John Wirthlin Hickey

Preprint · March 5, 2026 Spatially resolved omics technologies reveal tissue organization at single-cell resolution but remain limited by the cost of the assays, incomplete spatial coverage, 2D-only imaging, and experimental artifacts. These factors motivate the need for in silico ... Full text Link to item Cite

Alterations of the composition and spatial organization of the microenvironment following non-dysplastic Barrett’s esophagus through progression to cancer

Preprint · 2025 Barrett’s esophagus (BE), a metaplastic condition that is the only known precursor for esophageal adenocarcinoma (EAC), is relatively common, but progression to cancer is infrequent. BE is inflamed but the contribution of the immune system to the carcinoge ... Full text Cite

Fluid-Squid: DIY Multiplexed Imaging of Cells and Tissues

Preprint · 2025 Recent advances in multiplexed single-cell characterization have revolutionized our insight into cell biology, but many available technologies remain limited by high costs or a lack of customizability. To address these challenges, we developed Fluid-Squid, ... Full text Cite

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage

Preprint · 2024 The Human BioMolecular Atlas Program (HuBMAP) aims to construct a reference 3D structural, cellular, and molecular atlas of the healthy adult human body. The HuBMAP Data Portal ( https://portal.hubmapconsortium.org ) serves experimental datasets and suppo ... Full text Cite

Integrating Multiplexed Imaging and Multiscale Modeling Identifies Tumor Phenotype Transformation as a Critical Component of Therapeutic T Cell Efficacy.

Preprint · December 8, 2023 Cancer progression is a complex process involving interactions that unfold across molecular, cellular, and tissue scales. These multiscale interactions have been difficult to measure and to simulate. Here we integrated CODEX multiplexed tissue imaging with ... Full text Link to item Cite

A spatial map of human macrophage niches reveals context-dependent macrophage functions in colon and breast cancer.

Preprint · January 10, 2023 Tumor-associated macrophages (TAMs) display heterogeneous phenotypes. Yet the exact tissue cues that shape macrophage functional diversity are incompletely understood. Here we discriminate, spatially resolve and reveal the function of five distinct macroph ... Full text Link to item Cite

Annotation of Spatially Resolved Single-cell Data with STELLAR

Preprint · 2021 Accurate cell type annotation from spatially resolved single cells is crucial to understand functional spatial biology that is the basis of tissue organization. However, current computational methods for annotating spatially resolved single-cell data are t ... Full text Cite