Widely adopted Stochastic Neighbor Embedding (SNE) techniques like UMAP and tSNE have been used to make inferences in a range of scientific disciplines. Despite this, they are prone to producing visualizations that fragment underlying clusters ...Stochastic Neighbor Embedding (SNE) algorithms like UMAP and tSNE often produce visualizations that do not preserve the geometry of noisy and high dimensional data. In particular, they can spuriously separate connected components of the underlying data ...

We characterize the transcriptomic and morphological dynamics of enteric neurons emerging in the chick embryo gastrointestinal tract. Neurons elongating their projections express axon guidance gene programs that differ from those that guide ...The genetic programs directing nascent enteric nervous circuits and their unique architecture remain poorly characterized. To gain insight, we combined manipulations in the chick embryo model, whole gut three-dimensional (3D) imaging, and single-nucleus ...