Micromanager: use full channel name in file names when necessary

If the trimmed name (everything before the first '-') is not sufficient
for picking up TIFF files, then use the full channel name.  I suspect
this is only an issue for datasets produced with older versions of
Micromanager, but that may not be correct.
MM: trim the timepoint count if all files are missing beyond a certain point

Fixes ticket #11972.
Prevent empty StructuredAnnotations from being created

If Modulo annotations and original metadata are not present, there is no
need to create a StructuredAnnotations object.

Fixes #11867.
Leica .lei: fix file matching when there are multiple candidate series

This prevents a series with missing files from picking up files that
belong to a subsequent series.

Fixes #11683.
APNG: eliminate need for deinterleaving

By setting the 'interleaved' flag differently, the deinterleaving logic
can be removed, which prevents the reader from allocating another image
array.  This improves performance and memory usage for larger images.

Fixes #10796.
Prevent misleading IOException during config file parsing
FV1000: populate DeltaT based upon the start/end times

Fixes #11087.
APNG: fix tile pasting for images beyond the first
FV1000: parse position data from .pty files

This is a slightly modified version of the patch submitted by Patrick
Riley in this mailing list thread:

http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2014-March/002696.html
Resolve model references even if annotations are not populated

This should fix #12093.
merge dev_5_0 -D org: PR 972 (CZI: restrict dimension adjustment)
merge dev_5_0 -D org: PR 984 (Enable SDT plane preloading by default)
merge dev_5_0 -D org: PR 987 (Volocity: parse timestamps from .atsf files)
merge dev_5_0 -D org: PR 989 (ND2: always set the field index to 2)
merge dev_5_0 -D org: PR 993 (Update docs regarding BF and Eclipse (see #12127).)
merge dev_5_0 -D org: PR 998 (Micromanager fixes)
merge dev_5_0 -D org: PR 1000 (Metadata fixes)
merge dev_5_0 -D org

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 997 melissalinkert 'Make macro recording work with Exporter (rebased onto dev_5_0)' (status: error)
  # PR 979 melissalinkert 'SVS import and TIFF export fixes' (status: failure)
  # PR 951 ctrueden 'Fix up Bio-Formats POMs' (status: )
Updating bdc292c..366186a
Merged PRs (fast-forward):
  # PR 915 imunro 'Fix for single channel  meas_mode 13 data.'
  # PR 988 melissalinkert 'InCell: fix NPE when parsing Z positions'
  # PR 960 melissalinkert 'Cache OME-XML between ImagePluses (rebased onto dev_5_0)'

Merged PRs:
  # PR 972 melissalinkert 'CZI: restrict dimension adjustment'
  # PR 984 melissalinkert 'Enable SDT plane preloading by default'
  # PR 987 melissalinkert 'Volocity: parse timestamps from .atsf files'
  # PR 989 melissalinkert 'ND2: always set the field index to 2'
  # PR 993 bpindelski 'Update docs regarding BF and Eclipse (see #12127).'
  # PR 998 melissalinkert 'Micromanager fixes'
  # PR 1000 melissalinkert 'Metadata fixes'

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