Image mass cytometry (IMC) enables high-dimensional spatial profiling by combining mass cytometry's analytical power with spatial distributions of cell phenotypes. Recent studies leverage large language models (LLMs) to extract cell states by translating gene or protein expression into biological context. However, existing single-cell LLMs face two major challenges: (1) Integration of spatial information: they struggle to generalize spatial coordinates and effectively encode spatial context as text, and (2) Treating each cell independently: they overlook cell-cell interactions, limiting their ability to capture biological relationships. To address these limitations, we propose Spatial2Sentence, a novel framework that integrates single-cell expression and spatial information into natural language using a multi-sentence approach. Spatial2Sentence constructs expression similarity and distance matrices, pairing spatially adjacent and expressionally similar cells as positive pairs while using distant and dissimilar cells as negatives. These multi-sentence representations enable LLMs to learn cellular interactions in both expression and spatial contexts. Equipped with multi-task learning, Spatial2Sentence outperforms existing single-cell LLMs on preprocessed IMC datasets, improving cell-type classification by 5.98% and clinical status prediction by 4.18% on the diabetes dataset while enhancing interpretability. The source code can be found here: https://github.com/UNITES-Lab/Spatial2Sentence.

Imaging mass cytometry (IMC) is a relatively new technique for imaging biological tissue at subcellular resolution. In recent years, learning-based segmentation methods have enabled precise quantification of cell type and morphology, but typically rely on large datasets with fully annotated ground truth (GT) labels. This paper explores the effects of imperfect labels on learning-based segmentation models and evaluates the generalisability of these models to different tissue types. Our results show that removing 50% of cell annotations from GT masks only reduces the dice similarity coefficient (DSC) score to 0.874 (from 0.889 achieved by a model trained on fully annotated GT masks). This implies that annotation time can in fact be reduced by at least half without detrimentally affecting performance. Furthermore, training our single-tissue model on imperfect labels only decreases DSC by 0.031 on an unseen tissue type compared to its multi-tissue counterpart, with negligible qualitative differences in segmentation. Additionally, bootstrapping the worst-performing model (with 5% of cell annotations) a total of ten times improves its original DSC score of 0.720 to 0.829. These findings imply that less time and work can be put into the process of producing comparable segmentation models; this includes eliminating the need for multiple IMC tissue types during training, whilst also providing the potential for models with very few labels to improve on themselves. Source code is available on GitHub: https://github.com/kimberley/ISBI2024.