A novel channel invariant architecture for the segmentation of cells and nuclei in multiplexed images using InstanSeg

Abstract The quantitative analysis of bioimaging data increasingly depends on the accurate segmentation of cells and nuclei, a significant challenge for the analysis of high-plex imaging data. Current deep learning-based approaches to segment cells in multiplexed images require reducing the input to a small and fixed number of input channels, discarding imaging information in the process. We present Channel Net, a novel deep learning architecture for generating three-channel representations of multiplexed images irrespective of the number or ordering of imaged biomarkers. When combined with InstanSeg, ChannelNet sets a new benchmark for the segmentation of cells and nuclei on public multiplexed imaging datasets. We provide an open implementation of our method and integrate it in open source software. Our code and models are available on https://github.com/instanseg/instanseg .