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feat(pyramid): pyramids on images and label images; mantis-v2 adds them after tracking and QC (#359) - #430

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ieivanov merged 68 commits into

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feat/pyramid-labels

Oct 24, 2026

Merged

feat(pyramid): pyramids on images and label images; mantis-v2 adds them after tracking and QC (#359)#430
ieivanov merged 68 commits into
mainfrom
feat/pyramid-labels

Commits on Oct 8, 2026
- feat(track): write labels and tracks.geff into the assembled plate
  
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- build(deps): repin iohub dev/dca-labels after #485 drops its legacy labels field
  
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- build(deps): repin iohub dev/dca-labels after iohub#486 label-default fix
  
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Commits on Oct 9, 2026
- feat(track): keep no Ultrack databases by default
  
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- build(deps): pin iohub to iohub#486 now that #485 is on main
  
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- build(deps): repin iohub#486 after per-position label defaults fix
  
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- build(deps): repin iohub#486 after review fixes
  
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Commits on Oct 16, 2026
- build(deps): pin ultrack to royerlab main now that #288 and #289 merged
  
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- refactor(track): drop the tempfile redirect now that ultrack#289 merged
  
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- build(deps): pin iohub to main now that #486 merged
  
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Commits on Oct 17, 2026
- feat(project)!: biahub project CLI; segment and track no longer project
  
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Commits on Oct 19, 2026
- feat(nextflow): A549 project.yml projects every assembled channel; skill checks it
  
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- fix(project): float32 plate for any max/mean/sum channel; drop float64 accumulation
  
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- refactor(project): focus record keys are z and z_per_t
  
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- refactor(project)!: z selection is start/stop or center with below/above
  
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- docs(nextflow): cleanup never targets the projected plate
  
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- feat(project): chunks_czyx and shards_ratio; A549 writes 16-timepoint shards
  
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- perf(project): find the focus of the timepoints in a process pool
  
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- feat(nextflow): projected plate lives beside the assembled one as <ds>_proj.zarr
  
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Commits on Oct 20, 2026
- Preserve focus metadata
  
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- Validate existing output layout before reuse
  
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- Include channel order in settings fingerprint
  
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- fix(project): size RAM by the channels read
  
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- test(project): focus record carries the focus settings
  
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- fix(project): more RAM headroom per worker, calibrated on an A549 position
  
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- Merge feat/project-cli: labels and tracks.geff go into the plate track reads
  
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- build(deps): ultrack pin follows royerlab/ultrack#290's pyupgrade fix
  
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Commits on Oct 21, 2026
- Merge remote-tracking branch 'origin/main' into feat/project-cli
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- Merge branch 'feat/project-cli' into feat/track-labels-geff
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- feat(track)!: cellpose is the default segmentation method
  
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- feat(pyramid): pyramids on images and label images; mantis-v2 adds them last (#359)
  
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- feat(nextflow): QC is the last step; pyramids run after tracking and ahead of it
  
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- build(deps): iohub pin follows the #488 review fixes (label-safe defaults, pyramid_dims)
  
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- build(deps): iohub pin follows the second #488 review round
  
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- build(deps): iohub pin follows the third #488 review round
  
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- feat(segment,track)!: segmentation moves out of track into the plate
  
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- refactor(segment,track): scaffold labels with iohub's create_empty_labels; track on preempted
  
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- build(deps): iohub pin moves to the #461 branch (pyramid levels keep level-0 shard bytes)
  
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- feat(settings)!: shards replaces shards_ratio in the concatenate and project configs
  
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- Merge feat/track-labels-geff: segment writes the labels, track links them
  
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- feat(track): the tracked label image takes the source label's dtype as well
  
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- feat(segment,track)!: segment writes only into the plate; track's output_label
  
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- build(configs): concatenate chunks 1 x 8 x 256 x 256; iohub pin keeps level-0 chunks down the pyramid
  
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- feat(track)!: the tracked label image is labels/tracks_<labels>
  
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- Merge remote-tracking branch 'origin/main' into feat/project-cli
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- Merge branch 'feat/project-cli' into feat/track-labels-geff
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- Merge branch 'feat/track-labels-geff' into feat/pyramid-labels
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- fix(pyramid): size the task from the level-0 shard, measured on an A549 position
  
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Commits on Oct 22, 2026
- fix(pyramid): double a retried task's memory after an OOM kill
  
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- fix(project): double a retried task's memory after an OOM kill
  
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Commits on Oct 23, 2026
- fix(pyramid): request 14x the shard and 0.3 min per volume, from v9's 54 positions
  
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- fix(project): max keeps the input dtype; only mean/sum make the plate float32
  
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  c407462
- Merge remote-tracking branch 'origin/main' into feat/project-cli
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- Merge commit '3b689f99' into feat/track-labels-geff
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- build(deps): pin iohub to main at the #491 merge (80b20a6)
  
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- Merge branch 'feat/track-labels-geff' into feat/pyramid-labels
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  67e7156
- Merge remote-tracking branch 'origin/main' into feat/track-labels-geff
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- Merge branch 'feat/track-labels-geff' into feat/pyramid-labels
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- feat(segment,track)!: label images are (T, 1, Z, Y, X)
  
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- build(deps): pin iohub to czbiohub-sf/iohub#496 (labels are (T, 1, Z, Y, X))
  
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- build(deps): iohub pin follows czbiohub-sf/iohub#496's review fixes (9f21979)
  
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Commits on Oct 24, 2026
- build(deps): iohub pin follows czbiohub-sf/iohub#496 (eee7567)
  
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  fe09c0d
- build(deps): pin iohub to main at the #496 merge (0cb3e35)
  
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  d570380
- refactor(labels): size label shards with iohub's 200 MB target
  
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  0bc9f45
- build(deps): the iohub override follows the pin (0cb3e35)
  
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  6d9d19a
- Merge feat/track-labels-geff: label images are (T, 1, Z, Y, X); iohub pin 0cb3e35
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- style: ruff format
  
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- Merge remote-tracking branch 'origin/main' into feat/pyramid-labels
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Commits

Commits on Oct 8, 2026

Commits on Oct 9, 2026

Commits on Oct 16, 2026

Commits on Oct 17, 2026

Commits on Oct 19, 2026

Commits on Oct 20, 2026

Commits on Oct 21, 2026

Commits on Oct 22, 2026

Commits on Oct 23, 2026

Commits on Oct 24, 2026