glencoesoftware / raw2ometiff

Raw format to OME-TIFF converter
GNU General Public License v2.0
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Add --split-planes option to write one plane per file #108

Closed melissalinkert closed 10 months ago

melissalinkert commented 1 year ago

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:

e.g. for a 96 well x 4 fields x 3 channels plate, these options would result in 1, 384, and 1152 files respectively.

melissalinkert commented 1 year ago

Following discussion in PR review meeting, at this point need confirmation from @DavidStirling that the output with --split-planes is compatible with CellProfiler.

sbesson commented 11 months ago

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