Multimodal imaging

This python toolbox performs registration between 2-D microscopy images from the same tissue section or serial sections in several ways to achieve imaging mass spectrometry (IMS) experimental goals.

This code supports the following works and enables others to perform the workflows outlined in the following works, please cite them if you use this toolbox:

• Advanced Registration and Analysis of MALDI Imaging Mass Spectrometry Measurements through Autofluorescence Microscopy, 10.1021/acs.analchem.8b02884

• Next Generation Histology-directed Imaging Mass Spectrometry Driven by Autofluorescence Microscopy, 10.1021/acs.analchem.8b02885

BIRL stands for "Benchmark on Image Registration methods with Landmark validation". BIRL is a cross-platform framework for comparison of image registration methods with landmark validation (registration precision is measured by user landmarks). The project contains a set of sample images with related landmark annotations and experimental evaluation of state-of-the-art image registration methods.

Some key features of the framework:

• automatic execution of image registration of a sequence of image pairs
• integrated evaluation of registration performances using Target Registration Error (TRE)
• integrated visualization of performed registration
• running several image registration experiment in parallel
• resuming unfinished sequence of registration benchmark
• handling around dataset and creating own experiments
• rerun evaluation and visualisation for finished experiments

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

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