qust documentation

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Contents:

• QuST Prerequisites
• QuST Installing
• QuST Building
• Image Alignment
  • Load H&E Images into FIJI
  • H&E Color Deconvolution
  • Load DAPI Images into FIJI
  • Linear Image Stack Alignment using SIFT
  • Non-linear Image Stack Alignment using bUnwrap
  • Load Xenium data into QuST
• TUTORIAL
  • Tutorial Prerequisites
  • Create a new QuPath project
  • Image Registration
  • Sample prep
  • Loading Xenium Annotations
  • Generating Dataset
  • Applying a Trained Model
  • Running DBSCAN-CellX