Mapping Virtual Millitomes to Reference Organs

The millitome defines a guide for scaling up tissue registration by partitioning a human organ model and computationally registering the resulting tissue blocks into extraction sites within the Human Reference Atlas (HRA) three-dimensional (3D) reference system. The guide can be implemented using (1) detailed instructions for surgeons on how to extract tissues from a human body or (2) a 3D cutting mold to be used when entire organs are cut into extraction sites. In both cases, AutoMated Alignment and Projection (AMAP) toolkit documented in this GitHub repository (Cyberinfrastructure for Network Science, Indiana University 2023) is used to align cutting instructions or 3D molds to the HRA reference organs. Using a lookup table that assigns tissue specimen IDs to cut tissue blocks, data can be added and explored in the Exploration User Interface (EUI). This workflow reduces the time and increases the efficiency of registering tissue into the HRA. This Standard Operating Procedure (SOP) outlines the steps for aligning a virtual millitome to a 3D reference object in the HRA to register the sectioned blocks into extraction sites within the HRA 3D reference system. It generates the required files for ingestion into the HRA Knowledge Graph (HRA-KG) and publishes them in the EUI. The virtual millitome includes a 3D model (STL/GLB file) along with a sectioning protocol and a block assignment table used by the data provider. Fig. 1 provides a schematic overview of this process.