Thomas, Z. | Search bioRxiv

bioRxiv2026

QuantCell: machine learning based cell annotation from qualitative and quantitative imaging profiles

Recent advances in spatial omics enable high-resolution, multiplexed imaging of RNA and protein expression, but cell annotation remains challenging, particularly in complex tissues with numerous markers or rare cell types. Here, we present QuantCell, a machine learning framework that leverages quantitative imaging data to improve annotation derived from qualitative profiles. QuantCell evaluates multiple models and applies a user-defined false discovery rate to ensure high-confidence annotation. Using PhenoCycler imaging of mouse bone marrow, QuantCell increased annotated cells from 33.1% to 90.2% at 5% FDR, achieving 96.5% accuracy. QuantCell supports diverse imaging platforms and robustly detects rare cell populations.

bioinformatics↗

bioRxiv2024

Cellular and molecular networks of intercellular signaling in bone marrow hematopoiesis

Hematopoietic stem and progenitor cells (HSPCs) rely on intercellular signaling to maintain and adjust their production of blood and immune cells. This process occurs in the semi-fluidic bone marrow, hosting dozens of cell types that constantly migrate and interact. To elucidate the dynamic network of cell-cell interaction and signaling transduction underlying hematopoiesis, we developed an algorithm to measure Cell-cell Spatial Interaction Probability (CellSIP) by integrating data on ligand and receptor expression, cell type abundance, and cellular spatial positioning. Using new and published mouse datasets, we validated CellSIP and uncovered signaling transductions indicating feedback mechanisms underlying hematopoiesis. Moreover, we identified significant correlations between signaling pathways across individual HSPCs at the same hematopoiesis stage. These pathway correlations illuminate the organization of cellular and signaling networks underlying hematopoiesis, revealing new regulators through their associations with established ones. The signaling quantification and correlation data are available through the Hematopoiesis Intercellular Signaling Explorer (HISE).

bioinformatics↗