Section on High Resolution Optical Imaging (HROI)
The Section on High Resolution Optical Imaging (HROI) develops novel technologies for studying biological processes at unprecedented speed and resolution. Research includes improving the performance of 3D optical imaging microscopes, particularly with respect to resolution and depth (e.g. multifocal structured illumination microscopy, MSIM) and speed and phototoxicity (e.g. inverted selective plane illumination microscopy, iSPIM). We collaborate closely with intra- and extramural researchers (both academic and commercial) to ensure that our microscopes are both easily and widely used. Along with researchers at Sloan-Kettering (Zhirong Bao) and Yale University (Daniel Colon-Ramos), we are using one of our technologies (iSPIM) to construct the first atlas of 4D neurodevelopment in an animal.
- Furthering development of superresolution optical imaging techniques, particularly 3-D structured illumination microscopy(SIM)
Structured illumination microscopy techniques use patterned excitation light and post-processing to double the resolution of a conventional microscope. Unlike other super-resolution techniques, they provide resolution enhancement at a relatively low illumination dose, thus enabling high resolution imaging over tens – hundreds of volumes. Previous implementations of SIM were limited to samples of < 10 um, but we have developed a multifocal version (MSIM)1 that permits resolution-doubling at depths exceeding 50 um. Most recently, we have extended the speed of MSIM 100x, facilitating super-resolution imaging at hundreds of frames per second.1
- Improving the usability and resolution of selective plane illumination microscopy (SPIM)
Selective plane illumination microscopy techniques combine a perpendicular excitation/detection geometry with light-sheet excitation, drastically reducing photobleaching and damage while providing higher signal-to-noise ratio and acquisition rates than confocal microscopy. Nevertheless, widespread adoption of SPIM has been slow because (1) the geometry is cumbersome, usually requiring special sample preparation; (2) Axial resolution is usually 3x worse than confocal microscopy. To address the usability issue, we have developed inverted selective plane illumination microscopy (iSPIM)2, a module that can be mounted onto an epifluorescence microscope, thus allowing conventional sample mounting on glass coverslips while retaining the advantages of SPIM. iSPIM offers an approximate 30-fold improvement over spinning disk confocal microscopy in terms of acquisition speed, photobleaching, and total acquisition length when imaging live samples. We have recently developed a variation of iSPIM that enables isotropic imaging with 330 nm spatial resolution (~4x better axial resolution than previous implementations) and temporal resolution down to 3 ms.
- Construction of a 4-dimensional digital atlas of neuronal development in C. Elegans in collaboration with researchers at Yale University and Memorial Sloan-Kettering Cancer Center
Along with extramural neuroscientists, scientists, and developmental biologists, we are using iSPIM to follow all neurons in the developing nematode embryo. We intend to create the first digital atlas of neurodevelopment. Further information on this project may be obtained at www.wormguides.org
1. Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy. York AG, Parekh SH, Dalle Nogare D, Fischer RS, Temprine K, Mione M, Chitnis AB, Combs CA, Shroff H. Nat Methods. 2012 May 13;9(7):749-54. doi: 10.1038/nmeth.2025.
2. Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans. Wu Y, Ghitani A, Christensen R, Santella A, Du Z, Rondeau G, Bao Z, Colón-Ramos D, Shroff H. Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17708-13. doi: 10.1073/pnas.1108494108. Epub 2011 Oct 17.
The Shroff lab currently houses:
- A photoactivated localization microscope (PALM) for 3D super-resolution (25-50 nm in XY and 100 nm in z).
- A multifocal structured illumination microscope with 150 nm lateral, 350 nm axial resolution and a time resolution of 5 ms.
- Two selective plane illumination microscopes, with isotropic spatial resolution down to 330 nm and temporal resolution of 5 ms.
- Research Fellow
- Postdoc Fellow (Irta)
- Pre-Doctoral Irta (Graduate Student)
- Postdoc Fellow (Visiting Fellow)
- Post Baccalaureate
- Pre-Doctoral Irta (Graduate Student)
- Senior Investigator
- Staff Scientist
- Albumin/vaccine nanocomplexes that assemble in vivo for combination cancer immunotherapy. Zhu G, Lynn GM, Jacobson O, Chen K, Liu Y, Zhang H, Ma Y, Zhang F, Tian R, Ni Q, Cheng S, Wang Z, Lu N, Yung BC, Wang Z, Lang L, Fu X, Jin A, Weiss ID, Vishwasrao H, Niu G, Shroff H, Klinman DM, Seder RA, Chen X. Nat Commun. 2017 Dec 5.
- Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy. Wu Y, Kumar A, Smith C, Ardiel E, Chandris P, Christensen R, Rey-Suarez I, Guo M, Vishwasrao HD, Chen J, Tang J, Upadhyaya A, La Riviere PJ, Shroff H. Nat Commun. 2017 Nov 13.
- Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Kieffer-Kwon KR, Nimura K, Rao SSP, Xu J, Jung S, Pekowska A, Dose M, Stevens E, Mathe E, Dong P, Huang SC, Ricci MA, Baranello L, Zheng Y, Tomassoni Ardori F, Resch W, Stavreva D, Nelson S, McAndrew M, Casellas A, Finn E, Gregory C, St Hilaire BG, Johnson SM, Dubois W, Cosma MP, Batchelor E, Levens D, Phair RD, Misteli T, Tessarollo L, Hager G, Lakadamyali M, Liu Z, Floer M, Shroff H, Aiden EL, Casellas R. Mol Cell. 2017 Aug 17.
