bUnwarpJ: Consistent and
Elastic Registration in ImageJ.
1Biocomputing Unit, National Centre for Biotechnology (CSIC). Madrid, Spain
2Escuela Politécnica Superior. Universidad Autónoma de Madrid. Madrid, Spain
ImageJ User & Developer Conference 2008
User or developer?
What can this plugin offer me?
bUnwarpJ for users
(if you dare…)
Consistent and elastic registration
The plugin: main features
Source and target images
Speed vs. Accuracy
Energy function weights
Output info and save option
Image and deformation
representation: cubic B-splines
• Multi-resolution approach
• Spline deformation
• Spline interpolation
• Vectorial splines
So, what is the deformation
Multi-resolution: from “Very coarse” to “Super Fine”.
Meaning: from 20 x 20 = 1x1 intervals of B-spline
coefficients to 24 x 24 = 16x16 intervals.
Basically, more B-spline coefficients, more details.
Image similarity: MSE - Mean Square Error (grayscale
Landmarks: geometric error between landmark points.
Regularization: divergence and curl of the deformations.
Consistency: geometric distances between the pixel
coordinates after applying both transformations (direct and
E=w i E imgwE wd E dvgwr E rot w c E cons
Weights: similarity and
1.0 (if any).
The regularization weights penalize the
divergence and curl of the vector field.
Meaning: we penalize vector fields with many
points like this:
Result: we force the deformation to be smooth.
Weights: 0.1 and 0.1 when t