Computational protocol to assess the quality of sequencing-based microscopy networks using spatial coherence metrics

Sequencing-based microscopy captures spatial information as DNA barcode networks. Here, we present a protocol for measuring the spatial quality of such networks by estimating the intrinsic network dimension and Gram-matrix spectral scores from the network's shortest-path distances. We describe steps for installing the software, inputting the edge list of the network, and computing spatial coherence. We then detail procedures for transforming the network into an image. The pipeline handles fast strategies for large graphs and optionally reconstructs spatial layouts for visualization. For complete details on the use and execution of this protocol, please refer to Fernandez Bonet et al.¹.