Published by the Foundation for Open Access Statistics
Editors-in-chief: Bettina Grün, Torsten Hothorn, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
An Interactive Java Statistical Image Segmentation System: GemIdent | Holmes | Journal of Statistical Software
Authors: Susan Holmes, Adam Kapelner, Peter P. Lee
Title: An Interactive Java Statistical Image Segmentation System: GemIdent
Abstract: Supervised learning can be used to segment/identify regions of interest in images using both color and morphological information. A novel object identification algorithm was developed in Java to locate immune and cancer cells in images of immunohistochemically-stained lymph node tissue from a recent study published by Kohrt et al. (2005). The algorithms are also showing promise in other domains. The success of the method depends heavily on the use of color, the relative homogeneity of object appearance and on interactivity. As is often the case in segmentation, an algorithm specifically tailored to the application works better than using broader methods that work passably well on any problem. Our main innovation is the interactive feature extraction from color images. We also enable the user to improve the classification with an interactive visualization system. This is then coupled with the statistical learning algorithms and intensive feedback from the user over many classification-correction iterations, resulting in a highly accurate and user-friendly solution. The system ultimately provides the locations of every cell recognized in the entire tissue in a text file tailored to be easily imported into R (Ihaka and Gentleman 1996; R Development Core Team 2009) for further statistical analyses. This data is invaluable in the study of spatial and multidimensional relationships between cell populations and tumor structure. This system is available at together with three demonstration videos and a manual.

The code is now open-sourced and available on github at:

Page views:: 4161. Submitted: 2008-08-09. Published: 2009-06-25.
Paper: An Interactive Java Statistical Image Segmentation System: GemIdent     Download PDF (Downloads: 3691)
Supplements: GemIdent executables, source code, documentation, example images Download (Downloads: 2165; 11MB)

DOI: 10.18637/jss.v030.i10

This work is licensed under the licenses
Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.