Data Science For Health (DS4H)

Image Alignment Tool

Freely available Fiji plugin to align images based on a few markers manually defined


Data Science for Health (DS4H) Image Alignment is a user-friendly tool freely provided as an Fiji plugin. With DS4H Image Alignment, partially overlapping images can be easily co-registered by defining with a few clicks some well visible reference marks. The implemented least-squares method automatically approximates the solution of the mathematical overdetermined system, so to define the registration matrix then used for aligning the different images. It also considers rotations and scale changes in case the images to be aligned are dilated/shrinked. Finally, it provides an iterative subroutine for a fine alignment, to easily reach a very good image co-registration quality.


DS4H Image Alignment has been implemented in Java as a plugin for Fiji. It works with svs files, but also all the medical imaging formats included in Bio-Formats.


To install DS4H Image Alignment follow the instructions reported on the Video Tutorial. Basically, you have to copy the DS4H Image Alignment jar file in the plugins folder of Fiji.
Please, note that DS4H Image Alignment was tested using Fiji version Windows 64-bit release 2017 May 30.


Copyright (C) 2019, the Data Science for Health (DS4H) group. All rights reserved.

Image Alignment and the material available on the Image Alignment website is licensed under the: GNU General Public License version 3


We thanks all the University Students that helped in this project. In particular:


The Data Science for Health (DS4H) group: