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Rewrite codex() and add phenocycler() for Akoya CODEX / PhenoCycler-Fusion data - #429

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timtreis wants to merge 107 commits into

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feat/akoya-readers

Draft

Rewrite codex() and add phenocycler() for Akoya CODEX / PhenoCycler-Fusion data#429
timtreis wants to merge 107 commits into
mainfrom
feat/akoya-readers

Commits on Oct 16, 2026
- test: add synthetic Akoya qptiff, FCS and CODEX processor fixture writers
  
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  c4f414a
- feat: add QPTIFF metadata and lazy image core for Akoya readers
  
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  95eeaca
- fix: never guess QPTIFF scan-profile enrichment for ambiguous channels
  
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  125176b
- feat: add shared Akoya channel, transform and metadata helpers
  
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  d4ec437
- feat: add phenocycler reader for PhenoCycler-Fusion 1.x/2.x qptiff
  
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  8c6a8d2
- feat!: rewrite codex reader discovery and images for CODEX Processor and CIM outputs
  
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  08b73f1
- fix: tile uncompressed CODEX tiffs and harden legacy discovery
  
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  042695f
- feat: read CODEX Processor FCS/CSV cell tables with marker names and all regions
  
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  736c75f
- fix: skip unusable region-less CODEX tables and reject overlapping ones
  
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  afd5f24
- feat: ingest QuPath, mcquant and generic cell tables with mask labels in Akoya readers
  
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  c2b81cf
- fix: guard reserved obs keys, check masks and relax mapping keys in Akoya cell tables
  
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  3e1151b
- feat: rasterise QuPath cell polygons lazily into labels
  
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  8ccd9ff
- fix: reject QuPath polygons far from their cells' centroids
  
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  0d5cbb9
- feat: keep QuPath polygons and give unrelated Akoya regions their own coordinate systems
  
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  a8634af
- feat: add HuBMAP SPRM and inForm cell-table adapters
  
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  1bec2f8
- docs: document Akoya reader rewrite and add real-data tests
  
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  814f037
- fix(codex): find channelNames.txt and experiment.json case-insensitively
  
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  853509e
- fix: keep cell-table columns named region or cell_id as source_<name>
  
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  183685a
- fix: reject a mapping or an empty sequence as regions
  
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  82a2a72
- fix(phenocycler): ignore malformed or non-UTF-8 sidecars with a warning
  
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  a8d0358
- fix: make lazy qptiff, compressed-TIFF and mask arrays picklable
  
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  6eb8b27
- fix(codex): ignore region-named CSVs that are not CODEX cell tables
  
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  a32a8e3
- fix: convert µm cell coordinates with each region's own pixel size
  
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  90f15db
- fix(phenocycler): find .QPTIFF scans and datasets below raw/images/phenocycler
  
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  b0ed75d
- fix(qptiff): do not pair scan-profile records by position across markers
  
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  77953f1
- fix: name the file when a region's cells share an instance id
  
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  fc5fa05
- test(codex): write and re-read a two-region CODEX Processor read
  
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  8da35f2
- refactor: share the Akoya element assembly and qptiff region ids
  
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  f09f09b
- docs: describe the Akoya fixes in the changelog
  
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  97b1051
- fix: keep codex positional signature backward compatible
  
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  2bb33a0
- feat: auto-scale integer-downsampled Akoya masks
  
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  7fe106a
- fix: document and test the Akoya mask scaling precisely
  
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  6726129
- feat: optionally read both 8-bit and extended-range qptiffs
  
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  c6863a1
- feat: officially support Vectra, PhenoImager and inForm QPTIFFs
  
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  38b0e4a
- feat: read real QuPath, inForm and mcquant exports
  
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  ad02cb9
- fix: tighten QuPath detection and inForm defaults
  
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  7c75918
- fix: match R-exported QuPath measurement names
  
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  9330eb5
- fix: match raw region names against sanitised region ids
  
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  e8d6a04
- fix: sanitise user-given region ids and mapping keys
  
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  60973fb
- fix: read generic pixel tables in image pixels by default
  
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  d3e9bc7
- fix: keep QuPath morphology out of bare-marker fallback
  
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  290d57a
- test: cover read_all_bit_depths with masks and tables
  
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  9b2720c
Commits on Oct 18, 2026

Commits

Commits on Oct 16, 2026

Commits on Oct 18, 2026