Welcome to the documentation of spatialproteomics!

Contents:

• The preprocessing (pp) accessor
• The label (la) accessor
• The plot (pl) accessor
• The tool (tl) accessor

Tutorials:

• Example Workflow with spatialproteomics
  • 1. Getting Started
  • 2. Image Processing
  • 3. Cell Segmentation
  • 4. Quantifying Protein Expression per Cell
  • 5. Cell Type Prediction
  • 6. Plotting
• Subselecting Data
  • Slicing Channels and Spatial Coordinates
  • Slicing Labels
• Segmentation
  • Whole-Cell Segmentation with Cellpose
  • Whole-Cell Segmentation with Mesmer
  • Nuclear Segmentation with StarDist
  • Segmenting Multiple Channels with Cellpose
• Custom Cropping
  • Loading the image from a zarr file
  • Drawing in the healthy regions using TissueTag
  • Putting the mask into the spatialproteomics object
  • Using the mask to set every pixel intensity to 0 in that region
  • Using the mask to remove cells in that region
• Plotting
  • Plotting Channel Intensities
  • Rendering Segmentation Masks
  • Rendering Obs
  • Rendering Labels
  • Annotation of Regions or Cells
  • Expert Plotting
• Image Processing
• Cell Type Prediction
  • Image Processing
  • Cell Type Prediction with Argmax
  • Cell Type Prediction with Astir
  • Marker Binarization
• Interoparability
  • Importing Data
  • Exporting Data
  • Exporting to Zarr
  • Exporting Tables to CSV
  • Exporting to AnnData
  • Exporting to SpatialData
• Interactivity

Indices and tables

• Index

• Module Index

• Search Page