Fiji Build (MiniMaven): make sure that IJ1 plugins are put into plugins/

... and conversely, non-plugins are put into jars/...

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Update .gitignore after recent cleanups

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Woops. Put back a few files required for the TrakEM2 build

Oh how I wish TrakEM2 was Mavenized...

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Fix EOF newlines
Remove unused loci_tools dependency
Explicitly list Bio-Formats-related dependencies

This is cleaner than using loci_tools (the catch-all uber-jar collection
of all Bio-Formats stuff). It will also make the updater faster in the
future, because we will no longer need to ship a new loci_tools.jar
(~10MB) every time any piece of Bio-Formats code changes.
TrackMate_: WIP - taking the long path towards ImgLib2

It's going to be long and painfull, and manual.
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Merge remote-tracking branch 'origin/master' into track-mate
TrackMate_: WIP 2 - porting to ImgLib2

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
TrackMate_: WIP 3 - going on with imglib2, and some design changes

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
TrackMate_: successfully made it to imglib2

There is still some work to do: some parts belong to imblib2, not to
TrackMate.
Also there are still these annoying messages about the calibration not
being copied from ImagePlus.
Best the core of the job is done.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Fixed nasty multi-threaded bug in content-based fusion
Debugging interval can be chosen
Merge remote-tracking branch 'origin/master' into track-mate
Saving as slices is now part of SPIM Registration, add an additional "z" tag for each filename index
Simplification, removed empty interface
TrackMate_: prepare rewrite special cursors

Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Fixed some bugs that I missed
Merge branch 'track-mate' of ssh://pacific.mpi-cbg.de/srv/git/fiji into track-mate
Fixed a bug in computing output image size when only one image is part of the collection