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
Fix mis-merge

This resets all the files outside of TrackMate back to their previous
revision...

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bump to pom-scijava 1.62

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
importTrackMateTracks: a MATLAB script to import TrackMate track files.

From the file help:

importTrackMateTracks Import linear tracks from TrackMate

  This function reads a XML file that contains linear tracks generated by
  TrackMate (http://fiji.sc/TrackMate). Careful: it does not open the XML
  TrackMate session file, but the track file exported in TrackMate using
  the action 'Export tracks to XML file'. This file format contains less
  information than the whole session file, but is enough for linear tracks
  (tracks that do not branch nor fuse).

  SYNTAX

  tracks = importTrackMateTracks(file) opens the track file 'file' and
  returns the tracks in the variable 'tracks'. 'tracks' is a cell array,
  one cell per track. Each cell is made of 4xN double array, where N is the
  number of spots in the track. The double array is organized as follow:
  [ Ti, Xi, Yi, Zi ; ...] where T is the index of the frame the spot has been
  detected in. T is always an integer. X, Y, Z are the spot spatial
  coordinates in physical units.

  [tracks, metadata] = importTrackMateTracks(file) also returns 'metadata',
  a struct that contains the metadata that could be retrieved from the XML
  file. It is made of the following fields:
    - 'spaceUnits': a string containing the name of the physical spatial unit.
    - 'timeUnits': a string containing the name of the physical temporal unit.
    - 'frameInterval': a double whose value is the frame interval.
    - 'date': a string representation of the date the XML file has been generated.
    - 'source': a string representation of the TrackMate version this file
      has been generated with.

  OUTPUT

  The function offers two flags to change how the output is returned. As
  stated above, by default, it is returned as [ Ti, Xi, Yi, Zi ; ...] where
  T is the frame as an integer.

   tracks = importTrackMateTracks(file, clipZ) allows specifying whether to
   remove the Z coordinate entirely or not. TrackMate always return 3D
   coordinates, even for 2D motion. In the latter case, the Z coordinate is
   always 0. If 'clipZ' is set to true AND if all the particles have their
   Z coordinate to 0, then 'tracks' will be made of [ Ti, Xi, Yi ] arrays.

   tracks = importTrackMateTracks(file, clipZ, scaleT) allows specifying
   whether to scale the T coordinate by physical units. If scaleT is set to
   true AND if the frame interval metadata value could be retrieved, then
   the time will be returned in physical units, not in integer frame
   number.

  FILE FORMAT

  The XML file is expected to be formatted as follow:

  <?xml version="1.0" encoding="UTF-8"?>
  <Tracks nTracks="39" spaceUnits="pixel" frameInterval="5.0" timeUnits="s" generationDateTime="Thu, 8 Aug 2013 13:33:23" from="TrackMate v2.1.0">
    <particle nSpots="125">
        <detection t="0" x="69.3" y="151.0" z="0.0" />
        <detection t="1" x="70.0" y="153.0" z="0.0" />
            ... etc...
    </particle>
    <particle nSpots="99">
        ...
    </particle>
    ...
  </Tracks>

  Jean-Yves Tinevez <jeanyves.tinevez@gmail.com> - 2013
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Revert "importTrackMateTracks: a MATLAB script to import TrackMate track files."

This reverts commit 28a77b80d66f1d35a36bb2c166714f3a0b09d202.
Symbolic links are not carried away when git committing.
importTrackMateTracks: a MATLAB script to import TrackMate track files.

From the file help:

importTrackMateTracks Import linear tracks from TrackMate

  This function reads a XML file that contains linear tracks generated by
  TrackMate (http://fiji.sc/TrackMate). Careful: it does not open the XML
  TrackMate session file, but the track file exported in TrackMate using
  the action 'Export tracks to XML file'. This file format contains less
  information than the whole session file, but is enough for linear tracks
  (tracks that do not branch nor fuse).

  SYNTAX

  tracks = importTrackMateTracks(file) opens the track file 'file' and
  returns the tracks in the variable 'tracks'. 'tracks' is a cell array,
  one cell per track. Each cell is made of 4xN double array, where N is the
  number of spots in the track. The double array is organized as follow:
  [ Ti, Xi, Yi, Zi ; ...] where T is the index of the frame the spot has been
  detected in. T is always an integer. X, Y, Z are the spot spatial
  coordinates in physical units.

  [tracks, metadata] = importTrackMateTracks(file) also returns 'metadata',
  a struct that contains the metadata that could be retrieved from the XML
  file. It is made of the following fields:
    - 'spaceUnits': a string containing the name of the physical spatial unit.
    - 'timeUnits': a string containing the name of the physical temporal unit.
    - 'frameInterval': a double whose value is the frame interval.
    - 'date': a string representation of the date the XML file has been generated.
    - 'source': a string representation of the TrackMate version this file
      has been generated with.

  OUTPUT

  The function offers two flags to change how the output is returned. As
  stated above, by default, it is returned as [ Ti, Xi, Yi, Zi ; ...] where
  T is the frame as an integer.

   tracks = importTrackMateTracks(file, clipZ) allows specifying whether to
   remove the Z coordinate entirely or not. TrackMate always return 3D
   coordinates, even for 2D motion. In the latter case, the Z coordinate is
   always 0. If 'clipZ' is set to true AND if all the particles have their
   Z coordinate to 0, then 'tracks' will be made of [ Ti, Xi, Yi ] arrays.

   tracks = importTrackMateTracks(file, clipZ, scaleT) allows specifying
   whether to scale the T coordinate by physical units. If scaleT is set to
   true AND if the frame interval metadata value could be retrieved, then
   the time will be returned in physical units, not in integer frame
   number.

  FILE FORMAT

  The XML file is expected to be formatted as follow:

  <?xml version="1.0" encoding="UTF-8"?>
  <Tracks nTracks="39" spaceUnits="pixel" frameInterval="5.0" timeUnits="s" generationDateTime="Thu, 8 Aug 2013 13:33:23" from="TrackMate v2.1.0">
    <particle nSpots="125">
        <detection t="0" x="69.3" y="151.0" z="0.0" />
        <detection t="1" x="70.0" y="153.0" z="0.0" />
            ... etc...
    </particle>
    <particle nSpots="99">
        ...
    </particle>
    ...
  </Tracks>

  Jean-Yves Tinevez <jeanyves.tinevez@gmail.com> - 2013
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Updated mpicbg, fixed repainting and processor setting issue in
Stack_Rotate that destroyed the current stack and provided suboptimal
interactive experience.  Something changed in ImagePlus.updateAndDraw(),
but only for stacks---who knows...
Bump to pom-scijava 1.63

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Merge pull request #23 from robertb-r/master

Update to Correct_3D_drift.py
Bump to pom-scijava 1.64

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Merge remote-tracking branch 'origin/master' into track-mate