Closed melissalinkert closed 10 months ago
Following discussion in PR review meeting, at this point need confirmation from @DavidStirling that the output with --split-planes
is compatible with CellProfiler.
Capturing a former discussion with @melissalinkert and @muhanadz, the rationale behind https://github.com/glencoesoftware/raw2ometiff/pull/108#event-11236543153 is to re-evaluate specifically the interplay of this PR together with the recent work on RGB (#113).
Although the scenarios in https://github.com/glencoesoftware/raw2ometiff/pull/108#pullrequestreview-1676331880 should be minimally retested, the goal is to focus more specifically on brightfield digital pathology examples containing one or multiple whole slide images and/or multiple focal planes using both the --rgb
flag and some JPEG/JPEG-2000 compression as well as the --split
and --split-planes
options
Fixes #107.
Default and
--split
behavior should remain unchanged. Using--split-planes
writes each plane's pyramid to a separate file. If both--split-planes
and--split
are used,--split-planes
takes precedence.As mentioned in #107, I'd really prefer not to add more flexibility than this to the OME-TIFF layout; as we've seen with
bfconvert
, even seemingly simple configurability can add a lot of complexity. With this change, though, there are now 3 options:--split
)--split-planes
)e.g. for a 96 well x 4 fields x 3 channels plate, these options would result in 1, 384, and 1152 files respectively.