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RegistrationTree

Registration for very large 3D images stored in the BigDataViewer HDF5 or n5 formats.

  • Wrapper for BigWarp (https://github.com/saalfeldlab/bigwarp) and Elastix (https://elastix.lumc.nl/) allowing easy passing of images between the two (builds on top of Christian Tischer's elastix wrapper: https://github.com/embl-cba/elastixWrapper)

  • Cropped and downsampled regions can be selected interactively to send to elastix (minimising the amount of data that must be re-written / making it easier to use with very large images).

  • Registrations can be built up / viewed / compared in an arbitrary tree, allowing easy comparison of different registration options.

Currently only affine registrations are supported. Time series and multichannel images are not supported.

Designed for registration of 3D images, but 2D should also be supported (not tested explicitly!)

Installation

RegistrationTree is a Fiji plugin. If you haven't used Fiji/ImageJ before - you can download it from: https://imagej.net/Fiji
If you're using an existing Fiji installation, make sure it is up to date!
Go to Help > Update... in the imagej menu, and select Apply Changes.

Add the RegistrationTree update site

Go to Help > Update... in the imagej menu, and select 'Manage update sites'.
In the new window that pops up, select 'Add update site'. This will create a new row in the table. Fill this row out so it looks like below:

Then click 'Close'.
Then click 'Apply Changes'

User guide

A short user guide is provided in the wiki: https://github.com/K-Meech/RegistrationTree/wiki

Cite

If you use RegistrationTree in your work, please cite our paper on eLife