Feature-based registration

A python based tool for registering a template brain (from the Allen Reference Atlas) to the sample image, an extension of aMAP. Once this is complete, any other image in the template space can be aligned with the sample (such as region annotations, for segmentation of the sample image). The template to sample transformation can also be inverted, allowing sample images to be aligned in a common coordinate space. Current registration backend is niftyreg.

Component of BrainGlobe Initiative

A collection of Java tools and HTTP services (APIs) for rendering transformed image tiles that includes:

• a JSON data model for render, tile, and transform specifications,
• a Java stand-alone render application / library,
• a set of render web services that provide RESTful APIs to persisted collections of tile and transform specifications, and
• a set of Java clients for processing/rendering data that utilize the render web services to retrieve and/or store persisted specifications.
• Docker packaging for building the libraries and deploying the render web services

The basic concept is to render images (tiles) based on transformation files, without having to store the big generated image from an alignment of tiles (mosaicking).

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. 

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