Atlas Toolkit

We developed this software to integrate 3D imaging datasets that encompass different aspects of eye development, such as gene expression profiles, signalling pathway activities, cell dynamics and tissue geometry.

Atlas toolkit is a Fiji/ImageJ plugin for fast group-wise registration of 3D morphological datasets that does not rely on landmarks.

Paper: Grocott, T., Thomas, P., Munsterberg, A. (2016) Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks. Scientific Reports Full Text

ImageJ Wiki:

Source Code: on GitHub

Instructional videos

This video shows how Atlas Toolkit can be used to align (register) multiple image stacks together.

This particular tool generates two different outputs: 1) the aligned image stacks, and 2) an '.ots' file for each of the aligned image stacks.

The '.ots' file records the alignment process so that it can be repeated later.

This video shows how Atlas Toolkit can use the '.ots' files to reproduce a particular alignment. At the end of the video you can see a direct comparison of the same stack 'before' and 'after' alignment.

This is useful when you want to repeat an earlier alignment, but using different data channels from the same input image stack.

For example, say you aligned two or more tissues after labelling them - you could then apply that exact alignment to the raw image stacks, or to different processed versions.