CODEX® Support
  • Welcome
  • CODEX® Instrument Manager (CIM)
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      • Keyence BZ-X800 and BZ-X700
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  • CODEX® Processor
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      • Extended Depth of Field
      • Shading Correction
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      • Segmentation & Spillover
      • t-SNE
      • FCS Format
    • Troubleshooting
  • CODEX® Multiplex Analysis Viewer (MAV)
    • Overview
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      • Marker Manager
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      • FCS Format
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    • CODEX and microscope setup
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  • Appendix
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      • CIM
      • Processor
      • MAV
  • PhenoCycler Analysis
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  • Cell Segmentation
  • Spatial Spillover Compensation

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  1. CODEX® Processor
  2. Technical Notes

Segmentation & Spillover

PreviousTile RegistrationNextt-SNE

Last updated 5 years ago

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Cell Segmentation

Segmentation involves two steps, finding local maxima and region-growing using the maxima as seed points . Threshold values can be specified by the user to control the region growth. Cell volumes are grown in 3D to encompass all corresponding marker expression signal. Expression levels are integrated for each marker using all voxels within a cell.

Spatial Spillover Compensation

Cells may have spillover fluorescence expression from adjacent cells that may hamper efforts to differentiate positive and negative expressions. Spillover compensation is used to reassign such expression back to the correct cells using a Gabriel graph and adjacency matrices, improving separation of sub-populations.

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[2]
Goltsev, Y., Samusik, N., Kennedy-Darling, J., Bhate, S., Hale, M., Vazquez, G., ... & Nolan, G. P. (2018). Deep profiling of mouse splenic architecture with CODEX multiplexed imaging. Cell, 174(4), 968-981.