JOBIM 2024 mini-symposium on spatial transcriptomics (Université Toulouse III - Paul Sabatier)

JOBIM 2024 mini-symposium (thursday 27th june 2024)
Unraveling Cellular Landscapes: Advances in Spatial Transcriptomics (Marie Coutelier and Stephen Whitmarsh)

Abstract:
In the ever-evolving landscape of omics approaches, spatial transcriptomics has emerged as a revolutionary tool. While single-cell transcriptomics analyses offer unprecedented insight into the granularity of cell-specific gene expression patterns, they lack the spatial context crucial for understanding the intricacies of specific biological questions, such as developmental processes, tumor invasion, or insights into biological structures or rare cell types obtained from histology and fluorescence. Integrating near single-cell granular transcriptomic profiling and histological characterization of tissues allows for a comprehensive exploration of cellular heterogeneity and a nuanced understanding of molecular landscapes. However, spatial transcriptomics data analysis poses unique challenges in bioinformatic analysis that also rely strongly on new developments in data management, statistics and image analysis. Bioinformatic analyses need to address issues of scalability, data normalization, batch effect correction (e.g., between slides). At the same time, robust image processing and analysis are required to deal with image artefacts and deploy cutting-edge deep learning techniques for cell-segmentation and phenotyping based on large dataset and AI models. The objective of this symposium is to share insights from various experiences in managing all aspects of spatial transcriptomics data, perspectives on how to effectively integrate them, and scientific illustrations of how spatial considerations can prove relevant to biology. Presentations of analyses methods and pipelines from two core facilities will be followed by illustrations withtalks on specific scientific topics.

Access slide deck