Towards more accurate large-scale gene expression profiles

Laboratory of Neurodevelopmental Systems Biology (Dr. Gioele La Manno) and Bioimage Analysis and Computational Microscopy (Dr. Martin Weigert)

Spatial transcriptomics – a nascent field arising from the combination of cutting-edge microscopy with gene-specific in-situ labeling – can be used to generate large gene expression profiles of messenger RNA. This gives scientists an indication of the relative expression rates of different genes in the same environment. EPFL scientists at these two labs are are profiling the expression of up to two hundred genes simultaneously in the developing brain using Hybridization In Situ Sequencing (HybISS). This cutting-edge method relies on computational processing methods that are still immature, can be hard to use and error-prone.

In this project, Dr. La Manno and Dr. Weigert will develop a computational spatial transcriptomics framework – called Codebook-Aware ILP Detection and Tracking (CBAIDT) – that leverages modern computer vision techniques while using a novel tracking approach to substantially increase the accuracy and robustness of gene expression map generation.