Background: Advancements in genome editing technology and the globalization of life science research have highlighted the need for refined techniques in individualizing fertilized mouse eggs. Traditional embryo transfer surgery, which demands precise and objective success assessment, presents challenges for technical mastery and animal welfare. To address these issues, we developed a novel culture medium incorporating a dye library that enhances the visibility of ultrafine capillaries. Results: We screened 32 compounds based on their color properties and excluded those with clear cytotoxicity through colony formation inhibition tests. Five compounds demonstrated developmental outcomes comparable to those of the control group during embryo culture. Gene expression analysis revealed high correlation with control embryos, indicating no adverse developmental impact. No maternal toxicity was observed during and after embryo transfer using the dyed medium, which also produced normal offspring. A randomized survey confirmed improved visibility compared to conventional methods. Conclusion This study successfully identified nontoxic dyes that enhance the visibility of embryo transfer culture media, potentially improving precision and animal welfare in embryological research. Based on our findings, adding Brilliant Blue FCF or Fast Green FCF to the medium is recommended.