Spatial omics content

[AnnaChristina]

• [x] Introduction - scope 0.5-1 page

  • look into reviews
  • broad overview into the field
  • mention nature methods "method of the year 2020"
  • define axis: targeted/high-resolution vs unbiased/cell-aggregates

• [x] Technologies (depends heavily on what we show in the tutorial) - scope 0.5 page per method

  • ST, visium
  • MERFISH
  • IMC (Imaging Mass Cytometry)

• [x] tools (plus tutorial) - check current reviews - 1 page overall

  • squidpy
  • spectreMAP
  • giotto
  • ??

• [x] spot deconvolution (show two methods and tutorials for this) - 0.5 page

  • RCTD
  • SpotLight
  • Stereoscope
  • DestVI
  • cell2location

• [ ] Identification of Cells from mRNA spot - 0.5 page

• Baysor

• SSAM

• Sparcle

• ClusterMap

• [x] other (check where to put those, if even include)

  • tangram
  • cell type annotation
  • imputation

• [ ] downstream tools

  • ncem

[giovp]

From discussion at topic meeting:

Missing topics

• [x] spatially-aware clustering (e.g. bayespace and others)
• [ ] spatially-aware factorization (e.g. mefisto, non-negative spatial factorization and others)
• [x] spatially-variable genes (spatialDE2 and others)
• [ ] interactive visualization (napari, tissuumaps, isee)

Also important to define what's the lower-bound on pre-processing you want to add (e.g. starfish will be added or not?)

exciting, looking forward to take a look!