Include option to carry out registration on hyper stack in addition to virtual hyper stack
Improve dialog to give user choice of RAM or virtual memory
Copy image information, colour, and properties from original to registered hyperstack
Fixed typo that caused bug with single channel images
Descriptor-based registration: propagate single model to multiple time-points

This commit changes the behavior of the 'Descriptor-based registration'
plugin:

When a model was extracted from a pair of images with a single
time-point, the generated model could then be applied to another pair of
images. Unfortunately, it was applied only to the first time-point of
the new pair of images, even if they had several frames.

This commit allows a single model to be applied to all the time-points
of the new image pair.

The use-case targetted here is the correction for channel misalignment
in microscope able to capture several channels at once. The (typically)
two channels are often slightly misaligned. Users then image fluorescent
multi-color beads to assess this misalignement, then acquire a
time-lapse. They then want to correct the whole time-lapse from the
single image of the beads.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Merge branch 'db-registration-tl'

Conflicts:
	src-plugins/Descriptor_based_registration/src/main/java/process/OverlayFusion.java
fixed two bugs in the overlay fusion for the descriptor based registration
Updater_Fix.js: Make sure that ij.IJ is found

Noticed by Vassilis Kehayas in bug 631.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add a little utility to update the URLs in Updater_Fix.js

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Update the URLs in Updater_Fix.js to the newest, latest & greatest

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Trainable Weka Segmentation: added method to create instances in place.
Trainable Weka Segmentation: create instances in place to improve speed.
Merge branch 'trainable-seg-gui'

Merge last changes to improve speed and memory use.
Merge branch 'master' of https://github.com/fiji/fiji
difference-of-mean does not ignore minmaxset anymore
Merge branch 'master' of github.com:fiji/fiji
QuickPALM: fix NullPointerException

When the full count of threads was not needed, a couple of the elements
in the threads array are still null. Let's not try to join() these.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Build.sh: handle 'fiji' and 'ImageJ' target again

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Update .gitignore for current ImageJ2

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Weed out .gitignore some

I might have been overzealous in parts, but I always can but things
back...

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'quickpalm-npe'

This fixes a NullPointerException when not all available thread slots
were used.

From Ricardo:

	On Sat, 13 Jul 2013, Ricardo Henriques wrote:

	> Hi Johannes,
	> By all means, merge away. Thank you for looking into this.
	> Cheers,
	> -Ricardo

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>