The Cancer Complexity Knowledge Portal presents datasets, publications, and other resources generated by NCI interdisciplinary research programs. Scientists across these programs integrate synergistic approaches, work on data, and develop tools in collaboration to address important questions in basic and translational cancer research. This repository encompasses not only CCBIR (our parent consortium) but all under NCI.
We produce custom software to run our custom microscopes. ASLM is an open source Python package for control of light-sheet microscopes. It allows for easily reconfigurable hardware setups and automated acquisition routines. - courtesy of Dean Lab
Publications
A general algorithm for consensus 3D cell segmentation from 2D segmented stacks
Felix Y Zhou, Clarence Yapp, Zhiguo Shang, Stephan Daetwyler, Zach Marin, Md Torikul Islam, Benjamin Nanes, Edward Jenkins, Gabriel M. Gihana, Bo-Jui Chang, Andrew Weems, Michael Dustin, Sean Morrison, Reto Fiolka, Kevin Dean, Andrew Jamieson, Peter K. Sorger, and Gaudenz Danuser. bioRxiv (2024) preprint.
Mechanically sheared axially swept light-sheet microscopy
Jinlong Lin, Dushyant Mehra, Zach Marin, Xiaoding Wang, Hazel M. Borges, Qionghua Shen, Seweryn Galecki, John Haug, and Kevin M. Dean. bioRxiv (2024) preprint.
Adaptive optics in an oblique plane microscope
Conor McFadden, Zach Marin, Bingying Chen, Stephan Daetwyler, Xiaoding Wang, Divya Rajendran, Kevin M. Dean, and Reto Fiolka. bioRxiv (2024) preprint.
Stephan Daetwyler, Hanieh Mazloom-Farsibaf, Felix Y. Zhou, Dagan Segal, Etai Sapoznik, Jill M. Westcott, Rolf A. Brekken, Gaudenz Danuser, and Reto Fiolka. bioRxiv (2024) preprint.
navigate: an open-source platform for smart light-sheet microscopy
Zach Marin, Xiaoding Wang, Dax W. Collison, Conor McFadden, Jinlong Lin, Hazel Borges, Bingying Chen, Dushyant Mehra, Qionghua Shen, Seweryn Galecki, Stephan Daetwyler, Reto Fiolka, and Kevin M. Dean. bioRxiv (2024) preprint.
Multiplexed 3D analysis of immune states and niches in human tissue
Clarence Yapp, Ajit J. Nirmal, Felix Zhou, Zoltan Maliga, Juliann B. Tefft, Paula Montero Llopis, George F. Murphy, Christine G. Lian, Gaudenz Danuser, Sandro Santagata, and Peter K. Sorger. bioRxiv (2024) preprint.
Seed becoming soil: a new paradigm of the Ewing sarcoma tumor microenvironment
Christopher Kuo and James F. Amatruda. Clin Cancer Res (2023) 29 (24): 5002-5004.
Mesoscopic oblique plane microscopy via light-sheet mirroring
Stephan Daetwyler, Bo-Jui Chang, Bingying Chen, Fabian F. Voight, Divya Rajendran, Felix Zhou, and Reto Fiolka. Optica (2023) Vol 10, Issue 11, pp: 1571-1581.
Projective oblique plane structured illumination microscopy
Bo-Jui Chang, Douglas Shephard, Reto Fiolka. npj Imaging (2023) 1, Article number 2.
Blebs promote cell survival by assembling oncogenic signaling hubs
Andrew D. Weems, Erik S. Welf, Meghan K. Driscoll, Felix Y. Zhou, Hanieh Mazloom-Farsibaf, Bo-Jui Chang, Vasanth S. Murali, Gabriel M. Gihana, Byron G. Weiss, Joseph Chi, Divya Rajendran, Kevin M. Dean, Reto Fiolka & Gaudenz Danuser. Nature (2023) 615: 517–525.
Resolution doubling in light-sheet microscopy via oblique plane structured illumination
Bingying Chen, Bo Jui Chang, Philippe Roudot, Felix Zhou, Etai Sapoznik, Madeleine Marlar-Pavey, James B. Hayes, Peter T. Brown, Chih Wei Zeng, Talley Lambert, Jonathan R. Friedman, Chun Li Zhang, Dylan T. Burnette, Douglas P. Shepherd, Kevin M. Dean, and Reto P. Fiolka. Nature Methods (2022) 19: 1419–1426.
Increasing the field-of-view in oblique plane microscopy via optical tiling
Bingying Chen, Bo-Jui Chang, Felix Y. Zhou, Stephan Daetwyler, Etai Sapoznik, Benjamin A. Nanes, Isabella Terrazas, Gabriel Muhire Gihana, Lizbeth Perez Castro, Isaac S. Chan, Maralice Conacci-Sorrell, Kevin M. Dean, Alfred Millett-Sikking, Andrew G. York, and Reto Fiolka. Biomedical optics express (2022) 13 (11): 5616–5627.
In vivo 3D profiling of site-specific human cancer cell morphotypes in zebrafish
Dagan Segal, Hanieh Mazloom-Farsibaf, Bo-Jui Chang, Philippe Roudot, Divya Rajendran, Stephan Daetwyler, Reto Fiolka, Mikako Warren, James F. Amatruda, and Gaudenz Danuser.
J Cell Biol (2022) 221 (11): e202109100.