Reto Fiolka

Scientists at Janelia work together in multidisciplinary teams to solve challenging biological problems that are difficult to address in other research settings.

Many lab spaces at Janelia feature modular designs and natural light.

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Occupying 689 wooded acres along the Potomac River, Janelia Farm provides a variety of services and facilities to support its diverse community of scientists and staff—inside and outside the lab.

A view of the Janelia Farm Research Campus at dusk.

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The Janelia Farm model frees scientists of constraints commonly found in other research environments, providing access to world-class resources and a talented support staff.

Graduate scholar John Tuthill prepares a Drosophila specimen for imaging.

Credit: James Kegley

In addition to our resident scientists and fellows, we offer visiting scientists, graduate, and undergraduate candidates a range of scientific programs.

Graduate scholar Arbora Resulaj (left) and her mentor, Janelia Fellow Dmitry Rinberg (right).

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Janelia Farm regularly hosts scientific meetings, ranging from workshops to intensive, specialized conferences. See what's coming up and visit the archive of past events.

Janelia's large auditorium seats 250 people.

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Janelia provides outstanding employment opportunities, at all levels.

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Many tools developed in Janelia Farm labs are made freely available to outside researchers, while others are taking shape through collaborations with industry, academia, and government.

A virtual arena for the study of flight in insects.

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Janelia’s sense of community comes from a core belief that people of diverse disciplines and backgrounds can accomplish great things when working with a common purpose.

Research specialist Trevor Wardill (left) and group leader Vivek Jayaraman (right).

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Cui Lab

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Deep tissue imaging is a challenge, since abberations and random scattering prevent the formation of a proper focus. However, a properly designed wavefront that exactly compensates all the distortions in the sample can yield an ideal focus, independent of the complexity of the scattering. This principle is known as optical phase conjugation (OPC). The question is how to find this wavefront or an approximation that can do the job.

The aim of my research is to develop microscopy techniques that can rapidly estimate complex wavefront corrections for 2 photon imaging in brain tissue.

In my previous work at Janelia, I have built a fast multi-purpose structured illumination microscope (SIM). SIM allows to double the diffraction limited resolution in all three dimensions and combined with fast cameras (sCMOS) and spatial light modulators, it can be applied to live cell imaging.

My research interests encompass microscopy, interferometry, holography, light scattering, ultrafast laser optics and liquid crystals.

Education:

2001-2006: Undergraduate studies in Mechanical Engineering, ETH Zurich,

Switzerland

2006-2009: PhD studies at the Chair of Nanotechnology, ETH Zurich, Switzerland

April 2010: Visitor at the synchrotron of the Paul Scherrer Institute in Switzerland

In my PhD thesis I worked on improving the resolution in quantitative phase microscopy and fluorescence microscopy. In 2010, I shortly worked on a project for quantitative hard X-ray tomography at the Paul Scherrer Institute in Switzerland.

Publications

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Janelia Publications

Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination.
Proceedings of the National Academy of Sciences of the United States of America 2012 R. Fiolka, L. Shao, H. E. Rego, M. W. Davidson, and M. G L. Gustafsson Proceedings of the National Academy of Sciences of the United States of America, 109:5311-5 (2012)
doi:10.1073/pnas.1119262109

Previous implementations of structured-illumination microscopy (SIM) were slow or designed for one-color excitation, sacrificing two unique and extremely beneficial aspects of light microscopy: live-cell imaging in multiple colors. This is especially unfortunate because, among the resolution-extending techniques, SIM is an attractive choice for live-cell imaging; it requires no special fluorophores or high light intensities to achieve twice diffraction-limited resolution in three dimensions. Furthermore, its wide-field nature makes it light-efficient and decouples the acquisition speed from the size of the lateral field of view, meaning that high frame rates over large volumes are possible. Here, we report a previously undescribed SIM setup that is fast enough to record 3D two-color datasets of living whole cells. Using rapidly programmable liquid crystal devices and a flexible 2D grid pattern algorithm to switch between excitation wavelengths quickly, we show volume rates as high as 4 s in one color and 8.5 s in two colors over tens of time points. To demonstrate the capabilities of our microscope, we image a variety of biological structures, including mitochondria, clathrin-coated vesicles, and the actin cytoskeleton, in either HeLa cells or cultured neurons.

