The promise of SPATIAL BIOLOGY

Spatial biology provides greater insight into the complex biological interactions occurring within tissues. It integrates data on the physical arrangement of cells within tissues with information about the proteins and other biomolecules within these cells, including DNA modifications and RNA expression. This level of detail is not possible with conventional tissue microscopy (histology), which is widely used in research and diagnostic settings, or with dissociative single-cell sequencing. Instead, spatial biology requires a range of new technologies and computational methods based on machine learning. The development of tissue atlases also depends heavily on the expertise of practicing pathologists who use histology daily in the diagnosis and staging of disease.

The HTA team is committed to using the advances in high-plex tissue profiling that have been developed for research to improve disease diagnosis and management for patients. Ultimately, we aim to detect diseases, such as cancer, much earlier and enable its eradication; for more advanced diseases, we aim to develop new ways of matching individual patients to the therapies most likely to benefit them. Achieving this goal is facilitated by the fact that pathology in a clinical setting is undergoing a transition from conventional to fully digital methods. We expect the scientific advances made with tissue atlases to directly impact digital pathology practice.


The HTA is based on research performed in the Laboratory of Systems Pharmacology (LSP) at Harvard Medical School and the laboratories of its international collaborators. Much of our current work focuses on developing experimental and computational methods for using highly multiplexed tissue imaging, spatial transcriptomics, imaging mass spectrometry, and other technologies to transform spatial data into precise molecular and morphological information on cell types and states. Exemplary multi-dimensional datasets on melanoma and colorectal cancer have started to appear. We expect these to be consolidated into atlases later in 2022 and 2023.

HTA Atlases address different biological problems and types of disease, from tuberculosis to cancer, but they share a common set of technical, software, and educational resources available on this website. HTA resources are the work of molecular and systems biologists, clinicians, computer scientists, and software engineers, including graduate students and postdoctoral fellows. With very rare exceptions, the data and software generated by HTA projects are freely available under permissive Creative Commons or open-source software licenses.

The HTA is supported primarily by federal and foundation grants, but we welcome participation by commercial instrument and reagent companies interested in our work. We also welcome collaborations with biotechnology and pharmaceutical companies interested in applying spatial profiling to IND-enabling studies and clinical trials. Positions are available for students, postdocs, and research staff under the supervision of faculty with diverse skills and interests.

Read more about how the Harvard Tissue Atlas will move spatial biology forward by exploring our site. The best way to learn about the methods being used to build these atlases is via our webinar-based curriculum at the LEARN tab, by browsing our PUBLICATIONS, by reading about our DATA STANDARDS, or by accessing ATLAS DATASETS. You can view the full collection of data on the DATA EXPLORATIONS page. Visit the JOIN US page to learn more about available positions within the HTA, and collaboration opportunities.