Tutorials

Notebooks to showcase the use of Harpy for analyzing spatial proteomics data.

• General tutorials
  • Technology-specific advice
  • Scalable Spatial Transcriptomics Analysis with Harpy.
  • Highly-multiplexed image analysis with Harpy
  • Harpy support for InstanSeg segmentation model
  • Run FlowSOM for pixel and cell clustering
  • Generating single-cell representations from highly multiplexed images and integration with PyTorch
  • Highly-multiplexed image analysis with Harpy and Kronos.
  • Quality Control on IMC spatial proteomics with Harpy
  • Benchmark results Harpy
• Advanced tutorials
  • Quality Control on in-silico spatial proteomics with Harpy
  • Interactive napari cell annotation on spatial proteomics
  • Interactive napari pixel annotation on spatial proteomics
  • Harpy distance calculations
  • Working with multiple samples (and coordinate systems)
  • Rasterize and vectorize
  • Shallow feature extraction using Harpy.
  • Basic Spatial Transcriptomics Analysis with Harpy
  • Example spatial transcriptomics (Xenium)
  • Understanding Dask behaviour in SpatialData
• HPC tutorials
  • High Performance Computing
  • High Performance Computing on the VIB Data Core Compute.