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07/13/15 | Continuous volumetric imaging via an optical phase-locked ultrasound lens.
Kong L, Tang J, Little JP, Yu Y, Lämmermann T, Lin CP, Germain RN, Cui M
Nature Methods. 2015-Jul 13;12(8):759-62. doi: 10.1038/nmeth.3476

In vivo imaging at high spatiotemporal resolution is key to the understanding of complex biological systems. We integrated an optical phase-locked ultrasound lens into a two-photon fluorescence microscope and achieved microsecond-scale axial scanning, thus enabling volumetric imaging at tens of hertz. We applied this system to multicolor volumetric imaging of processes sensitive to motion artifacts, including calcium dynamics in behaving mouse brain and transient morphology changes and trafficking of immune cells.

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07/13/15 | High-resolution in vivo imaging of mouse brain through the intact skull.
Park JH, Sun W, Cui M
Proceedings of the National Academy of Sciences of the United States of America. 2015-Jul 13;112(30):9236-41. doi: 10.1073/pnas.1505939112

Multiphoton microscopy is the current method of choice for in vivo deep-tissue imaging. The long laser wavelength suffers less scattering, and the 3D-confined excitation permits the use of scattered signal light. However, the imaging depth is still limited because of the complex refractive index distribution of biological tissue, which scrambles the incident light and destroys the optical focus needed for high resolution imaging. Here, we demonstrate a wavefront-shaping scheme that allows clear imaging through extremely turbid biological tissue, such as the skull, over an extended corrected field of view (FOV). The complex wavefront correction is obtained and directly conjugated to the turbid layer in a noninvasive manner. Using this technique, we demonstrate in vivo submicron-resolution imaging of neural dendrites and microglia dynamics through the intact skulls of adult mice. This is the first observation, to our knowledge, of dynamic morphological changes of microglia through the intact skull, allowing truly noninvasive studies of microglial immune activities free from external perturbations.

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03/23/15 | Numerical study of multi-conjugate large area wavefront correction for deep tissue microscopy.
Wu TW, Cui M
Optics Express. 2015 Mar 23;23(6):7463-70. doi: 10.1364/OE.23.007463

Wavefront distortion fundamentally limits the achievable imaging depth and quality in thick tissue. Wavefront correction can help restore the diffraction limited focus albeit with a small field of view (FOV), which limits its imaging applications. In this work, we numerically investigate whether the multi-conjugate configuration, originally developed for astronomical adaptive optics, may increase the correction FOV in random turbid media. The results show that the multi-conjugate configuration can significantly improve the correction area compared to the widely adopted pupil plane correction. Even in the simple case of single-conjugation, it still outperforms the pupil plane correction. This study provides a guideline for designing the optimal wavefront correction system in deep tissue imaging.

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03/09/15 | In vivo neuroimaging through the highly scattering tissue via iterative multi-photon adaptive compensation technique.
Kong L, Cui M
Optics Express. 2015 Mar 9;23(5):6145-50. doi: 10.1364/OE.23.006145

For in vivo deep tissue imaging, high order wavefront measurement and correction is needed for handling the severe wavefront distortion. Towards such a goal, we have developed the iterative multi-photon adaptive compensation technique (IMPACT). In this work, we explore using IMPACT to perform calcium imaging of neocortex through the intact skull of adult mice, and to image through the highly scattering white matter on the hippocampus surface.

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12/22/14 | In vivo fluorescence microscopy via iterative multi-photon adaptive compensation technique.
Kong L, Cui M
Optical Express. 2014 Oct 6;22(20):23786-94. doi: 10.1364/OE.22.023786

Iterative multi-photon adaptive compensation technique (IMPACT) has been developed for wavefront measurement and compensation in highly scattering tissues. Our previous report was largely based on the measurements of fixed tissue. Here we demonstrate the advantages of IMPACT for in vivo imaging and report the latest results. In particular, we show that IMPACT can be used for functional imaging of awake mice, and greatly improve the in vivo neuron imaging in mouse cortex at large depth (~660 microns). Moreover, IMPACT enables neuron imaging through the intact skull of adult mice, which promises noninvasive optical measurements in mouse brain.

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07/29/14 | A self-adaptive method for creating high efficiency communication channels through random scattering media.
Hao X, Martin-Rouault L, Cui M
Science Reports. 2014 Jul 29;4:5874. doi: 10.1038/srep05874

Controlling the propagation of electromagnetic waves is important to a broad range of applications. Recent advances in controlling wave propagation in random scattering media have enabled optical focusing and imaging inside random scattering media. In this work, we propose and demonstrate a new method to deliver optical power more efficiently through scattering media. Drastically different from the random matrix characterization approach, our method can rapidly establish high efficiency communication channels using just a few measurements, regardless of the number of optical modes, and provides a practical and robust solution to boost the signal levels in optical or short wave communications. We experimentally demonstrated analog and digital signal transmission through highly scattering media with greatly improved performance. Besides scattering, our method can also reduce the loss of signal due to absorption. Experimentally, we observed that our method forced light to go around absorbers, leading to even higher signal improvement than in the case of purely scattering media. Interestingly, the resulting signal improvement is highly directional, which provides a new means against eavesdropping.

