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Lightsheet pyramids: ingest from OME-Zarr or SmartSPIM, chunk materialization, cloud round trip, and napari viewing - #979

Merged

stevevanhooser merged 120 commits into

mainfrom

claude/lightsheet-zarr-ndi-viewer-djp5vk

Oct 14, 2026

Merged

Lightsheet pyramids: ingest from OME-Zarr or SmartSPIM, chunk materialization, cloud round trip, and napari viewing#979
stevevanhooser merged 120 commits into
mainfrom
claude/lightsheet-zarr-ndi-viewer-djp5vk

Commits on Sep 9, 2026
- Add lightsheet OME-Zarr NDI document type + LightsheetZarrManager (scaffold)
  
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  5ab84f3
- readViewport scaffold: initialize outputs and mark unused args
  
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  282f92d
- writeChunkFile scaffold: initialize outputs and mark unused args
  
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  9bbf265
- Drop unused nChunks assignment in lightsheet makePyramid.makeOneLevel
  
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  27a8f78
- Drop the readViewport scaffold from the PR
  
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  2207091
- Drop the writeChunkFile scaffold from the PR
  
  stevevanhooser
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  037a4b3
- Drop the materializeChunks branch from makePyramid
  
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  8f8af4e
- README: drop removed scaffolds; point at WDS/NDI-python
  
  stevevanhooser
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  claude
  committed
  6a0ef06
- Add the two missing _schema.json validators for the lightsheet doc pair
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  committed
  6a03187
- Use NaN (not null) for unbounded matrix parameters in the lightsheet schemas
  
  stevevanhooser
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  claude
  committed
  59d3b62
- Merge branch 'main' into claude/lightsheet-zarr-ndi-viewer-djp5vk
  stevevanhooser
  authored
  49b1187
- Restructure lightsheet pyramid: one parent per source volume, per-level reduction_function, dedupe shared level 0
  
  stevevanhooser
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  claude
  committed
  30dfd8a
- Address Code Analyzer: paren-index perEntryReduction instead of brace-wrap
  
  stevevanhooser
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  claude
  committed
  1af66bb
- Re-tile OME-Zarr on ingest to an 8 MB per-chunk byte budget
  claude
  committed
  c8f3479
- Cover the lightsheet builders and manager statics
  claude
  committed
  c92b92a
- Fix element-wise axis test in chooseTileShape
  claude
  committed
  1d11302
- Store axes_units and channel_names as strings, not matrices
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  committed
  04293e3
Commits on Sep 10, 2026
Commits on Sep 11, 2026
- makePyramid: stream per-chunk reads instead of loading each level whole
  claude
  committed
  74a8588
- clevel: cap validation at 9, not 22 (Blosc wrapper limit)
  claude
  committed
  8578add
Commits on Sep 13, 2026
Commits on Sep 14, 2026
Commits on Sep 15, 2026
- Merge origin/main into claude/lightsheet-zarr-ndi-viewer-djp5vk
  claude
  committed
  b379744
Commits on Sep 16, 2026
Commits on Sep 20, 2026
Commits on Sep 21, 2026
- ProgressBarWindow: per-bar Timeout; list_binary_files and zipForUpload guard the handle
  claude
  committed
  b367283
- cloud upload: verbose diagnostics on the pre-upload cloud check + final status
  claude
  committed
  4e45d96
Commits on Sep 23, 2026
- Merge remote-tracking branch 'origin/main' into claude/lightsheet-zarr-ndi-viewer-djp5vk
  claude
  committed
  2280b03
Commits on Sep 24, 2026
- cloud download: fast + visible series-ingest reconstruction
  claude
  committed
  58cbdee
- cloud download: employ listFilesAll for uid validation on the remote path
  claude
  committed
  9467a0a
Commits on Sep 25, 2026
- Merge remote-tracking branch 'origin/main' into claude/lightsheet-zarr-ndi-viewer-djp5vk
  claude
  committed
  249bf5d
- LightsheetZarrManager: pull Levels + Reduction from the child level docs
  claude
  committed
  60a79cf
Commits on Sep 27, 2026
Commits on Sep 28, 2026
Commits on Sep 30, 2026
- TestPublishWithDocsAndFiles: poll getFileDetails until uploaded=true
  claude
  committed
  d5e43d3
Commits on Oct 4, 2026
- lightsheet pyramid: default tile budget 8 MB -> 32 MB
  claude
  committed
  5c9e8a8
Commits on Oct 11, 2026
- Merge origin/main into claude/lightsheet-zarr-ndi-viewer-djp5vk
  claude
  committed
  37afa16
Commits on Oct 12, 2026
Commits on Oct 13, 2026

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Commits on Oct 12, 2026

Commits on Oct 13, 2026