Difference between revisions of "DS4H Image Alignment"

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| category              = [[:Category:Registration]]
 
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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.
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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With DS4H Image Alignment images can be easily aligned (i.e. co-registered) by defining with a few clicks some well visible reference marks.  
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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 the [[Bio-formats]] library.
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DS4H Image Alignment is freely available at: [www.filippopiccinini.it/DS4H-IA.html], together with a sample dataset and a video tutorial.
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== Contact Us ==
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The Data Science for Health (DS4H) group:
  
It also considers rotations and scale changes in case the images to be aligned are dilated/shrinked.
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Filippo Piccinini
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Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola (FC), Italy
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filippo.piccinini@irst.emr.it
  
Finally, it provides an iterative subroutine for a fine alignment, to easily reach good image co-registration quality.  
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Antonella Carbonaro
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Department of Computer Science and Engineering (DISI), University of Bologna, Bologna, Italy
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antonella.carbonaro@unibo.it
  
== Image support ==
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Stefano Belli
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Master's Degree Student in Computer Sciences, University of Bologna, Italy
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stefano.belli4@studio.unibo.it
  
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.
 
  
 
[[Category:Tutorials]]
 
[[Category:Tutorials]]
 
[[Category:Plugins]]
 
[[Category:Plugins]]
 
[[Category:Registration]]
 
[[Category:Registration]]

Revision as of 10:50, 21 August 2019

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



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 the Bio-formats library.

DS4H Image Alignment is freely available at: [www.filippopiccinini.it/DS4H-IA.html], together with a sample dataset and a video tutorial.


Contact Us

The Data Science for Health (DS4H) group:

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

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

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