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Prior Publications (6)

Simplified approach to diffraction tomography in optical microscopy.
Optics Express 2009 R. Fiolka, K. Wicker, R. Heintzmann, and A. Stemmer Optics Express, 17:12407-17 (2009)

We present a novel microscopy technique to measure the scattered wavefront emitted from an optically transparent microscopic object. The complex amplitude is decoded via phase stepping in a common-path interferometer, enabling high mechanical stability. We demonstrate theoretically and practically that the incoherent summation of multiple illumination directions into a single image increases the resolving power and facilitates image reconstruction in diffraction tomography. We propose a slice-by-slice object-scatter extraction algorithm entirely based in real space in combination with ordinary z-stepping. Thereby the computational complexity affiliated with tomographic methods is significantly reduced. Using the first order Born approximation for weakly scattering objects it is possible to obtain estimates of the scattering density from the exitwaves.

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Variable phase retarder made of a dielectric elastomer actuator.
Optics Letters 2009 M. Beck, R. Fiolka, and A. Stemmer Optics Letters, 34:803-5 (2009)

We present a polymeric optical phase retarder that is electrically tunable by a dielectric elastomer actuator. The soft material device affords a large tuning range (14pi at lambda=488 nm) combined with high accuracy in optical path length and low drift rate (8.3 nm/min). Furthermore, the phase retarder is not sensitive to polarization, introduces a wavefront distortion141 kW/cm2). We show the dynamics for periodic phase modulation and demonstrate a simple drive technique for fast phase stepping. The polymer-based device is inexpensive, easy to fabricate, and its design can be adapted to specific applications.

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Even illumination in total internal reflection fluorescence microscopy using laser light.
Microscopy Research and Technique 2008 R. Fiolka, Y. Belyaev, H. Ewers, and A. Stemmer Microscopy Research and Technique, 71:45-50 (2008)
doi:10.1002/jemt.20527

In modern fluorescence microscopy, lasers are a widely used source of light, both for imaging in total internal reflection and epi-illumination modes. In wide-field imaging, scattering of highly coherent laser light due to imperfections in the light path typically leads to nonuniform illumination of the specimen, compromising image analysis. We report the design and construction of an objective-launch total internal reflection fluorescence microscopy system with excellent evenness of specimen illumination achieved by azimuthal rotation of the incoming illuminating laser beam. The system allows quick and precise changes of the incidence angle of the laser beam and thus can also be used in an epifluorescence mode.

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Structured illumination in total internal reflection fluorescence microscopy using a spatial light modulator.
Optics Letters 2008 R. Fiolka, M. Beck, and A. Stemmer Optics Letters, 33:1629-31 (2008)

In wide-field fluorescence microscopy, illuminating the specimen with evanescent standing waves increases lateral resolution more than twofold. We report a versatile setup for standing-wave illumination in total internal reflection fluorescence microscopy. An adjustable diffraction grating written on a phase-only spatial light modulator controls the illumination field. Selecting appropriate diffraction orders and displaying a sheared (tilted) diffraction grating allows one to tune the penetration depth in very fine steps. The setup achieves 91 nm lateral resolution for green emission.

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Widefield fluorescence microscopy with extended resolution.
Histochemistry and Cell Biology 2008 A. Stemmer, M. Beck, and R. Fiolka Histochemistry and Cell Biology, 130:807-17 (2008)
doi:10.1007/s00418-008-0506-8

Widefield fluorescence microscopy is seeing dramatic improvements in resolution, reaching today 100 nm in all three dimensions. This gain in resolution is achieved by dispensing with uniform Köhler illumination. Instead, non-uniform excitation light patterns with sinusoidal intensity variations in one, two, or three dimensions are applied combined with powerful image reconstruction techniques. Taking advantage of non-linear fluorophore response to the excitation field, the resolution can be further improved down to several 10 nm. In this review article, we describe the image formation in the microscope and computational reconstruction of the high-resolution dataset when exciting the specimen with a harmonic light pattern conveniently generated by interfering laser beams forming standing waves. We will also discuss extensions to total internal reflection microscopy, non-linear microscopy, and three-dimensional imaging.

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Virtual slit scanning microscopy.
Histochemistry and Cell Biology 2007 R. Fiolka, A. Stemmer, and Y. Belyaev Histochemistry and Cell Biology, 128:499-505 (2007)
doi:10.1007/s00418-007-0342-2

We present a novel slit scanning confocal microscope with a CCD camera image sensor and a virtual slit aperture for descanning that can be adjusted during post-processing. A very efficient data structure and mathematical criteria for aligning the virtual aperture guarantee the ease of use. We further introduce a method to reduce the anisotropic lateral resolution of slit scanning microscopes. System performance is evaluated against a spinning disk confocal microscope on identical specimens. The virtual slit scanning microscope works as the spinning disk type and outperforms on thick specimens.