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Contents:

  • Overview
  • Getting Started
  • Detecting Nuclei
    • Estimating the Centres of Nuclei
    • Filtering Prior to Nuclear Segmentation
    • Background Subtraction Prior to Nuclear Segmentation
    • Segmenting Nuclei
  • Segmenting Cells
  • Making Measurements
  • Running the Complete Analysis
  • Test Data
  • Running GIANI Headlessly
GIANI
  • Detecting Nuclei
  • View page source

Detecting Nuclei

The detection and segmentation of nuclei is broken up into four stages:

  • Estimating the Centres of Nuclei
    • Overview
    • Simple Nuclear Blob Detector
    • Advanced Nuclear Blob Detector
    • Ilastik (Beta)
    • StarDist (Beta)
  • Filtering Prior to Nuclear Segmentation
  • Background Subtraction Prior to Nuclear Segmentation
  • Segmenting Nuclei
    • Nuclear Volume Marker
    • Nuclear Membrane Marker
    • Preview Segmentation
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