Tutorials

Notebooks to showcase the use of SPArrOW for analyzing spatial transcriptomics data.

• General tutorials
  • How to start
  • Analyzing MERFISH Data from the MERSCOPE Platform
  • Analysis of NanoString CosMx data
  • Tutorial for the Analysis of Visium HD Data
• Advanced tutorials
  • Working with multiple samples and coordinate systems
  • Using SPArrOW with a retrained Cellpose model
  • 1. Using a pretrained Cellpose model
  • 2. Acquiring the data for retraining
  • 3. Retraining the Cellpose model
  • Using multiple stains on Xenium data
  • Read in data
  • Cell segmentation: DAPI (only nuclei)
  • Cell segmentation: hierarchical approach
  • Cell segmentation: combined Cellpose
• HPC tutorials
  • High Performance Computing
  • High Performance Computing on the VIB Data Core Compute