Merge pull request #5 from ncihtan/st-update

Generalize spatial_transcriptomics.md

data_model/spatial_transcriptomics.md

@@ -4,16 +4,17 @@ order: 994
 
 # Spatial Transcriptomics
 
-The HTAN data model for spatial transcriptomics data is based upon the both imaging and single cell sequencing data models. These form a collection of  metadata fields where transcriptomic levels (or gene or protein level measures) can be mapped to locations on a tissue slide and were developed in consultation with the data generating centers who are both experts in imaging metadata (e.g., DICOM and OME) and multiple large-scale atlas projects.
+The HTAN data model for spatial transcriptomics data is based upon both imaging and single cell sequencing data models. These form a collection of metadata fields where transcriptomic levels (or gene or protein level measures) can be mapped to locations on a tissue slide, and were developed in consultation with the data generating centers who are both experts in imaging metadata (e.g. DICOM and OME) and multiple large-scale atlas projects.
 
-For further information on spatial transcriptomics see the [10X guide on ST](https://www.10xgenomics.com/spatial-transcriptomics). The HTAN data model for spatial transcriptomics was intended initially for 10X Visium, but in the near future more platforms will be supported including Nanostring GeoMX, Pick-Seq, 
+The HTAN data model currently supports 10X Visium data, but additional platforms will be added in the near future including Nanostring GeoMX and Pick-Seq.
 
-As with other data model, 10X Visium data levels are provided as follows:
+Spatial transcriptomic datasets are typically comprised of RNA-sequencing data at varying levels, coupled with imaging data and an auxiliary set of files used in or generated by processing workflows for spatial transcriptomics:
 
 | Level | Description                                                                                                                              |
 | --------------- | ------------------------------------------------------------------------------------------------------------------------------ |
-| RNA-seq Level 1 | Files contain raw RNA-seq data associated with spot/slide data.                                                                |
-| RNA-seq Level 2 | Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.                                                     |
-| Auxiliary Files | Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.  |
-| RNA-seq Level 3 | Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.             |
-| RNA-seq Level 4 | Processed data files based on Spatial Transcriptomics RNA-seq Level 3.
+| Spatial Transcriptomics RNA-seq Level 1 | Files contain raw RNA-seq data associated with spot/slide data.                                                                |
+| Spatial Transcriptomics RNA-seq Level 2 | Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.                                                     |
+| Spatial Transcriptomics RNA-seq Level 3 | Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.             |
+| Spatial Transcriptomics RNA-seq Level 4 | Processed data files based on Spatial Transcriptomics RNA-seq Level 3.                                                         |
+| Spatial Transcriptomics Auxiliary Files | Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.  |
+| Imaging Level 2 | Imaging data compiled into a single file format, preferably a tiled and pyramidal OME-TIFF. |