Data in this directory is used by the vignette and the examples of functions
in the package. It corresponds to Xenium by 10x genomics (mouse brain FF
tissue), CosMx by Nanostring (human lung NSCLC) and Merscope by Vizgen (human
ovarian cancer).

+ XENIUM
- Downloaded from:
https://www.10xgenomics.com/resources/datasets/fresh-frozen-mouse-brain-replicates-1-standard

- Download date: 8th Feb 2023

- Modifications: Raw csv.gz files were uncompressed and only the transcripts
and boundaries from a patch of 20µm x 20µm were used. 
    - x_min <- 4900, x_max <- 4920
    - y_min <- 6400, y_max <- 6420

+ MERSCOPE
- Downloaded from:
https://console.cloud.google.com/storage/browser/vz-ffpe-showcase/HumanOvarianCancerPatient2Slice2?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false

- Download date: 27th Feb 2023

- Modifications: raw transcripts file was filtered to only contain molecules
present in a 80µm x 80µm patch.
    - x_min <- 8000, x_max <- 8080
    - y_min <- 8000, y_max <- 8080 

+ COSMX
- Downloaded from:
https://nanostring.com/products/cosmx-spatial-molecular-imager/nsclc-ffpe-dataset/

- Download date: 27th Feb 2023

- Modifications: raw transcript file had coordinates in pixels. To standardise
data we converted the data to µm units. CosMx specifies that 1 pixel is equal
to 0.18 µm. Thus, a 20µm x 20µm patch corresponded to 100 x 100 pixel patch.
    - x_min <- 10000, x_max <- 10100
    - y_min <- 140000, y_max <- 140100
