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Introduction

In our preprint, we used an E13 mouse head sample to benchmark the precision, sensitivity, and spatial resolution of RNA capture due to the high availability of published gene expression data (RNA-seq, in-situ hybridization, ST, etc.) and the possibility to maintain RNA quality by controlling sample handling and timing.

In the following sections, we explore how to reproduce the preprocessing steps for this data, and provide an example notebook for exploratory data analysis of the data using standard single cell tools.