In Gnomon, Forms are archetypes of data structures that are commonly used to represent the state of a developing biological system. Several examples of such Forms are provided by the platform, defining a generic interface of how to interact with various computational representations, independently of their underlying implementation.

Available Forms

The following Forms interfaces are currently supported by the Gnomon platform:

  • Image (multi-channel 3D intensity images)

  • CellImage (connected-regions 3D labelled images)

  • BinaryImage (“black or white” 3D binary mask images)

  • PointCloud (3D point clouds with point attributes)

  • LString (branching structure proceeding from a L-System)

  • Mesh (3D meshes made of polygonal or polyhedral cells)

  • DataFrame (multi-row data table of named columns)

  • DataDict (flexible key-value structure)

Adding Custom Forms

It is possible to extend the possible forms, yet it currently requires significant additions to the source code of Gnomon, for which we detail the procedure: Defining a new Form to implement a data structure