General Plugins

The “general” plugin group includes several plugins which may be applied to several different types of spatial –omics techniques.

CreateAnnotation

This CLI includes several operations that can be applied to annotations to create “new” annotations.

This includes operations such as “+” and “-” where you can add or subtract regions covered by different annotations to/from each other. On the more advanced side, you can also combine several operations together in JSON format and also include property filters and the “within” predicate.

ExportAnnotations

This CLI lets users generate annotations in different formats using the “export_annotations” function in fusion-tools.

Available export formats include Aperio XML, GeoJSON, and large-image (default in Histomics/DSA). After running this plugin, the exported annotations are added to the “files” for that item where they can be downloaded.

FeatureExtraction

This CLI is used for calculating “pathomics” features for each structure in a slide. These features include quantitative measures of morphology (size and shape), color (color channel statistics), texture (by color channel), and distance transform (thickness).

Sub-compartment extraction is used to separately extract regions corresponding to Hematoxylin and Eosin stains. For more flexibility in other stains or to define other sub-compartments, see the “feature_extraction” submodule in fusion-tools.

SpatialAggregation

Spatial aggregation is used to project properties to intersecting structures. An example of this would be for projecting spatial –omics data (10x Visium spots or segmented cells with labels) to segmented/annotated structures.