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Φ Φ-Space: continuous phenotyping of single-cell multi-omics data
The prevalence of single-cell multi-omics datasets calls for automated cell type annotation methods that can characterize novel cell states. We developed Φ Φ-Space, a computational framework for the continuous phenotyping of single-cell multi-omics data. We adopt a highly versatile modeling strategy to characterize query cell identity in a low-dimensional phenotype space, defined by reference phenotypes. The phenotype space embedding enables various downstream analyses, including insightful visualizations, clustering, and cell type labeling. Φ Φ-Space is applicable to a wide range analytical tasks beyond cell type transfer. Its ability to model complex phenotypic variations will facilitate biological discoveries from different omics types.
Journal Article
Representation in Scientific Practice Revisited
Representation in Scientific Practice, published by the MIT Press in 1990, helped coalesce a long-standing interest in scientific visualization among historians, philosophers, and sociologists of science and remains a touchstone for current investigations in science and technology studies. This volume revisits the topic, taking into account both the changing conceptual landscape of STS and the emergence of new imaging technologies in scientific practice. It offers cutting-edge research on a broad array of fields that study information as well as short reflections on the evolution of the field by leading scholars, including some of the contributors to the 1990 volume. The essays consider the ways in which viewing experiences are crafted in the digital era; the embodied nature of work with digital technologies; the constitutive role of materials and technologies -- from chalkboards to brain scans -- in the production of new scientific knowledge; the metaphors and images mobilized by communities of practice; and the status and significance of scientific imagery in professional and popular culture.ContributorsMorana Alac, Michael Barany, Anne Beaulieu, Annamaria Carusi, Catelijne Coopmans, Lorraine Daston, Sarah de Rijcke, Joseph Dumit, Emma Frow, Yann Giraud, Aud Sissel Hoel, Martin Kemp, Bruno Latour, John Law, Michael Lynch, Donald MacKenzie, Cyrus Mody, Natasha Myers, Rachel Prentice, Arie Rip, Martin Ruivenkamp, Lucy Suchman, Janet Vertesi, Steve Woolgar
eBook
