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. 2019 Oct 21;21:428–435. doi: 10.1016/j.isci.2019.10.035

Figure 1.

Figure 1

Detecting ecDNA in DAPI-Stained Images

(A and B) Copy number amplification of EGFR in a glioblastoma cell line due to extrachromosomal DNA (ecDNA) formation.

(C and D) Copy number amplification of EGFR in a glioblastoma cell line with no ecDNA. Note that the sequence-based reconstruction does not distinguish between ecDNA (A) and homogeneously stained regions (C).

(E) Identification of ecDNA in DAPI-stained images of cells in metaphase. Although a FISH signal for EGFR is also shown, only the DAPI signals are used for calling ecDNA using the Watershed method, ecDetect, manually annotated ground truth, and ecSeg.

(F) A neural network architecture for semantic segmentation of the pixel into ecDNA, chromosomes, nuclei, and background, as described in Transparent Methods.