These weights are not restricted to be between 0 and 1, and they may take any value as long as it is non-negative. The different weights of the goal function control the relative weight of each one of the terms. This is very useful when registering large images. the image dimensions can be reduced by a factor of 2 0 = 1 to 2 7 = 128. The image subsampling parameter can be chosen between 0 and 7, i.e. The registration will be then calculated using the subsampled versions of the images but the results will be applied to the original ones. Since bUnwarpJ 2.5 there is a new parameter on the main window to allow subsampling the input images. As you increase the deformation level, the number of splines is doubled in each direction (horizontal and vertical). “Very coarse” corresponds to 4 splines (one in each corner of the image). The “Initial” and “Final” deformation lists allow you to select the coarsest and finest scale of the spline deformation field. This panel gives you access to most of the internal parameters of the algorithm. More internal options can be modified in the “Advanced Options” panel. The two registration modes “Accurate” and “Fast” involve performing bidirectional registration and affect the stopping criteria internally used by the program. The registration mode “ Mono” (included since version 2.5) makes the program to perform only unidirectional registration, i.e. The registration mode can be “Accurate”, “Fast” and “Mono”. If so, the maing dialog window of the plugin will open.īoth selected images will work simultaneously as source and target, their tags are there only for the sake of clarification. Two images ( 8, 16, 32-bit grayscale or RGB Color) need to be opened in order to be able to use the plugin. The plugin can be called from the main ImageJ/Fiji menu under Plugins › Registration › bUnwarpJ. The optimization process is a Levenberg–Marquardt algorithm minimization enhanced by a Broyden–Fletcher–Goldfarb–Shanno algorithm estimate of the local Hessian of the goal function, and both, images and deformations are represented by B-spline. Where the weights of every term are set by the user in the main window of the plugin. This image registration algorithm is based on the minimization of an energy functional that includes the dissimilarity between the source and target images -in both directions- \(E_\] Two images are given as a result: the deformed versions of A and B images. Image A is elastically deformed in order to look as similar as possible to image B, and, at the same time, the “inverse” transformation (from B to A) is also calculated so a pseudo-invertibility of the final deformation could be guaranteed. It performs a simultaneous registration of two images, A and B. General DescriptionīUnwarpJ is an algorithm for elastic and consistent image registration developed as an ImageJ plugin. The invertibility of the deformations is enforced through a consistency restriction.įor a quick start, you can have a look at the video tutorial (awarded at the Second ImageJ User & Developer Conference). This ImageJ/Fiji plugin performs 2D image registration based on elastic deformations represented by B-splines. If you’d like to help, check out the how to help guide!īUnwarpJ scheme: bidirectional Unwarping in Java. Get this file from the ImageJ website: ģ) Extend the java classpath to mij.jar, e.g using the Matlab command: javaaddpath 'C:\Program Files\MATLAB\R2009b\java\mij.jar'.Ĥ) Extend the java classpath to ij.jar, e.g using the Matlab command: javaaddpath 'C:\Program Files\MATLAB\R2009b\java\ij.jar'.ĥ) Start MIJ by running the Matlab command: MIJ.start or MIJ.The content of this page has not been vetted since shifting away from MediaWiki. With MIJ, ImageJ acts as an image-processing library of Matlab.ĭaniel Sage, Dimiter Prodanov, Jean-Yves Tinevez and Johannes Schindelin, "MIJ: Making Interoperability Between ImageJ and Matlab Possible", ImageJ User & Developer Conference, 24-26 October 2012, Luxembourg.ġ) Put mij.jar into the java directory of Matlab (e.g for Window Machine 'C:\Program Files\MATLAB\R2009b\java\').Ģ) Copy also ij.jar (ImageJ) in the java directory of Matlab. Thanks to the Fiji team, MIJ is now super-easy to use with a Matlab script Miji.m which is integrated in Fiji. MIJ allows also to access to all built-in functions of ImageJ and to third-part plugins of ImageJ. MIJ is a Java package mij.jar that provides static methods to convert images (2D) and volumes (3D) in Matlab arrays. MIJ offers the missing link between imaging software: ImageJ, Fiji and Matlab.
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