Spatial Process & Relationship Modeling Documentation

Contents:

• Introduction
  • Inputs
  • Requirements
  • Contact
• Release Notes
  • SPRM v1.5.1
  • SPRM v1.4.4
• SPRM Preprocessing & Analysis
  • Preprocessing
  • Image Analysis
  • Mask Analysis
  • Downstream Analysis (Statistical, Spatial, Clustering, and Subtyping)
• SPRM Outputs
  • OME-TIFFs showing pixel level results (remapping of channels) [3 per input image]
  • CSV showing interpolated cell outlines & polygons [2 per input image]
  • CSVs containing features for each cell [4 per image]
  • CSVs containing features for each segmentation [12 per image]
  • Master CSV containing clustering results for each cell (row) for each method (column) [1 per input image]
  • CSVs containing mean values of “markers” for each cluster for each clustering method [5 per input image]
  • PNGs showing coloring by cluster [10 per input image]
  • CSV containing the signal to noise ratios of the image per channel [1 per input image]
  • CSV containing PCA and Silhouette analysis of the image [2 per input image]
  • CSV containing the summary file [3 per run]
• SPRM Options Parameters
  • SPRM Options Table
  • Additional Information

Indices and tables