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CP1: CellProfiler plugin modules convert; undeclared modules stay in the pipeline - #1237

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feature/CP1-cellprofiler-plugins

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CP1: CellProfiler plugin modules convert; undeclared modules stay in the pipeline#1237
trissim wants to merge 9 commits into
mainfrom
feature/CP1-cellprofiler-plugins

Commits on Oct 12, 2026
- CP1 receipt: plugin usage ranking, today's behaviour, target
  
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- A .cppipe with an undeclared module imports; absent dependencies named at compile
  
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- Plugin modules HistogramEqualization, DistanceTransform, HistogramMatching
  
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- RunCellpose, RunStarDist, Runilastik declared: they convert, compile names what is missing
  
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- CP1 receipt: what is done, blocked and remaining
  
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- Declared requirements come from the code that is running
  
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- Stop ignoring every JSON file
  
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- Built-ins LoadData, LabelImages, SaveCroppedObjects, CreateBatchFiles: 94 of 94 declared
  
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- WIP: checkpoint when the agent stopped at the usage limit (2026-10-12); tree may be mid-edit, tests not run
  
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