almost seven years ago, I started the Fiji project to address the need for
a user-friendly distribution of ImageJ with life-science specific plugins
on the one side and for a developer-friendly platform on which new image
processing and analysis components can be built on the other.
A lot happened in the meantime!
- Many useful plugins were added to the Fiji distribution, e.g. the
Trainable Segmentation (sporting advanced machine learning "hidden"
behind a very intuitive and easy-to-use graphical user interface) or
several bleeding-edge plugins to process and analyze light-sheet
microscopy (SPIM) images.
- We saw that the updater was the singularly most popular feature – both
for developers and users, because it made the interaction between these
two groups of scientists much easier – and extended its functionality
e.g. to allow for personal update sites.
- We saw the need for a robust next-generation data processing library and
came up first with ImgLib, later with the even better ImgLib2.
- We then joined ranks with the ImageJ2 project, lifting the complete Fiji
project to a new level of professional, industry-grade software
- During a hackathon with representatives of KNIME, OMERO and Icy, the
SciJava project was started, identifying commonly needed functionality
and putting it into highly reusable, robustly developed software
- An incredibly successful paper was published in Nature Methods, cited
almost a thousand times at the time of writing (according to Google
- Many development techniques and best practices emerged that now benefit
the entire developer community.
- Developer and web resources are now provided by LOCI in Madison, WI,
USA, being much more scalable than our first server.
- The Fiji wiki was transmogrified into the Fiji/ImageJ wiki, with the two
entry points http://fiji.sc and http://imagej.net being backed by the
same, community-driven content.
- Fiji development is busier than ever, and the web site access numbers
have climbed from a humble 4,870 unique visitors in January 2009 to
320,365 unique visitors in October 2014.
For me personally, Fiji has landed me a job at the MPI-CBG in Dresden,
Germany, getting free reign to work on Fiji for one year, then getting the
opportunity to use Fiji extensively while leading the image processing
facility for two years. I had the flattering invitation to work with Kevin
Eliceiri and Curtis Rueden at the University Wisconsin-Madison originally
intended for two years, then extended to a third year, and I just returned
to Dresden to work with PAvel Tomancak.
The work on Fiji put me in touch with many excellent scientists in all
kinds of exciting places (Barcelona, New York, Paris, San Francisco, and
many more) and while funding was always a concern, I had many an
encouraging feedback from literally hundreds of users.
After such a long time of sustained committment and dedication, it is time
to take a slightly belated sabbatical for me.
The Fiji maintenance will be in good hands, as my good friend and
colleague Curtis Rueden agreed to step in for me; His unquestioned
integrity and skill will undoubtedly keep this project running very
Here's to keeping the community spirit alive!
ImageJ-devel mailing list
If I had a bottle of champagne, I'd crack it across the bow of the good ship Dscho to send it on it's well-deserved way. Thanks for holding things together for so long, hope to see you refreshed and ready for more when you pull back into port. If you find your way to Boston, don't be a stranger, doesn't have to be about work.
On Fri, Nov 14, 2014 at 1:27 PM, Johannes Schindelin <[hidden email]> wrote:
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