUnwarpJ this is defined by the number of B-splines used to represent the deformations:
If images start very far away from the right alignment, it is usually a good idea to go from "Very Coarse" to "Very Fine". If they start close to the right alignment, using a very coarse initial deformation could cause the algorithm to fail. So, in that case, it would be enough to set initial deformation to "Fine" and final deformation to "Very Fine". Use "Super Fine" only when you need a very high level of accuracy, because it makes the algorithm quite slower depending on the image sizes. Description taken from https://imagej.net/BUnwarpJ | ||||||||||||
| Final deformation mode | See description for "Initial deformation mode" | ||||||||||||
| Divergence weight | Regularizes the deformation by penalizing the divergence of the deformation vector field. If you see that your transformations get too rough, it is a good idea to use this parameter. A value of 0.1 is usually good if there's no prior knowledge about the deformation shape. Description taken from https://imagej.net/BUnwarpJ | ||||||||||||
| Curl weight | Regularizes the deformation by penalizing the curl of the deformation vector field. If you see that your transformations get too rough, it is a good idea to use this parameter. A value of 0.1 is usually good if there's no prior knowledge about the deformation shape. Description taken from https://imagej.net/BUnwarpJ | ||||||||||||
| Landmark weight | Forces the deformations to fit the landmark points. Set it to 1.0 unless you're not using landmarks. Description taken from https://imagej.net/BUnwarpJ | ||||||||||||
| Image weight | The weight to control the pixel values difference. Leave it at 1.0 unless you want to do, for instance, landmark-only registration. Description taken from https://imagej.net/BUnwarpJ | ||||||||||||
| Consistency weight | Forces the resulting deformations to be one (source to target) as close as possible to the inverse of the other one (target to source). Values between 10.0 and 30.0 usually work fine. It is only taken into account for registration modes "Fast" or "Accurate". Description taken from https://imagej.net/BUnwarpJ | ||||||||||||
| Stop threshold | Stops the optimization process at each multiresolution level when the error relative change is not larger than this threshold. Description taken from https://imagej.net/BUnwarpJ | ||||||||||||
| Point selection mode | The source for points to be used in calculation of image registration:
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