- Adaptive optics improves multiphoton super-resolution imaging. Zheng W, Wu Y, Winter P, Fischer R, Nogare DD, Hong A, McCormick C, Christensen R, Dempsey WP, Arnold DB, Zimmerberg J, Chitnis A, Sellers J, Waterman C, Shroff H. Nat Methods. 2017 Sep.
- Visualizing Calcium Flux in Freely Moving Nematode Embryos. Ardiel EL, Kumar A, Marbach J, Christensen R, Gupta R, Duncan W, Daniels JS, Stuurman N, Colón-Ramos D, Shroff H. Biophys J. 2017 May 9.
- Immunogenic cancer cell death selectively induced by near infrared photoimmunotherapy initiates host tumor immunity. Ogawa M, Tomita Y, Nakamura Y, Lee MJ, Lee S, Tomita S, Nagaya T, Sato K, Yamauchi T, Iwai H, Kumar A, Haystead T, Shroff H, Choyke PL, Trepel JB, Kobayashi H. Oncotarget. 2017 Feb 7.
- Correction: Influenza A Virus Assembly Intermediates Fuse in the Cytoplasm. Lakdawala SS, Wu Y, Wawrzusin P, Kabat J, Broadbent AJ, Lamirande EW, Fodor E, Altan-Bonnet N, Shroff H, Subbarao K. PLoS Pathog. 2016 Dec.
- Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy. Wu Y, Chandris P, Winter PW, Kim EY, Jaumouillé V, Kumar A, Guo M, Leung JM, Smith C, Rey-Suarez I, Liu H, Waterman CM, Ramamurthi KS, La Riviere PJ, Shroff H. Optica. 2016 Aug 20.
- Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM). Kumar A, Christensen R, Guo M, Chandris P, Duncan W, Wu Y, Santella A, Moyle M, Winter PW, Colón-Ramos D, Bao Z, Shroff H. Biol Bull. 2016 Aug.
- Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium. Dundon SE, Chang SS, Kumar A, Occhipinti P, Shroff H, Roper M, Gladfelter AS. Mol Biol Cell. 2016 Jul 1.
- Untwisting the Caenorhabditis elegans embryo. Christensen RP, Bokinsky A, Santella A, Wu Y, Marquina-Solis J, Guo M, Kovacevic I, Kumar A, Winter PW, Tashakkori N, McCreedy E, Liu H, McAuliffe M, Mohler W, Colón-Ramos DA, Bao Z, Shroff H. Elife. 2015 Dec 3.
- Drosophila germ granules are structured and contain homotypic mRNA clusters. Trcek T, Grosch M, York A, Shroff H, Lionnet T, Lehmann R. Nat Commun. 2015 Aug 5.
- Construction of an instant structured illumination microscope. Curd A, Cleasby A, Makowska K, York A, Shroff H, Peckham M. Methods. 2015 Oct 15.
- WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration. Santella A, Catena R, Kovacevic I, Shah P, Yu Z, Marquina-Solis J, Kumar A, Wu Y, Schaff J, Colón-Ramos D, Shroff H, Mohler WA, Bao Z. BMC Bioinformatics. 2015 Jun 9.
- Incoherent structured illumination improves optical sectioning and contrast in multiphoton super-resolution microscopy. Winter PW, Chandris P, Fischer RS, Wu Y, Waterman CM, Shroff H. Opt Express. 2015 Feb 23.
- Two-photon instant structured illumination microscopy improves the depth penetration of super-resolution imaging in thick scattering samples. Winter PW, York AG, Nogare DD, Ingaramo M, Christensen R, Chitnis A, Patterson GH, Shroff H. Optica. 2014 Sep 20.
- Dual-view plane illumination microscopy for rapid and spatially isotropic imaging. Kumar A, Wu Y, Christensen R, Chandris P, Gandler W, McCreedy E, Bokinsky A, Colón-Ramos DA, Bao Z, McAuliffe M, Rondeau G, Shroff H. Nat Protoc. 2014 Nov.
- Asymmetric division and differential gene expression during a bacterial developmental program requires DivIVA. Eswaramoorthy P, Winter PW, Wawrzusin P, York AG, Shroff H, Ramamurthi KS. PLoS Genet. 2014 Aug.
- Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Wu Y, Wawrzusin P, Senseney J, Fischer RS, Christensen R, Santella A, York AG, Winter PW, Waterman CM, Bao Z, Colón-Ramos DA, McAuliffe M, Shroff H. Nat Biotechnol. 2013 Nov.
- Instant super-resolution imaging in live cells and embryos via analog image processing. York AG, Chandris P, Nogare DD, Head J, Wawrzusin P, Fischer RS, Chitnis A, Shroff H. Nat Methods. 2013 Nov.
- Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy. York AG, Parekh SH, Dalle Nogare D, Fischer RS, Temprine K, Mione M, Chitnis AB, Combs CA, Shroff H. Nat Methods. 2012 May 13.
- Microscopy in 3D: a biologist's toolbox. Fischer RS, Wu Y, Kanchanawong P, Shroff H, Waterman CM. Trends Cell Biol. 2011 Dec.
- Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans. Wu Y, Ghitani A, Christensen R, Santella A, Du Z, Rondeau G, Bao Z, Colón-Ramos D, Shroff H. Proc Natl Acad Sci U S A. 2011 Oct 25.
- Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes. York AG, Ghitani A, Vaziri A, Davidson MW, Shroff H. Nat Methods. 2011 Apr.