Organ Scaffolds

The SPARC DRC provides organ scaffolds which are used to register data, models, and connectivity knowledge into a common spatial coordinate system. The scaffolds are each published as datasets on the SPARC Portal.


Many visceral organs of the body, including all of the high-priority organs for SPARC (heart, lungs, bladder, stomach, colon), undergo large deformations. Hearts beat, lungs breathe, the bladder fills and empties, and the stomach and colon, like the rest of the gut, are subject to large propagating waves of contraction. It is therefore imperative that any attempt to map the neurons within these organs must define the neurons and their cell bodies with respect to a 3D material coordinate system within each organ (see Figure 1). The organs themselves also move with the body that contains them, and the body moves with respect to the outside world. The embedding of organs within the body is described at the end of this section.

The Finite Element Method (FEM) that is widely used in the engineering world is a compelling way to capture the intricacies of anatomical domains. The basic idea is that a physical domain (in this case an anatomical region of the body) is divided into subdomains (“elements”) joined via common nodes as illustrated in Figure 1 (this is called a finite element "mesh"). The field within an element is an interpolation using element basis functions of values of the field defined at the nodes (called the "nodal parameters"). The material space (represented by the element coordinates) can be refined to any degree to ensure that sufficient nodal parameters are available to match the resolution of the experimental data being mapped on that mesh.

An essential feature of a 3D material coordinate system for organs is that it can deal with anatomical differences both within a species (individual differences) and across multiple species to enable cross-species comparisons. This can prove difficult when different species exhibit topological differences – for example, the varying numbers of pulmonary veins that enter the left atrium of the heart (typically 3 for rat, 4 for human, and 2 for pig). Another feature of mammals is that anatomical structures are generally smooth – there are none of the sharp edges typical of engineering structures.

To meet these requirements, we have developed configurable scripts for generating high-quality smooth models of organs and other anatomy, made available in the Scaffold Mapping Tools’ Scaffold Creator. Key to these models is that they define a permanent 3D material coordinate system for the anatomy of interest, allowing equivalent material points (e.g. representing the equivalent piece of tissue) to be identified across specimens and even species, independently of its location in 3D space or how distorted it is. This is a prerequisite for performing any population study of anatomical shape and distributions of embedded structures.

We could use the term "tissue coordinates" rather than "material coordinates," but the idea is more general. For example, a material coordinate position inside a deforming human body locates a unique material point in the body, but this is not necessarily part of a tissue (e.g., it could be in the middle of an airway). We call the 3D model together with its material coordinate system for an organ a "scaffold" because it is a coordinate framework into which many different aspects of tissue structure can be assembled, including muscle fiber orientations, vascular geometry, neural pathways, and the spatial distributions of genomic data. The anatomical scaffolds are generated from simple-shaped connected elements to follow the features of an organ or other anatomical part.

Organ Scaffold Heart

Figure 1. An example of mapping from material space to physical space. A tri-cubic Hermite space to a 3D volume in 3D physical space using the heart scaffold (a-b). The initial heart scaffold is (a) deformed (b) to illustrate the fact that a material point (e.g., the red sphere in a-b) retains the same material coordinates throughout a translation and deformation of the tissue. A scalar field from material space (c) to physical space (d) on a 3D domain is also shown for both geometric and scalar fields. In addition, an example of a domain refinement (e) of the deformed cube into subdomains or "elements" is illustrated.

To generate anatomical scaffolds, you will need to install the Scaffold Mapping Tools on your local machine. Documentation for the scaffold mapping tools is available from ABI-Mapping-Tools. The following are quick links to the specific tools used in the SPARC default organ scaffolds workflow:

Detailed information about the variants, coordinates, and annotations used for each specific organ scaffold can be found in the documentation for the scaffoldmaker library.

The latest version of the datasets and associated PMR exposures for each of the generic scaffold datasets are listed below. Each of these datasets contains:

  • the mapping tool provenance data file which lists the version of the tools used to produce the organ scaffold in the dataset, and

  • exported versions of the scaffolds in webGL formats. The webGL export is primarily intended for use in visualizing and interacting with the scaffolds on the SPARC Portal. The webGL visualization export is a format that ScaffoldVuer can consume and render in a browser. ScaffoldVuer is the javascript front end component written using the Vue.JS framework to visualize, amongst other things, scaffolds. The sparc-app uses the ScaffoldVuer component to show scaffolds in the SPARC Portal.

What’s Next

For more information on reuse of the generic organ scaffolds, please visit: