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Eliceiri Lab

Kevin Eliceiri, University of Wisconsin-Madison

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Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison

ImageJ is an open source image processing package popular in microscopy, medical imaging, plant sciences and other areas of scientific imaging. ImageJ's greatest strength is its flexible plugin mechanism, allowing scientists to extend its functionality by writing plugins and scripts to perform custom processing. Despite the flexibility and modularity of ImageJ, it lacks an image informatics infrastructure. Fixing this deficiency is the goal of this project. Both OMERO and ImageJ are designed to work with the same sorts of image data. The difference is that OMERO provides a robust server infrastructure for centralized storage and analysis of life sciences images, while ImageJ is a standalone tool for use on desktop workstations. However, both support life sciences data via the Bio-Formats library, and both handle datasets of up to five dimensions (X, Y, Z, time and channel). Further, increasingly popular multidimensional modalities such as spectral and lifetime imaging require image analysis software to support dimensions beyond these five. As such, both OMERO and ImageJ are now actively developing support for additional dimensions of image analysis.

LOCI's ImageJ-OMERO project seeks to extend ImageJ for easier interoperability with OMERO. OMERO should be capable of executing ImageJ plugins for multidimensional image processing within the OMERO server, using ImageJ as a library. And ImageJ should be able to access image data from OMERO data, process it locally, and then upload the results back to the OMERO server. OMERO benefits from ImageJ's easy extensibility and large collection of existing scripts and plugins, and ImageJ benefits from OMERO's centralized storage and unified metadata model. With this synergy, this is clearly a great opportunity to bring the full power of community-based image processing to bench scientists.

Further information is available on the ImageJ-OMERO project page.

Kevin Eliceiri Kevin Eliceiri is Director of the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison. LOCI is an NSF and NIH-funded instrumentation group with the mission of developing advanced optical and computational techniques for imaging and experimentally manipulating living specimens. Kevin leads these efforts and is working on utilizing the OME system as a visualization framework for multidimensional biological image data.

Curtis Rueden Curtis Rueden is a software architect at LOCI at the University of Wisconsin-Madison. Together with Kevin, Curtis directs LOCI's software efforts as a whole. Curtis is also the maintainer of the SciJava software stack including ImageJ, Fiji, SCIFIO and SciJava Common. Curtis designed the original Bio-Formats library API, and spearheaded the original OME-TIFF file format. Before joining LOCI, Curtis was part of UW-Madison's SSEC Visualization Project as a developer of the VisAD Java component library.

Alison Walter Alison Walter is a student programmer at LOCI. She works on several projects, including ImageJ Ops and ImageJ-OMERO.

Past OME Developers at LOCI

Mark Hiner Mark Hiner was a software developer at LOCI from September 2010 - June 2016. Mark worked on ImageJ and SCIFIO.

Johannes Schindelin Johannes Schindelin was a senior software developer at LOCI from September 2011 - September 2014. Johannes focused on developing software tools to help biologists analyze microscopy data. These days, Johannes works for Microsoft on the Git for Windows project.

Kristin Briney Kristin Briney was a Library Sciences student at LOCI, working to streamline the acquisition of experimental data beyond the biological image. She helped drive LOCI metadata efforts, and corresponding improvements to the OME data model.

Melissa Linkert — Melissa has moved to work on Bio-Formats for Glencoe Software.

Jason Palmer

Eric Alexander

Andrew Johnson

Caitlin Sticco

Eric Kjellman

Christopher Peterson

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