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09/01/13 | Three-dimensional live microscopy beyond the diffraction limit.
Fiolka R
Journal of Optics. 2013 Sep;15:094002. doi: 10.1088/2040-8978/15/9/094002

In fluorescence microscopy it has become possible to fundamentally overcome the diffraction limited resolution in all three spatial dimensions. However, to have the most impact in biological sciences, new optical microscopy techniques need to be compatible with live cell imaging: image acquisition has to be fast enough to capture cellular dynamics at the new resolution limit while light exposure needs to be minimized to prevent photo-toxic effects. With increasing spatial resolution, these requirements become more difficult to meet, even more so when volumetric imaging is performed. In this review, techniques that have been successfully applied to three-dimensional, super-resolution live microscopy are presented and their relative strengths and weaknesses are discussed.

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01/01/13 | High speed phase distortion measurement and compensation for focusing in space and time.
Fiolka R, Cui M
Proceedings of SPIE. 2013;8589:85890V. doi: 10.1117/12.2001121

Random scattering and aberrations severely limit the imaging depth in optical microscopy. We introduce a rapid, parallel wavefront compensation technique that efficiently compensates even highly complex phase distortions. Using coherence gated backscattered light as a feedback signal, we focus light deep inside highly scattering brain tissue. We demonstrate that the same wavefront optimization technique can also be used to compensate spectral phase distortions in ultrashort laser pulses using nonlinear iterative feedback. We can restore transform limited pulse durations at any selected target location and compensate for dispersion that has occurred in the optical train and within the sample.

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10/22/12 | Parallel wavefront measurements in ultrasound pulse guided digital phase conjugation.
Fiolka R, Si K, Cui M
Optics Express. 2012 Oct 22;20(22):24827-34. doi:

Ultrasound pulse guided digital phase conjugation has emerged to realize fluorescence imaging inside random scattering media. Its major limitation is the slow imaging speed, as a new wavefront needs to be measured for each voxel. Therefore 3D or even 2D imaging can be time consuming. For practical applications on biological systems, we need to accelerate the imaging process by orders of magnitude. Here we propose and experimentally demonstrate a parallel wavefront measurement scheme towards such a goal. Multiple focused ultrasound pulses of different carrier frequencies can be simultaneously launched inside a scattering medium. Heterodyne interferometry is used to measure all of the wavefronts originating from every sound focus in parallel. We use these wavefronts in sequence to rapidly excite fluorescence at all the voxels defined by the focused ultrasound pulses. In this report, we employed a commercially available sound transducer to generate two sound foci in parallel, doubled the wavefront measurement speed, and reduced the mechanical scanning steps of the sound transducer to half.

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10/01/12 | Breaking the spatial resolution barrier via iterative sound-light interaction in deep tissue microscopy.
Si K, Fiolka R, Cui M
Scientific Reports. 2012 Oct;2:748. doi: doi:10.1038/srep00748

Optical microscopy has so far been restricted to superficial layers, leaving many important biological questions unanswered. Random scattering causes the ballistic focus, which is conventionally used for image formation, to decay exponentially with depth. Optical imaging beyond the ballistic regime has been demonstrated by hybrid techniques that combine light with the deeper penetration capability of sound waves. Deep inside highly scattering media, the sound focus dimensions restrict the imaging resolutions. Here we show that by iteratively focusing light into an ultrasound focus via phase conjugation, we can fundamentally overcome this resolution barrier in deep tissues and at the same time increase the focus to background ratio. We demonstrate fluorescence microscopy beyond the ballistic regime of light with a threefold improved resolution and a fivefold increase in contrast. This development opens up practical high resolution fluorescence imaging in deep tissues.

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08/01/12 | Fluorescence imaging beyond the ballistic regime by ultrasound-pulse-guided digital phase conjugation.
Si K, Fiolka R, Cui M
Nature Photonics. 2012 Aug;6:657. doi: doi:10.1038/nphoton.2012.205

Fluorescence imaging has revolutionized biomedical research over the past three decades. Its high molecular specificity and unrivalled single-molecule-level sensitivity have enabled breakthroughs in a number of research fields. For in vivo applications its major limitation is its superficial imaging depth, a result of random scattering in biological tissues causing exponential attenuation of the ballistic component of a light wave. Here, we present fluorescence imaging beyond the ballistic regime by combining single-cycle pulsed ultrasound modulation and digital optical phase conjugation. We demonstrate a near-isotropic three-dimensional localized sound–light interaction zone. With the exceptionally high optical gain provided by the digital optical phase conjugation system, we can deliver sufficient optical power to a focus inside highly scattering media for not only fluorescence imaging but also a variety of linear and nonlinear spectroscopy measurements. This technology paves the way for many important applications in both fundamental biology research and clinical studies.

