Extended Data Fig. 3: OmiCLIP’s robustness for image quality and sequencing depth.

a, Example image with low-quality region marked in red line and simulated low-quality image by adding Gaussian noise. b, Cosine similarity of paired transcriptomic and image embeddings using OmiCLIP (original image and simulated low-quality image), PLIP (original image), and OpenAI CLIP (original image). In the box plots, the middle line represents the median, the box boundaries indicate the interquartile range, and the whiskers extend to data points within 1.5× the interquartile range. Sample sizes are 10 for each simulated condition. c, Cosine similarity of the paired image with transcriptomic embeddings using OmiCLIP (original transcriptomes and down sampled transcriptome from high sequencing depth to middle sequencing depth, middle sequencing depth to low sequencing depth, and high sequencing depth to low sequencing depth, respectively), PLIP (original transcriptome), and OpenAI CLIP (original transcriptome). In the box plots, the middle line represents the median, the box boundaries indicate the interquartile range, and the whiskers extend to data points within 1.5× the interquartile range, n = 500.