U-CIE [/juː ‘siː/]: Color encoding of high-dimensional data

Abstract

U-CIE is a visualization method that encodes arbitrary high-dimensional data as colors using a combination of dimensionality reduction and the CIELAB color space to retain the original structure to the extent possible. We illustrate its broad applicability by visualizing single-cell data on a protein network and metagenomic data on a world map and on scatter plots. U-CIE is available as a web resource at https://u-cie.jensenlab.org/ and as an R package.

Spatial Transcriptomics Sequencing of Mouse Liver at 2µm Resolution Using a Novel Spatial DNA Chip

“…x 20 x 20 µm in diameter in adult mice 56,57 . In order to better visualize the spatial composition of the tissue, Cell2location 29 and U-CIE 58 were used to generate cell type spatial and cluster maps. Cell2location is a spatial deconvolution method used here to interpret gene expression data within liver tissue sections, as referenced from the Liver Cell Atlas.…”

“…U-CIE 58 is utilized for visualizing gene expression with UMAP 59 condensing high-dimensional data into three dimensions 60 . This maintains the spatial integrity of gene expression patterns.…”

“…For reference, a bin size of 5, corresponding to 10 x 10 µm regions, was used to generate the images in Figures 2 and 3. Hepatocytes are approximately 8,000 µm 3 or 20 x In order to better visualize the spatial composition of the tissue, Cell2location 29 and U-CIE 58 were used to generate cell type spatial and cluster maps (Fig. 4-5).…”

“…No reuse allowed without permission. In order to better visualize the spatial composition of the tissue, Cell2location 29 and U-CIE 58 were used to generate cell type spatial and cluster maps (Fig. 4-5).…”