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Re: Funded ImageJ development effort: Imagejdev.org

Posted by lechristophe on Dec 09, 2009; 8:49am
URL: http://imagej.273.s1.nabble.com/Funded-ImageJ-development-effort-Imagejdev-org-tp3690128p3690137.html

Curtis,

These are great news. As a rather average user I'm looking forward to see
ImageJ grow and strengthen, keeping the openness and flexibility that have
always been keys to its success. I also want to add that you and LOCI have
done an incredible job with Bio-Formats. It is one of the best exemple of
what open source can bring to the scientific community. I remember a few
years ago when you were strictly tied to specific vendor software because of
proprietary formats, these days are gone thanks to Bio-Formats.
I wish you great success in refactoring ImageJ and hope I will be able to
help in some way.

Christophe

On Wed, Dec 9, 2009 at 1:16 AM, Curtis Rueden <[hidden email]> wrote:

> 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
> http://imagejdev.org/funding). We also have letters of support from both
> Wayne Rasband and the Fiji development group (http://pacific.mpi-cbg.de/)
> 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 (http://imagejdev.org/) 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 Imagejdev.org. 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 imagejdev.org 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: http://imagejdev.org/plan]
>      * Grant Harris has successfully refactored ImageJ's GUI into an
> interface-centric design and replaced the AWT interface with Swing. [see:
> http://imagejdev.org/files/imagejdev.org/ImageJX_Mar09.pdf]
>      * Raymond Martin is also actively researching this issue. [see:
>
> http://n2.nabble.com/ImageJ-development-involvement-contributions-td4102492.html
> ]
>   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:
>
> http://groups.google.com/group/imagejx/browse_thread/thread/3ac4cd10a7f1ec3c
> ]
>   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:
> http://imagejdev.org/aims.
> 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
> imagejdev.org 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!
>
> Regards,
> Curtis
>