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 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.

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.

Duncan LHMoyle MWShao LSengupta TIkegami RKumar AGuo MChristensen RSantella ABao ZShroff HMohler WColón-Ramos DA
J Vis Exp
2019 Jun 06

Vogt EJTokuhiro KGuo MDale RYang GShin SWMovilla MJShroff HDean J
Nat Commun
2019 May 22





Guo MChandris PGiannini JPTrexler AJFischer RChen JVishwasrao HDRey-Suarez IWu YWu XWaterman CMPatterson GHUpadhyaya ATaraska JWShroff H
Nat. Methods
2018 Jun


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
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2017 Dec 05

Zhu GMei LVishwasrao HDJacobson OWang ZLiu YYung BCFu XJin ANiu GWang QZhang FShroff HChen X
Nat Commun
2017 Nov 14

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


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2015 Jun 09


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


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Ingaramo MYork AGHoogendoorn EPostma MShroff HPatterson GH
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