Pre-release dependency updates

[melissalinkert]

This should allow picking up the update in glencoesoftware/bioformats2raw#309.

Not assigning reviewers yet, just opening so I don't forget to do this. Propose the following plan:

• get bioformats2raw 0.12.0 tagged (when we're ready)
• get the rest of 0.10.0 here merged (again, when we're ready)
• bump to bioformats2raw 0.12.0 here
• then test this PR to make sure that progress bars are working as expected per the discussion in Update progressbar to 0.10.2 bioformats2raw#309, merge, and tag 0.10.0

[melissalinkert]

Think I have caught all of the necessary dependency updates here to match bioformats2raw 0.12.0, so this should be the last thing to check for 0.10.0. Testing should be a matter of picking your favorite test data, converting with bioformats2raw 0.12.0 (both NGFF versions), then converting with this PR using -p (to check progress bars) and not-default --log-level (to check logback update).

[sbesson]

CI and changes all look good. Tested as suggested by converting a few sample Zarr v2 & v3 datasets generated using bioformats2raw 0.12.0 using the -p option:

omero@ngff:/mnt/data/seb/raw2ometiff_154$ /opt/omero/apps/raw2ometiff/raw2ometiff-0.10.0-SNAPSHOT/bin/raw2ometiff CMU-1_v2.zarr/ CMU-1_v2.ome.tiff -p
[0/0] 100% [==========================================================================================================] 4455/4455 (0:00:29 / 0:00:00) 
[0/1] 100% [==========================================================================================================] 1173/1173 (0:00:07 / 0:00:00) 
[0/2] 100% [============================================================================================================] 324/324 (0:00:02 / 0:00:00) 
[0/3] 100% [==============================================================================================================] 90/90 (0:00:00 / 0:00:00) 
[0/4] 100% [==============================================================================================================] 27/27 (0:00:00 / 0:00:00) 
[0/5] 100% [==============================================================================================================] 12/12 (0:00:00 / 0:00:00) 
[0/6] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[0/7] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[0/8] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[1/0] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[1/1] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[2/0] 100% [================================================================================================================] 6/6 (0:00:00 / 0:00:00) 
[2/1] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[2/2] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[2/3] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
omero@ngff:/mnt/data/seb/raw2ometiff_154$ /opt/omero/apps/raw2ometiff/raw2ometiff-0.10.0-SNAPSHOT/bin/raw2ometiff CMU-1_v3.zarr/ CMU-1_v3.ome.tiff -p
[0/0] 100% [==========================================================================================================] 4455/4455 (0:00:29 / 0:00:00) 
[0/1] 100% [==========================================================================================================] 1173/1173 (0:00:06 / 0:00:00) 
[0/2] 100% [============================================================================================================] 324/324 (0:00:01 / 0:00:00) 
[0/3] 100% [==============================================================================================================] 90/90 (0:00:00 / 0:00:00) 
[0/4] 100% [==============================================================================================================] 27/27 (0:00:00 / 0:00:00) 
[0/5] 100% [==============================================================================================================] 12/12 (0:00:00 / 0:00:00) 
[0/6] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[0/7] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[0/8] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[1/0] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[1/1] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[2/0] 100% [================================================================================================================] 6/6 (0:00:00 / 0:00:00) 
[2/1] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[2/2] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00) 
[2/3] 100% [================================================================================================================] 3/3 (0:00:00 / 0:00:00)

or --log-level

omero@ngff:/mnt/data/seb/raw2ometiff_154$ /opt/omero/apps/raw2ometiff/raw2ometiff-0.10.0-SNAPSHOT/bin/raw2ometiff NIRHTa+001_v2.zarr/ NIRHTa+001_v2.ome.tiff --log-level INFO
2026-04-23 11:24:38,968 [main] INFO  c.g.p.PyramidFromDirectoryWriter - Creating tiled pyramid file NIRHTa+001_v2.ome.tiff
2026-04-23 11:24:39,639 [main] INFO  c.g.pyramid.PyramidSeries - Number of resolution levels: 2
2026-04-23 11:24:39,667 [main] INFO  c.g.p.PyramidFromDirectoryWriter - Adding metadata for resolution: 0
2026-04-23 11:24:39,668 [main] INFO  c.g.p.PyramidFromDirectoryWriter - Adding metadata for resolution: 1
...
2026-04-23 11:46:06,885 [main] INFO  org.perf4j.TimingLogger - start[1776944766698] time[187] tag[fullResolution-2303]
2026-04-23 11:46:06,885 [main] INFO  org.perf4j.TimingLogger - start[1776944143812] time[623072] tag[fullResolutionIFDs]
2026-04-23 11:46:06,885 [main] INFO  org.perf4j.TimingLogger - start[1776943553425] time[1213459] tag[writeIFDs]
2026-04-23 11:46:06,885 [main] INFO  org.perf4j.TimingLogger - start[1776943492857] time[1274028] tag[convertToPyramid]

[erindiel]

Zarr v2 and v3 conversions were both successful as in @sbesson 's tests.

-rw-r--r--  1 erindiel  staff  1642003696 Apr 24 13:09 2.ome.tiff
-rw-r--r--  1 erindiel  staff  1642003696 Apr 24 13:09 3.ome.tiff

There were no visual differences in the output when viewed in FIJI.

Progress bar also looked good with -p 👍🏻

[sbesson]

Just in time for OME 2026 😄 All yours @melissalinkert