[ImageJ-devel] Funded ImageJ development effort: Imagejdev.org

Badri Roysam roysam at ecse.rpi.edu
Wed Dec 9 16:29:45 CST 2009

Congratulations Curtis. The FARSIGHT team will work with you to help
bring state of the art image analysis algorithms. They are written in C++ 
but can be wrapped for the new imageJ with your help. cheers,

Badri Roysam
Professor, Department of Electrical, Computer and Systems Engineering
Associate Director, NSF Center for Subsurface Sensing & Imaging Systems (CenSSIS ERC)
Co-Director, Rensselaer Center for Open Source Software
Rensselaer Polytechnic Institute
110 8th Street, Troy, New York 12180-3590, USA.
Office(JEC 7010): 518-276-8067, Assistant: 518-276-8525, Lab(JEC 6308): 518-276-8207, Fax: 518-276-8715
Email: roysam at ecse.rpi.edu, Web: http://www.ecse.rpi.edu/~roysam

----- Original Message -----
From: Curtis Rueden [mailto:ctrueden at wisc.edu]
To: ImageJ Interest Group [mailto:IMAGEJ at list.nih.gov]
Cc: Imagejdev.org Developers [mailto:imagej-devel at imagejdev.org], Tony Collins [mailto:tcollins at macbiophotonics.ca], Andreas Jahnen [mailto:andreas.jahnen at tudor.lu], Joachim Walter [mailto:jw at walter-witzenhausen.de], Dimiter Prodanov [mailto:dimiterpp at gmail.com], Wilhelm Burger [mailto:wilbur at ieee.org], Gábor Bakos [mailto:aborgabor at gmail.com], Raymond Martin [mailto:laseray at gmail.com], Johan Henriksson [mailto:mahogny at areta.org], Nico Stuurman [mailto:nico at cmpmail.ucsf.edu], Nenad Amodaj [mailto:nenad at amodaj.com], Daniel James White [mailto:white at mpi-cbg.de], Lassi Paavolainen [mailto:lassi.paavolainen at jyu.fi], Jason Swedlow [mailto:jason at lifesci.dundee.ac.uk], Chris Allan [mailto:callan at blackcat.ca], Josh Moore [mailto:josh.moore at gmx.de], Jean-Marie Burel [mailto:j.burel at dundee.ac.uk], Melissa Linkert [mailto:melissa at glencoesoftware.com], Badri Roysam [mailto:roysam at ecse.rpi.edu], Isaac Abbott [mailto:Isaac.Abbott at gmail.com], Johannes Schindelin [mailto:Johannes.Schindelin at gmx.de]
Subject: Funded ImageJ development effort: Imagejdev.org

> 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

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