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

Daniel James White white at mpi-cbg.de
Thu Dec 10 04:22:23 CST 2009

Dear Curtis,

Thats wonderful news!

I'm, very much looking forward to working with you guys and other  
interested parties
on the future of ImageJ.

Of course, the Fiji project has ImageJ at its core (as Ubuntu has  
linux at its core)
so we are very happy to hear this news!

the next major version of BioImageXD will be in built using Java,
and be properly modular with separated GUI, algorithms and data,
so there is good chance for interoperability.

The mission goals are all laudable,
and its great that we are mostly all pushing in the same directions.

Here is chance to rebuild the ImageJ dev community in a productive and  
collaborative way.



On Dec 9, 2009, at 1:16 AM, Curtis Rueden 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

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108

+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net 	BioImageXD
http://pacific.mpi-cbg.de		Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk		Dan's Homepages
https://ifn.mpi-cbg.de 			Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

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