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
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.
Merge pull request #324 from melissalinkert/dev-docs

Documentation updates
Adding request for example files
Changing wording to discourage email attachments
Merge pull request #331 from hflynn/file-requests

Adding request for example files
Add support for JPEG-2000 compression with code 34712

Fixes #9618.
Fix min/max display range for resliced images

Fixes #10092.
Leica LIF: fix ROI indices

Reported by Nicolas Brouilly.
Use better schema documentation links
merge dev_4_4 --exclude conflict needs-fixes broken: PR 328 (Sprint 4 bug fixes, part 2)
merge dev_4_4 --exclude conflict needs-fixes broken: PR 332 (Add support for JPEG-2000 compression with code 34712)
merge dev_4_4 --exclude conflict needs-fixes broken: PR 334 (Use better schema documentation links)
merge dev_4_4 --exclude conflict needs-fixes broken

Repository: openmicroscopy/bioformats
Updating 03770c0..ef5725b
Merged PRs:
  # PR 328 melissalinkert 'Sprint 4 bug fixes, part 2'
  # PR 332 melissalinkert 'Add support for JPEG-2000 compression with code 34712'
  # PR 334 melissalinkert 'Use better schema documentation links'

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