Deformable registration

Correlia is an open-source ImageJ/FIJI plug-in for the registration of 2D multi-modal microscopy data-sets. The software is developed at ProVIS - Centre for Correlative Microscopy and is specifically designed for the needs of chemical microscopy involving various micrographs as well as chemical maps at different resolutions and field-of-views.

Align two images using intensity correlation, feature matching, or control point mapping

Together, Image Processing Toolbox™ and Computer Vision Toolbox™ offer four image registration solutions: interactive registration with a Registration Estimator app, intensity-based automatic image registration, control point registration, and automated feature matching. 

It is an interactive front-end visualization for registration software based on Elasix (VTK/ITK)

Non linear registration intensity based for MRI brain exams. To be applied after FLIRT

Elastix is a toolbox for rigid and nonrigid registration of (medical) images.

Elastix is based on the ITK library, and provides additional algorithms for image registration. 

The software can be run as a single-line command, making it easy to include in larger scripts or workflows. The user needs to edit a configuration file that contains all relevant parameters for registration: transformation model, metric used to comapre images, optimization algorithm, mutliscale pyramidal representation of images...

Nowadays elastix is accompanied by SimpleElastix, making it available in other languages like C++, Python, Java, R, Ruby, C# and Lua.

Working version of a simple GUI frontend for CMTK image registration tools in Fiji

ANTs computes high-dimensional mappings to capture the statistics of brain structure and function.

Image Registration

Diffeomorphisms: SyN, Independent Evaluation: Klein, Murphy, Template Construction (2004)(2010), Similarity Metrics, Multivariate registration, Multiple modality analysis and statistical bias

Image Segmentation

Atropos Multivar-EM Segmentation (link), Multi-atlas methods (link) and JLF, Bias Correction (link), DiReCT cortical thickness (link), DiReCT in chimpanzees

A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O.

The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model).

Bigwarp is a tool for manual, interactive, landmark-based deformable image alignment. It uses the BigDataViewer for visualization and navigation, and uses a Thin Plate Spline implemented in Java to build a deformation from point correspondences.

This plugin allows to compute a similarity (translation/rotation/scaling and flipping) transform from pair of points. It is updating the transformed image interactively such that the user get immediate feedback. The transformation is saved and can be applied to any other stack/image. Non rigid deformation can also be applied in 2D or 3D.

3D/3D,2D/3D or 3D /2D can be handled .

3D ROI are enabled, and can be checked with the 3D vtk view (size of ROI can be changed using the ROI stroke width).

Some prealignment by rotating in 3D the volume is possible.

Transformations can be applied directly or combined through Block Protocols (search for apply transformation).

It's also provide information about the predicted Error (based on statistical prediction), either as a full color mapping, either on each points used as landmarks, and error on the discrepancy in position between points.

There are video tutorials available in the web.

The Virtual Brain Explorer (ViBE-Z) is a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. It automatically detects 14 predefined anatomical landmarks for aligning data. It also offers a database and atlas. The ViBE-Z database, atlas and software are provided via a web interface. A data preparation step is needed in order to provide the right input data and format.

Free-D is a three-dimensional (3D) reconstruction and modeling software. It allows to generate, process and analyze 3D point and surface models from stacks of 2D images. Free-D is an integrated software, offering in a single graphical user interface all the functionalities required for 3D modeling. It runs on Linux, Windows, and MacOS. Free-D is developed by the Modeling and Digital Imaging team of the Institut Jean-Pierre Bourgin, INRA Versailles, France.

TrakEM2 is an ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation (Fiji comes with TrakEM2). It supports arbitrary-sized datasets. 

2D Image registration method based on elastic deformations represented by B-splines.