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Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)
Charles Comiter, Eeshit Dhaval Vaishnav, Metamia Ciampricotti, Bo Li, Yiming Yang, Scott J. Rodig, Madison Turner, Kathleen L. Pfaff, Judit Jané-Valbuena, Michal Slyper, Julia Waldman, Sebastian Vigneau, Jingyi Wu, Timothy R. Blosser, Åsa Segerstolpe, Daniel Abravanel, Nikil Wagle, Xiaowei Zhuang, Charles M. Rudin, Johanna Klughammer, Orit Rozenblatt-Rosen, Koseki J. Kobayash-Kirschvink, Jian Shu, Aviv Regev
doi: https://doi.org/10.1101/2023.03.21.533680
Charles Comiter
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
2Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02142, USA
3Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
Eeshit Dhaval Vaishnav
5Sequome Inc., 10113 Berkshire Court, Cupertino, CA 95014, USA
Metamia Ciampricotti
6Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
Bo Li
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
13Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
14Department of Medicine, Harvard Medical School, Boston, MA, USA
17Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
Yiming Yang
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
13Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
17Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
Scott J. Rodig
7Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
Madison Turner
8Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
16Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
Kathleen L. Pfaff
8Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
Judit Jané-Valbuena
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Michal Slyper
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Julia Waldman
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Sebastian Vigneau
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Jingyi Wu
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Timothy R. Blosser
9Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
Åsa Segerstolpe
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Daniel Abravanel
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
15Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
Nikil Wagle
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
15Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
Xiaowei Zhuang
9Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
10Howard Hughes Medical Institute
Charles M. Rudin
6Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
Johanna Klughammer
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
11Gene Center and Department of Biochemistry, Ludwig-Maximilians-University, Munich, Germany
Orit Rozenblatt-Rosen
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
13Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
Koseki J. Kobayash-Kirschvink
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
12Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Jian Shu
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
3Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
Aviv Regev
1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
4Department of Biology, MIT, Cambridge, MA 02140, USA
10Howard Hughes Medical Institute
17Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
Article usage
Posted March 23, 2023.
Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)
Charles Comiter, Eeshit Dhaval Vaishnav, Metamia Ciampricotti, Bo Li, Yiming Yang, Scott J. Rodig, Madison Turner, Kathleen L. Pfaff, Judit Jané-Valbuena, Michal Slyper, Julia Waldman, Sebastian Vigneau, Jingyi Wu, Timothy R. Blosser, Åsa Segerstolpe, Daniel Abravanel, Nikil Wagle, Xiaowei Zhuang, Charles M. Rudin, Johanna Klughammer, Orit Rozenblatt-Rosen, Koseki J. Kobayash-Kirschvink, Jian Shu, Aviv Regev
bioRxiv 2023.03.21.533680; doi: https://doi.org/10.1101/2023.03.21.533680
Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)
Charles Comiter, Eeshit Dhaval Vaishnav, Metamia Ciampricotti, Bo Li, Yiming Yang, Scott J. Rodig, Madison Turner, Kathleen L. Pfaff, Judit Jané-Valbuena, Michal Slyper, Julia Waldman, Sebastian Vigneau, Jingyi Wu, Timothy R. Blosser, Åsa Segerstolpe, Daniel Abravanel, Nikil Wagle, Xiaowei Zhuang, Charles M. Rudin, Johanna Klughammer, Orit Rozenblatt-Rosen, Koseki J. Kobayash-Kirschvink, Jian Shu, Aviv Regev
bioRxiv 2023.03.21.533680; doi: https://doi.org/10.1101/2023.03.21.533680
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