Difference between revisions of "DS4H Image Alignment"

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== Description ==
 
== Description ==
  
Data Science for Health (DS4H) Image Alignment is a plugin developed to align biological images by manually specifying visible reference marks.
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"Data Science for Health (DS4H) Image Alignment" is a user-friendly tool freely provided as an ImageJ/Fiji plugin. With DS4H Image Alignment,images can be easily aligned (i.e. co-registered) by defining with a few clicks some well visible reference marks.  
Warping of the single original images is done according to a least-squares method that approximates the solution of the mathematical overdetermined system, so to define the registration matrix then used for aligning the different images.
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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.
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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 Bio-Formats. It is freely available at: www.filippopiccinini.it/DS4H-IA.html, together with a sample dataset and a video tutorial.
  
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 good image co-registration quality.
 
  
 
== Image support ==
 
== Image support ==

Revision as of 10:36, 21 August 2019

DS4H Image alignment (ImageJ)
Author Stefano Belli; Antonella Carbonaro; Filippo Piccinini
Maintainer Template:DS4H
Source on GitHub
Initial release 08/06/2019
Latest version 13/08/2019
Development status stable
Category Category:Registration



Description

"Data Science for Health (DS4H) Image Alignment" is a user-friendly tool freely provided as an ImageJ/Fiji plugin. With DS4H Image Alignment,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.

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 Bio-Formats. It is freely available at: www.filippopiccinini.it/DS4H-IA.html, together with a sample dataset and a video tutorial.


Image support

All the most common biological image formats (like .tiff, .svs, .ndpi2, etc.) are supported and openable directly from the plugin. This has been possible thanks to the use of the Bio-formats library.