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Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets

Figure 3

Light contamination in in-situ hybridization luminescence data.

Panel A shows the raw fluorescent microscopy capture of the gene Ascl's expression for one layer in the brain of Platynereis. Panel B shows the light intensity measured along the red line in panel A. Panel C shows the expected light intensity profile without light contamination. Because of the small scale of study, voxels surrounded by other voxels expressing a particular gene will have a higher intensity values because of nearby light contamination. Panel D shows errors introduced by the voxel cell model. Path a shows how regions with highly expressed genes can introduce errors through light contamination. Path b shows how some voxels may appear artificially void of expression because of the uneven distribution of transcripts inside the cytoplasm especially for large cells.

Figure 3