Deconvolution of cell types and states in spatial multiomics utilizing TACIT

Identifying cell types and states remains a time-consuming, error-prone challenge for spatial biology. While deep learning increasingly plays a role, it is difficult to generalize due to variability at the level of cells, neighborhoods, and niches in health and disease. To address this, we develop TACIT, an unsupervised algorithm for cell annotation using predefined signatures that operates without training data. TACIT uses unbiased thresholding to distinguish positive cells from background, focusing on relevant markers to identify ambiguous cells in multiomic assays. Using five datasets (5,000,000 cells; 51 cell types) from three niches (brain, intestine, gland), TACIT outperforms existing unsupervised methods in accuracy and scalability. Integrating TACIT-identified cell types reveals new phenotypes in two inflammatory gland diseases. Finally, using combined spatial transcriptomics and proteomics, we discover under- and overrepresented immune cell types and states in regions of interest, suggesting multimodality is essential for translating spatial biology to clinical applications.