BUnwarpJ

Revision as of 09:17, 16 December 2015 by Iarganda (talk | contribs) (Generalities: add description of verbose mode)
bUnwarpJ (Fiji)
Author Ignacio Arganda-Carreras
Maintainer Ignacio Arganda-Carreras (iargandacarreras@gmail.com)
File sc.fiji:bUnwarpJ_
Source on GitHub
Initial release July 20th, 2006
Latest version 2.6.3, June 25th, 2015
Development status stable, active
Category Registration
Website bUnwarpJ
bUnwarpJ scheme: bidirectional Unwarping in Java.

This ImageJ/Fiji plugin performs 2D image registration based on elastic deformations represented by B-splines. The invertibility of the deformations is enforced through a consistency restriction.

For a quick start, you can have a look at the video tutorial (awarded at the Second ImageJ User & Developer Conference).


General Description

bUnwarpJ is an algorithm for elastic and consistent image registration developed as an ImageJ plugin. It performs a simultaneous registration of two images, A and B. 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. Two images are given as a result: the deformed versions of A and B images.

Technical Explanations

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_{img}, an optional landmark constraint E_{\mu}, a regularization term (E_{div} + E_{rot}), and an energy term E_{cons} that accounts for the geometrical consistency between the elastic deformation in both directions. Namely, the energy function is given by

 E = w_iE_{img} + w_{\mu}E_{\mu} + (w_dE_{div} + w_rE_{rot}) + w_cE_{cons}

Where the weights of every term are set by the user in the main window of the plugin. The optimization process is a Levenberg-Marquardt minimization enhanced by a Broyden-Fletcher-Goldfarb-Shanno (BFGS) estimate of the local Hessian of the goal function, and both, images and deformations are represented by cubic B-splines.

User Manual

Generalities

The plugin can be called from the main ImageJ/Fiji menu under Plugins > Registration > bUnwarpJ. Two images (8, 16, 32-bit grayscale or RGB Color) need to be opened in order to be able to use the plugin. If so, the following window will open:

bUnwarpJ main dialog


Both selected images will work simultaneously as source and target, their tags are there only for the sake of clarification. The registration mode can be "Accurate", "Fast" and "Mono". The registration mode "Mono" (included since version 2.5) 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. More internal options can be modified in the "Advanced Options" panel. This panel gives you access to most of the internal parameters of the algorithm. The "Initial" and "Final" deformation lists allow you to select the coarsest and finest scale of the spline deformation field. "Very coarse" corresponds to 4 splines (one in each corner of the image). As you increase the deformation level, the number of splines is doubled in each direction (horizontal and vertical).

Since bUnwarpJ 2.5 there is a new parameter on the main window to allow subsampling the input images. The registration will be then calculated using the 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 20 = 1 to 27 = 128. This is very useful when registering large images.

The different weights of the goal function control the relative weight of each one of the terms. These weights are not restricted to be between 0 and 1, and they may take any value as long as it is non-negative. You can see a description of the different function weights in the presentation "bUnwarpJ: Consistent and Elastic Registration in ImageJ. Methods and Applications.", given at the Second ImageJ User & Developer Conference (2008) or have a look at the FAQ section.

The stop threshold is used by the algorithm to stop the optimization process at each multiresolution level when the error relative change is not larger than this threshold.

RGB Color images will be converted to grayscale during the registration process but the resulting transformations will be applied to the original color images.

If you want to exit the plugin, press "Cancel". When you want the plugin to perform the registration press "OK". After running the plugin (on "Accurate" or "Fast" mode), the results are two stacks with the following three images:

  1. One image (warping image) registered as to fit the other image (fixed image);
  2. The fixed image;
  3. The warping mask with the same deformation as the warping image.

The final registration values appear in a separate ("Results") window.

The following figure shows one of the resulting stacks from registering a source (moving) Lena image to a target (fixed) warped version of the same image:

From left to right, consecutive slices of the resulting stack: elastic-transformed image, original moving image and warped moving mask.


The verbose mode produces more information:

  1. The elastic deformation as a vector field. Each point in the fixed image must be deformed according to this field to fit into the warping image;
  2. The grid obtained after deforming the fixed image with the vector field described above;
  3. The step values of the optimization process in a separate ("Results") window.
From left to right: the last consecutive slices of the resulting stack in verbose mode (deformation field and deformation grid) and the Log window with the optimization steps, final optimal values and execution time.

Downloads

The latest stable distribution of bUnwarpJ can always be found included within Fiji and the latest released JARs are available in the GitHub repository. If you detect any bug, please feel free to contact the maintainer. Any feedback will be very appreciated.

API documentation

The API documentation can be reached online.

Installation

In Fiji, bUnwarpJ comes installed by default. In ImageJ, you must simply download the latest bUnwarpJ_.jar to the Plugins folder of ImageJ, restart ImageJ and there will be a new "Registration > bUnwarpJ" command in the Plugins menu.

To execute bUnwarpJ as a macro or from the command line, see the description in the User Manual.

References

The algorithm implemented on bUnwarpJ and its technical explanations are detailed on the paper:

The related paper of the previous work (UnwarpJ) is:

  • C.Ó. Sánchez Sorzano, P. Thévenaz, M. Unser, "Elastic Registration of Biological Images Using Vector-Spline Regularization", IEEE Transactions on Biomedical Engineering, vol. 52, no. 4, pp. 652-663, April 2005.

License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.txt).

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.