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saenopy 1.0.7 documentation
saenopy 1.0.7 documentation

Contents

  • 3D TFM
    • Interface
    • Parameters
      • Detect Deformations
      • Create Finite Element Mesh
      • Material Parameters
      • Regularisation Parameters
    • Theory
      • Material
      • Regularization Mode
    • Examples
      • Classic TFM (liver fibroblasts)
      • Dynamic TFM (immune cells)
      • Microbeads to Detect Matrix Deformations
      • Multicellular TFM (intestinal organoids)
      • Brightfield TFM & Cropped Input
    • API
      • Read Files with Pyhton
  • 2.5D Spheroid
    • Theory
    • Interface
    • Parameters
      • Detect Deformations
      • Calculate Forces
    • API
  • 2.5D Orientation
    • Theory
    • Interface
    • Parameters
      • Segmentation
      • Orientation
    • API
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Parameters¶

  • Detect Deformations
    • window size
    • overlap
    • n_min, n_max
    • segmentation threshold
    • continous_segmentation
  • Calculate Forces
    • Lookup Table
    • r_min, r_max
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Detect Deformations
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Interface
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