EPFL | Biomedical Imaging Group | Software for ImageJ

Advanced Image Processing and Analysis Using ImageJ

M. Unser

Proceedings of the Eighth European Light Microscopy Initiative Meeting (ELMI'08), Davos GR, Swiss Confederation, May 27-30, 2008, pp. 34.

ImageJ is a widely-used public-domain image-processing software that was developed by Wayne Rasband from the NIH, USA. ImageJ has an open architecture that provides extensibility via Java plugins, recordable operations and macros; this greatly facilitates the dissemination of algorithms for biological image analysis. In this presentation, we describe some ImageJ plugins that were developed by the researchers of EPFL's Biomedical Imaging Group during the past five years. While these algorithms typically rely on sophisticated mathematical tools such as splines, wavelets, and steerable filters, special efforts have been made to make them accessible to non-expert users via a friendly interface. Specifically, we present efficient image analysis procedures for tracking fluorophores (SpotTracker), for segmenting cells (Snakuscule), for directional image analysis (SteerableJ) including filament detection, and for tracing neurites (NeuronJ). We describe a wavelet-based software (EDF) for extended depth of focus from of focal series of images (z-stack). We introduce a new 3D deconvolution package (Deconvolution lab) that implements most of the state-of-the-art algorithms in the field: Wiener filter, Richardson-Lucy, and various flavors of constrained least-squares deconvolution. We also cover the important topic of image registration and describe a collection of high-end algorithms for motion compensation (TurboReg, StackReg), building image mosaics (MosaicJ), and elastic registration (UnwarpJ).

This is joint work with Daniel Sage, Philippe Thévenaz, François Aguet, Cédric Vonesch, as well as many other members of the laboratory who have contributed to this effort over the years.

@INPROCEEDINGS(http://bigwww.epfl.ch/publications/unser0808.html,
AUTHOR="Unser, M.",
TITLE="Advanced Image Processing and Analysis Using {ImageJ}",
BOOKTITLE="Eighth European Light Microscopy Initiative Meeting
	({ELMI'08})",
YEAR="2008",
editor="",
volume="",
series="",
pages="34",
address=" Davos GR, Swiss Confederation",
month="May 27-30,",
organization="",
publisher="",
note="")

© 2008 ELMI. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from ELMI. This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.