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feat/v1.1.0#28

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yousefkotp merged 8 commits into
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feat/v1.1.0-slide-patient-encoders
Apr 9, 2026
Merged

feat/v1.1.0#28
yousefkotp merged 8 commits into
mainfrom
feat/v1.1.0-slide-patient-encoders

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@yousefkotp yousefkotp commented Apr 6, 2026

  • Added encode-slide.
  • Added encode-patient.
  • process remains patch-only.
  • Added built-in slide encoders: titan, prism, moozy.
  • Added built-in patient encoder: moozy.
  • Patch features remain in patches/<stem>.h5 under features/<patch_encoder>.
  • Slide embeddings are written to slide_features/<slide_encoder> inside the per-slide H5.
  • Patient embeddings are written to patient_features/<encoder>/<case_id>.h5.
  • encode-slide reuses existing slide H5 files and computes missing required patch features when needed.
  • encode-patient reuses existing slide H5 files and computes missing required patch features when needed.
  • Added optional install extras:
    • atlas-patch[patch-encoders]
    • atlas-patch[titan]
    • atlas-patch[prism]
    • atlas-patch[moozy]
    • atlas-patch[slide-encoders]
    • atlas-patch[patient-encoders]

@yousefkotp yousefkotp merged commit 9cb1223 into main Apr 9, 2026
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