RESOLVE_analysis

Tentative set of tools and scripts for analysing spatial transcriptomic data with the resolve platform.

Seurat Loading

• Functions for loading resolve data
• Example script

The script is based on this Seurat vignette.

The script currently requires a development version of Seurat from the feat/imaging branch

Assumes the input cell segmentation was generated with: https://codebase.helmholtz.cloud/resolve_tools/resolve-processing

However, it should be adaptable to use segmentation output from other tools.

The ReadResolve function expects a folder with the following files:

• *-cell_data.csv: csv file with this header:

  cell,area,centroid.y,centroid.x,label,GENE1,GENE2,...
  

  • cell = table index, not used.
  • centroid.y,centroid.x = centroid coordinates (µm or pixel, see the use.micron argument)
  • area = area in pixel^2
  • GENE1,GENE2,...= transcript counts per cell.
• *-filtered_transcripts.txt (either the raw output from resolve or the deduplicated output from MindaGap): csv file with no header and these column:
  • x: pixels
  • y: pixels
  • z: not used, but required
  • gene name
  • quality: not used, optional
• *-roi.zip (optional, if not provided the centroids are used), zip format used by FiJi.
• *_mask.tiff: segmentation mask from cellpose or similar tool (tiff file, used only to get the total width and height, so any image would work)
• *-gridfilled.tiff: optional image to be added to the Seurat object for visualization. Generally we use the output from MindaGap, but any image would work.