Esteban Miglietta

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• Beth Cimini 🔬💻📊@bethcimini.bsky.social26-06-2026 14:50

  Levin, aided by local DL expert @gnodar.bsky.social, designed several variational autoencoders (VAEs), incorporating the transcripts, nuclear image, cell membrane image, or some combo. Figuring out the joint representations took some doing, but eventually we got some models that worked nicely (4/x)

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• Beth Cimini 🔬💻📊@bethcimini.bsky.social26-06-2026 14:50

  Because we're us, we were excited about image-based ST and including information from the images themselves, which spun the project into a new direction - what information could we add to spatial transcriptomics by the images themselves? (3/x)

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• Beth Cimini 🔬💻📊@bethcimini.bsky.social26-06-2026 14:50

  This project was initially conceived in computer-science-land by the fantastic co-first author Levin Moser, and then brought to biology-land by the fantastic co-first author Kamal Hamid. Levin had worked on Piximi, and wanted to work on graph neural networks for spatial transcriptomics (ST). (2/x)

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• Beth Cimini 🔬💻📊@bethcimini.bsky.social26-06-2026 14:50

  A week-overdue 🧵on the newest paper from the Cimini lab- do you ever do spatial transcriptomics? If you do, and you want free extra phenotypic info, step in to learn more about "Evaluating integrative strategies for incorporating phenotypic features in spatial transcriptomics". 🧪 (1/x)

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• Anne Carpenter@drannecarpenter.bsky.social11-05-2026 17:49

  Such an amazing opportunity! Your alumni go on to such nice jobs after.

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