Katy Börner’s team from the Luddy School of Informatics, Computing, and Engineering’s Cyberinfrastructure for Network Science Center has made significant contributions to constructing a Human Reference Atlas and has led or co-authored six research articles in a just-released HuBMAP package in Nature.

Börner, Victor H. Yngve distinguished professor of engineering and data science, and CNS director, leads certainly one of the 2 mapping components throughout the NIH-funded Human BioMolecular Atlas Program. Her team includes experts from Indiana University, Stanford University, California Institute of Technology, Harvard Medical School, and the EMBL’s European Bioinformatics Institute within the UK.

The attitude, “Advances and Perspectives for the Human BioMolecular Atlas Program (HuBMAP),” provides an summary of recent accomplishments and detailed maps at single-cell resolution.

Ellen Quardokus, research scientist at IU, and Andrea Radtke, senior scientist at NIH, each members of the MC-IU team, lead the trouble that resulted in “Organ Mapping Antibody Panels (OMAPs): A community resource for standardized multiplexed tissue imaging.”

Organ Mapping Antibody Panels (OMAPs) and accompanying Antibody Validation Reports (AVRs) reflect the labor and dedication of a team of domain experts in academia, industry, and government. Together, we now have worked to beat the price, time, and expertise required to map human tissues using multiplexed antibody-based imaging. Along with providing data on a whole bunch of community-validated antibodies for diverse imaging methods equivalent to CODEX, IBEX, and Cell DIVE, OMAPs are aligned to data within the Human Reference Atlas, providing evidence for cell types in specific anatomical structures. We’re excited to share these resources with the growing spatial biology community and sit up for accelerating discovery together.”

Andrea Radtke, senior scientist at NIH

Yingnan Ju, Luddy School PhD candidate, and Börner collaborated with the GE research team on “3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging”.

“This paper seamlessly bridges the gap between practical industrial applications and my academic pursuits” Ju said. “We successfully integrated data visualization and machine learning, synthesizing the invaluable insights from my GE internship with my research at Indiana University. This collaboration has not only laid a solid foundation for future exploration but in addition added substantial value to my Ph.D. experience. I’m excited and sit up for further collaboration.”

CNS Research Scientist Andreas Bueckle was a contact creator for “Tissue Registration and Exploration User Interfaces in support of a Human Reference Atlas.” The paper details the registration and exploration user interfaces that empower users to spatially register their data to certainly one of the 66 3D reference organs and semantically and spatially explore the hundreds of tissue blocks now mapped to the HRA. Users can try this in a 3D environment, deployed to an internet browser and reachable by anyone with a web connection and with hooks into the HuBMAP Data Portal.

“Constructing a Human Reference Atlas is a huge endeavor that requires skills and talents from a various set of experts,” Bueckle said. “This necessitates tools with state-of-the-art user interfaces.”

Yashvardhan Jain, CNS Research Software Engineer is the lead creator of “Robust and generalizable segmentation of human functional tissue units.”

“Construction of the Human Reference Atlas (HRA) requires a mix of human intelligence and machine intelligence,” Jain said. “Detecting and segmenting structures equivalent to functional tissue units in human tissue images is a crucial step and wishes efficient machine learning algorithms that may automate such tasks, enabling processing and evaluation of datasets at scale.”

Jain said global data science competition platforms equivalent to Kaggle could be leveraged to have interaction data scientists, machine learning engineers and researchers across the globe to speed up the event of efficient, generalizable and scalable algorithms that may aid the event of such automated tools.

Griffin Weber, Harvard Medical School lead the team that published “Anatomical structures, cell types, and biomarkers of the healthy human blood vasculature”.

“The Human Reference Atlas-Vasculature Common Coordinate Framework (HRA-VCCF) dataset is the primary open, computer-readable, and comprehensive database of the adult human blood vasculature,” he said. “It accommodates an inventory of blood vessels and their branching relationships, in addition to associated cell types and biomarkers, the vessel type, anastomoses, portal systems, microvasculature, functional tissue units, links to 3D reference objects, vessel geometries (length, diameter), and mappings to anatomical structures the vessels supply or drain. Since the vasculature extends to all parts of the body, this database forms a core a part of the Human Reference Atlas (HRA), linking together organ-specific datasets.”

You possibly can explore a video of the envisioned VCCF.

The MC-IU team authored, “Specimen, Biological Structure, and Spatial Ontologies in Support of a Human Reference Atlas.”

The Human Reference Atlas is a multiscale, pan-tissue, three-dimensional digital atlas of the healthy human body. It provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions linked to existing ontologies. As of July 2023, the atlas comprises 30 organs with 4,340 named anatomical structures, 1,474 cell types, and three,842 characteristic biomarkers plus greater than 1,200 anatomically correct reference objects. All data is on the market free of charge on the HRA Portal.

“We’re excited to see the atlas grow in coverage and quality in the course of the HuBMAP Production phase,” Börner said.

Their work was amongst a set of nine scientific papers released within the Nature family of journals describing breakthroughs in high resolution, multiscale and multimodal mapping of the human body in two and three dimensions.

HuBMAP researchers have published greater than 270 scientific papers, presenting advances in software and experimental technologies, creating maps of healthy human tissues on the cellular level.