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05/29/12 | Superpenetration optical microscopy by iterative multiphoton adaptive compensation technique.
Tang J, Germain RN, Cui M
Proceedings of the National Academy of Sciences of the United States of America. 2012 May 29;109(22):8434-9. doi: 10.1073/pnas.1119590109

Biological tissues are rarely transparent, presenting major challenges for deep tissue optical microscopy. The achievable imaging depth is fundamentally limited by wavefront distortions caused by aberration and random scattering. Here, we report an iterative wavefront compensation technique that takes advantage of the nonlinearity of multiphoton signals to determine and compensate for these distortions and to focus light inside deep tissues. Different from conventional adaptive optics methods, this technique can rapidly measure highly complicated wavefront distortions encountered in deep tissue imaging and provide compensations for not only aberration but random scattering. The technique is tested with a variety of highly heterogeneous biological samples including mouse brain tissue, skull, and lymph nodes. We show that high quality three-dimensional imaging can be realized at depths beyond the reach of conventional multiphoton microscopy and adaptive optics methods, albeit over restricted distances for a given correction. Moreover, the required laser excitation power can be greatly reduced in deep tissues, deviating from the power requirement of ballistic light excitation and thus significantly reducing photo damage to the biological tissue.

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04/03/12 | Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination.
Fiolka R, Shao L, Rego H, Davidson MW, Gustafsson MGL
Proceedings of the National Academy of Sciences of the United States of America. 2012 Apr 3;109(14):5311-5. 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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01/01/12 | Complex wavefront corrections for deep tissue focusing using low coherence backscattered light.
Fiolka R, Si K, Cui M
Optics Express. 2012;20(15):16532-43. doi: 10.1364/OE.20.016532

Aberrations and random scattering severely limit optical imaging in deep tissue. Adaptive optics can in principle drastically extend the penetration depth and improve the image quality. However, for random scattering media a large number of spatial modes need to be measured and controlled to restore a diffraction limited focus. Here, we present a parallel wavefront optimization method using backscattered light as a feedback. Spatial confinement of the feedback signal is realized with a confocal pinhole and coherence gating. We show in simulations and experiments that this approach enables focusing deep into tissue over up to six mean scattering path lengths. Experimentally the technique was tested on tissue phantoms and fixed brain slices.

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07/04/11 | Phase resolved interferometric spectral modulation (PRISM) for ultrafast pulse measurement and compression.
Wu TW, Tang J, Hajj B, Cui M
Optics Express. 2011 Jul 4;19(14):12961-8. doi: 10.1364/OE.19.012961

We show through experiments and simulations that parallel phase modulation, a technique developed in the field of adaptive optics, can be employed to quickly determine the spectral phase profile of ultrafast laser pulses and to perform phase compensation as well as pulse shaping. Different from many existing ultrafast pulse measurement methods, the technique reported here requires no spectrum measurements of nonlinear signals. Instead, the power of nonlinear signals is used directly to quickly measure the spectral phase, a convenient feature for applications such as two-photon fluorescence microscopy. The method is found to work with both smooth and even completely random distortions. The experimental results are verified with MIIPS measurements.

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03/15/11 | Parallel wavefront optimization method for focusing light through random scattering media.
Cui M
Optics Letters. 2011 Mar 15;36(6):870-2. doi: 10.1364/OL.36.000870

A parallel wavefront optimization method is demonstrated experimentally to focus light through random scattering media. The simultaneous modulation of multiple phase elements, each at a unique frequency, enables a parallel determination of the optimal wavefront. Compared to a pixel-by-pixel measurement, the reported parallel method uses the target signal in a highly efficient way. With 441 phase elements, a high-quality focus was formed through a glass diffuser with a peak-to-background ratio of \~{}270. The accuracy and repeatability of the system were tested through experiments.

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A large number of degrees of freedom are required to produce a high quality focus through random scattering media. Previous demonstrations based on spatial phase modulations suffer from either a slow speed or a small number of degrees of freedom. In this work, a high speed wavefront determination technique based on spatial frequency domain wavefront modulations is proposed and experimentally demonstrated, which is capable of providing both a high operation speed and a large number of degrees of freedom. The technique was employed to focus light through a strongly scattering medium and the entire wavefront was determined in 400 milliseconds,  three orders of magnitude faster than the previous report.

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