DS4H Image Alignment

Revision as of 02:28, 22 August 2019 by DS4H (talk | contribs)
DS4H Image alignment (ImageJ)
Author Stefano Belli; Antonella Carbonaro; Filippo Piccinini
Maintainer DS4H
Source on GitHub
Initial release 08/06/2019
Latest version 13/08/2019
Development status stable
Category Category:Registration


"Data Science for Health (DS4H) Image Alignment" is a user-friendly tool freely provided as an ImageJ/Fiji plugin. With DS4H Image Alignment, 2D images can be easily aligned (i.e. 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 of object dilation/shrink. Finally, it provides an iterative subroutine for a fine alignment, to easily reach a very good image co-registration quality.

File:Http://filippopiccinini.altervista.org/FP/DS4H IA Modified TsujikawaCellReports2017.png


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


DS4H Image Alignment is freely available, together with a sample dataset and a video tutorial.

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 Imagej/Fiji.

- ImageJ/Fiji plugin (".jar" file), to be copied in the plugins folder of Imagej/Fiji.

- Sample dataset (1 MB), with a few images useful to test DS4H Image Alignment.

- Video tutorial, to learn how to use DS4H Image Alignment:

Contact Us

The Data Science for Health (DS4H) group:

- Antonella Carbonaro Department of Computer Science and Engineering (DISI), University of Bologna, Bologna, Italy antonella.carbonaro@unibo.it

- Filippo Piccinini Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola (FC), Italy filippo.piccinini@irst.emr.it

- Stefano Belli Master's Degree Student in Computer Sciences, University of Bologna, Italy stefano.belli4@studio.unibo.it