User Tools

Site Tools


Annotation ROI 3D

The Annotation ROI 3D plug-in is a plug-in designed to aid in annotating 3D image stacks. The plug-in identifies unique 3D regions, assigns them an ID and allows comments to be made relating to each region. Comments and data about the regions can then be exported in XML data format for analysis.


William Grimes (william dot grimes dot 12 at ucl dot ac dot uk)

Supervised by: Professor Asanobu Kitamoto


To install the plug-in download the Annotation_ROI_3D-1.0.0.jar file and place it in the Plugins folder of ImageJ.



Sharmili Roy, Xi Liang, Asanobu Kitamoto, Masaru Tamura, Toshihiko Shiroishi, Michael S. Brown, “Phenotype Detection in Morphological Mutant Mice using Deformation Features,” Medical Image Computing and Computer Assisted Intervention (MICCAI'13), Sep 2013


For information about the development of this plug-in please see the following report, which includes a user manual in the appendix. thesis.pdf

About Us

This project was completed at the National Institute of Informatics. As Japan's only general academic research institution seeking to create future value in the new discipline of informatics, the National Institute of Informatics (NII) seeks to advance integrated research and development activities in information-related fields, including networking, software, and content. These activities range from theoretical and methodological work through applications. As an inter-university research institute, NII promotes the creation of a state-of-the-art academic-information infrastructure (the Cyber Science Infrastructure, or CSI) that is essential to research and education within the broader academic community, with a focus on partnerships and other joint efforts with universities and research institutions throughout Japan, as well as industries and civilian organizations.

National Institute of Informatics

plugin/utilities/annotation_roi_3d/start.txt · Last modified: 2019/04/12 13:13 by

Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki