TIFF: tweak the JPEG YCbCr settings

Reported by Marc Lartaud.
ICS: separate RGB-stored channels that have wavelength data

Reported here: http://www.openmicroscopy.org/community/viewtopic.php?t=3115

Conflicts:

	components/scifio/src/loci/formats/in/ICSReader.java
Adjust the sizes if '-timepoint', '-channel', or '-z' are used
Reset ifdCounts on close; stopped tweaking IFDs

When a writer is 'closed', the current ifdCounts map has all present
entries reset to 0. This map is referenced in populateImage, but if you
change output files (multi-file dataset), the stored IFD count is used to
populate the TiffData elements in each series. Each subsequent file would
cause the old TiffData IFDs to be replaced with a new sequence beginning
at the old maximum.

Also, the IFDs for series 0 were being reduced by 1. This caused each IFD
in series 0 to be identical.

Signed-off-by: Luke Stuyvenberg <stuyvenberg@wisc.edu>
Make sure that the BigTIFF value is set when fixing IFD offsets
Use the known min/max if a global min/max is unavailable

The global minimum and maximum values are only available if every plane
in the series has been read.  In some cases (e.g. if "Specify range..."
was specified), we need autoscaled images but have not read all of the
planes.

Fixes #10088.
Fix min/max display range for resliced images

Fixes #10092.
Leica LIF: fix ROI indices

Reported by Nicolas Brouilly.
Leica TCS: fix a few file grouping bugs

Fixes QA #4832/#4833.
ICS: fix potential NPE

Conflicts:

	components/scifio/src/loci/formats/in/ICSReader.java
Add method to disable YCbCr correction for JPEG TIFFs

This is what 49a3ec6455e2bb4ed846cc8d65ea04a4ec5e0b99 should have done.
merge develop -D org -I include -E conflict -E needs-fixes -E broken: PR 340 (Use better schema documentation links (rebased onto develop))
merge develop -D org -I include -E conflict -E needs-fixes -E broken: PR 341 (Docs enhancements (rebased onto develop))
merge develop -D org -I include -E conflict -E needs-fixes -E broken: PR 344 (Sprint4.2 bug fixes develop)
merge develop -D org -I include -E conflict -E needs-fixes -E broken

Repository: openmicroscopy/bioformats
Updating 55cf7fd..221be61
Merged PRs:
  # PR 340 melissalinkert 'Use better schema documentation links (rebased onto develop)'
  # PR 341 melissalinkert 'Docs enhancements (rebased onto develop)'
  # PR 344 melissalinkert 'Sprint4.2 bug fixes develop'

Generated by OMERO-merge-develop#117 (http://hudson.openmicroscopy.org.uk/job/OMERO-merge-develop/117/)