Funded ImageJ development effort:

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Curtis Rueden

Dec 8, 2009, 7:16:54 PM12/8/09
to ImageJX discussion group
Hi everyone,

Most of you know me, but for those who don't, my name is Curtis Rueden of the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison. Together with Glencoe Software and the Open Microscopy Environment (OME) consortium, LOCI releases the Bio-Formats library for reading microscopy file formats. Many of you know this software as a suite of ImageJ plugins which allow you to import pixels and metadata in more than 70 formats into ImageJ.

Recently, together with the Marine Biological Laboratory (MBL) at Woods Hole and the Broad Institute of MIT and Harvard, LOCI submitted a successful proposal to NIH to fund ImageJ development (for details, see We also have letters of support from both Wayne Rasband and the Fiji development group ( at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG). The project is still in the early planning stage, but we have launched a website ( describing the project aims, with we will heavily expand upon in coming weeks.

As of now, the actively involved people include: Wayne Rasband of NIH; Curtis Rueden of LOCI and Grant Harris of MBL as technical project leads; Lee Kamentsky and Adam Fraser of Broad's CellProfiler project; an additional 3-4 LOCI full-time staff programmers being brought on board within the next month; Fiji developers Albert Cardona, Johannes Schindelin and Stephan Preibisch; and principal investigators Kevin Eliceiri (LOCI), Anne Carpenter (Broad) and Rudolf Oldenbourg (MBL).

There has been a recent surge of interest in ImageJ and related projects: ImageJ itself, Fiji/ImageJA, ImageJX, VisBio, TrakEM2, Endrov, and now of course There are also many other projects with at least some interest in ImageJ as it evolves into the future: BioImageXD, CellProfiler, FARSIGHT, Micro-Manager, OME, and many more. As such, I have CCed participants in all of these projects, in the hope of maintaining an open dialogue as the project moves forward. Please forward on to anyone else who might be interested.

The mission of is:
  * To lead ImageJ development with a clear vision.
  * To continue developing one official version of ImageJ to keep the user community unified and happy.
  * To collaborate with other interested parties and institutions wherever useful.
  * To ensure ImageJ remains useful and relevant to the broadest possible community.
  * To maintain backwards compatibility with the current ImageJ as close to 100% as possible.
  * To avoid duplication of effort and instead leverage each others' work wherever practical.
  * To provide a central online resource for ImageJ: program downloads, a plugin repository, developer resources and more.

These goals will require careful planning and hard work to deliver, but will be well worth the effort. There is great potential to use ImageJ as a library, provide interoperability, or otherwise share code and ideas between these efforts. Now is the time to guide ImageJ's future development.

For those interested in the technical goals, they are:

Aim I – Improve the ImageJ core architecture
   a. Separate the data model from the user interface
      * Interface-driven, MVC design. Support AWT, Swing, headless/console, etc. [see:]
      * Grant Harris has successfully refactored ImageJ's GUI into an interface-centric design and replaced the AWT interface with Swing. [see:]
      * Raymond Martin is also actively researching this issue. [see:]
   b. Introduce an extensions framework for algorithms
      * Dimiter Prodanov proposed a revised PluginPlus interface on the ImageJX mailing list that would serve as a reasonable starting point for this aim, though there are many other questions and issues surrounding the architecture of such an extensions framework. [see:]
   c. Broaden the image data model
      * Stephan Preibisch of Fiji has developed a Generic Image Processing Library that could serve as a foundation for the broadened image data model.

Aim II – Expand functionality by interfacing ImageJ with existing open-source programs

Aim III – Grow community-driven development while maintaining compatibility

For more details, you can read about the aims at: Soon, we will also post the accepted grant proposal in its entirety.

Over the next few days, Grant Harris and I will be responding to a number of technical discussions that have cropped up on the ImageJ and ImageJX development lists, as well as replying to a few private emails from some of you as well. We apologize for the delay on these replies, but it has been a very hectic time. Moving forward, you can expect many additions to the website and associated tools, and a solidifying development plan as we meet with colleagues and discussion the best way forward for these efforts.

In the meantime, please let us know if you have any questions or ideas for collaboration!


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