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)

Thi is a picutre of fluorescently labeled microtubules fixed in a cell. The microtubules are less than 150 nm.

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)

This is a picture of GFP-histones in a live nematode embryo.  It shows both a top and bottom view of the embryo.

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

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.

This is an image of the laser configuration in the Section for High Resolution Optical Imaging

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.
Zhu GLynn GMJacobson OChen KLiu YZhang HMa YZhang FTian RNi QCheng SWang ZLu NYung BCWang ZLang LFu XJin AWeiss IDVishwasrao HNiu GShroff HKlinman DMSeder RAChen X
Nat Commun
2017 Dec 05

Wu YKumar ASmith CArdiel EChandris PChristensen RRey-Suarez IGuo MVishwasrao HDChen JTang JUpadhyaya ALa Riviere PJShroff H
Nat Commun
2017 Nov 13

Kieffer-Kwon KRNimura KRao SSPXu JJung SPekowska ADose MStevens EMathe EDong PHuang SCRicci MABaranello LZheng YTomassoni Ardori FResch WStavreva DNelson SMcAndrew MCasellas AFinn EGregory CSt Hilaire BGJohnson SMDubois WCosma MPBatchelor ELevens DPhair RDMisteli TTessarollo LHager GLakadamyali MLiu ZFloer MShroff HAiden ELCasellas R
Mol. Cell
2017 Aug 17

Zheng WWu YWinter PFischer RNogare DDHong AMcCormick CChristensen RDempsey WPArnold DBZimmerberg JChitnis ASellers JWaterman CShroff H
Nat. Methods
2017 Sep

Ardiel ELKumar AMarbach JChristensen RGupta RDuncan WDaniels JSStuurman NColón-Ramos DShroff H
Biophys. J.
2017 May 09

Ogawa MTomita YNakamura YLee MJLee STomita SNagaya TSato KYamauchi TIwai HKumar AHaystead TShroff HChoyke PLTrepel JBKobayashi H
2017 Feb 07

Lakdawala SSWu YWawrzusin PKabat JBroadbent AJLamirande EWFodor EAltan-Bonnet NShroff HSubbarao K
PLoS Pathog.
2016 Dec

Wu YChandris PWinter PWKim EYJaumouillé VKumar AGuo MLeung JMSmith CRey-Suarez ILiu HWaterman CMRamamurthi KSLa Riviere PJShroff H
2016 Aug 20

Kumar AChristensen RGuo MChandris PDuncan WWu YSantella AMoyle MWinter PWColón-Ramos DBao ZShroff H
Biol. Bull.
2016 Aug

Dundon SEChang SSKumar AOcchipinti PShroff HRoper MGladfelter AS
Mol. Biol. Cell
2016 Jul 01

Christensen RPBokinsky ASantella AWu YMarquina-Solis JGuo MKovacevic IKumar AWinter PWTashakkori NMcCreedy ELiu HMcAuliffe MMohler WColón-Ramos DABao ZShroff H
2015 Dec 03

Trcek TGrosch MYork AShroff HLionnet TLehmann R
Nat Commun
2015 Aug 05

Curd ACleasby AMakowska KYork AShroff HPeckham M
2015 Oct 15

Santella ACatena RKovacevic IShah PYu ZMarquina-Solis JKumar AWu YSchaff JColón-Ramos DShroff HMohler WABao Z
BMC Bioinformatics
2015 Jun 09

Winter PWYork AGNogare DDIngaramo MChristensen RChitnis APatterson GHShroff H
2014 Sep 20

Kumar AWu YChristensen RChandris PGandler WMcCreedy EBokinsky AColón-Ramos DABao ZMcAuliffe MRondeau GShroff H
Nat Protoc
2014 Nov

Eswaramoorthy PWinter PWWawrzusin PYork AGShroff HRamamurthi KS
PLoS Genet.
2014 Aug

Wu YWawrzusin PSenseney JFischer RSChristensen RSantella AYork AGWinter PWWaterman CMBao ZColón-Ramos DAMcAuliffe MShroff H
Nat. Biotechnol.
2013 Nov

York AGChandris PNogare DDHead JWawrzusin PFischer RSChitnis AShroff H
Nat. Methods
2013 Nov

York AGParekh SHDalle Nogare DFischer RSTemprine KMione MChitnis ABCombs CAShroff H
Nat. Methods
2012 May 13

Fischer RSWu YKanchanawong PShroff HWaterman CM
Trends Cell Biol.
2011 Dec

Wu YGhitani AChristensen RSantella ADu ZRondeau GBao ZColón-Ramos DShroff H
Proc. Natl. Acad. Sci. U.S.A.
2011 Oct 25