Adaptive optics stochastic optical reconstruction microscopy (AO-STORM) by particle swarm optimization

Tehrani, Kayvan Forouhesh; Zhang, Yiwen; Shen, Ping; Kner, Peter

doi:10.1364/boe.8.005087

Cited by 43 publications

(32 citation statements)

References 38 publications

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“…To analyze the mitochondrial network organization, we developed an angular Fourier filtering (AFF) method, based on a Fourier metric previously used for sensorless Adaptive Optics (70). Transforming an image from the spatial domain ( fig.…”

Section: -Photon Scanning Microscopymentioning

confidence: 99%

PGC-1α overexpression partially rescues impaired oxidative and contractile pathophysiology following volumetric muscle loss injury

Southern

Nichenko

Tehrani

et al. 2019

Preprint

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Volumetric muscle loss (VML) injury is characterized by a non-recoverable loss of muscle fibers due to ablative surgery or severe orthopaedic trauma, that results in chronic functional impairments of the soft tissue. Currently, the effects of VML on the oxidative capacity and adaptability of the remaining injured muscle are unclear. A better understanding of this pathophysiology could significantly shape how VML-injured patients and clinicians approach regenerative medicine and rehabilitation following injury. Herein, the data indicated that VML-injured muscle has diminished mitochondrial content and function (i.e. oxidative capacity), loss of mitochondrial network organization, and attenuated oxidative adaptations to exercise. However, forced PGC-1 overexpression rescued the deficits in oxidative capacity and muscle strength. This implicates physiological activation of PGC1-α as a limiting factor in VML-injured muscle adaptive capacity and provides a mechanistic target for regenerative rehabilitation approaches to address the skeletal muscle dysfunction.Oxidative capacity is a cornerstone of skeletal muscle health, and for the past 40 years, we have known that the most robust physiologic adaptation to regularly scheduled physical activity (i.e., exercise/overload training) is an increase in oxidative capacity (1,2). Improvements in muscle oxidative capacity are made possible with exercise training through adaptations affecting the density and function of the intramuscular mitochondrial network. The signaling pathways that initiate and coordinate mitochondrial improvements with exercise are complex, but advancements in molecular biology in the last two decades have revealed many of the key players involved (see for review (3)). Most notably, the transcription factor PGC-1 (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha) is considered a critical molecular modulator of skeletal muscle oxidative plasticity because it regulates gene expression patterns for expansion of the mitochondrial network (i.e. mitochondrial biogenesis), angiogenesis, and motor neuron associated adaptations with exercise training(4-6). Expansion of the vasculature and mitochondrial network with exercise training enhances the functional capacity of the muscle (e.g., fatigue resistance), and in general, this physiologic type of acclimation is considered beneficial for human performance and health (7,8).Large-scale skeletal muscle trauma, such as volumetric muscle loss (VML) injury, is unique in that the muscle is not able to regenerate muscle fibers with endogenous repair systems and as a result, cannot fully recover strength. The loss of muscle function (i.e., contractility) can exceed the loss of tissue mass(9), and this permanent functional deficit leaves patients with lifelong disability(10) for which there is currently no corrective physical rehabilitation guidelines. Furthermore, the extent to which the remaining skeletal muscle can adapt to rehabilitation is unclear. Recent preclinical work has investigated various...

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Section: -Photon Scanning Microscopymentioning

confidence: 99%

PGC-1α overexpression partially rescues impaired oxidative and contractile pathophysiology following volumetric muscle loss injury

Southern

Nichenko

Tehrani

et al. 2019

Preprint

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“…where their movement is affected by the individually best solution it found so far, as well as the groups best solution. Particle-swarm optimization was implemented via MATLAB particleswarm with a swarm size of 25 as suggested [8] with a maximum of 20 iterations for a maximum of 300 acquisitions. We used an initial swarm spansize of 0.1 rad and a maximum spansize of 0.75 rad.…”

Section: Particle-swarm Optimization Uses a Collection Of Solutions Mmentioning

confidence: 99%

REALM: AO-based localization microscopy deep in complex tissue

Siemons

Hanemaaijer

Kole

et al. 2020

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Performing Single-Molecule Localization Microscopy (SMLM) in complex biological tissues, where sample-induced aberrations hamper detection and localization, has remained a challenge. Here we establish REALM (Robust and Effective Adaptive Optics in Localization Microscopy), which corrects aberrations of ≤1 rad RMS using 297 frames of blinking molecules to improve single-molecule localization. We demonstrate this method by resolving the periodic cytoskeleton of the axon initial segment at  m depth in brain tissue. Results and discussionSingle-Molecule Localization Microscopy (SMLM) [1][2][3] enables exploring the nanoscale organization of cellular structures through repetitive localization of different sparse subsets of fluorophores. While this has provided many new insights into the organization of individual cultured cells, performing SMLM deep inside tissue or organoids has remained challenging. Accurate localization requires sufficient signal to noise and a non-aberrated point-spreadfunction (PSF) [4], both of which are compromised when imaging in biological tissue, in which a range of distinct cellular components cause complex light scattering [5]. A way to overcome this is the use of intensity-based Adaptive Optics (AO), which uses a deformable mirror in the emission path to compensate for tissue-induced wave-front distortions. The required shape of the mirror can be found iteratively by optimizing the contrast of the image (or guide star when possible) [6]. However, in SMLM the acquisitions are noisy and contain a strongly fluctuating amount of signal photons, rendering traditional approaches unusable. Various AO-methods have been proposed to overcome these issues [7-9], but the exact performance of these different AO-methods has not been consistently established and it has remained unclear what level of aberrations these methods can correct and under which conditions. Here we introduce REALM (Robust and Effective Adaptive Optics in Localization Microscopy), which corrects aberrations of up to 1 rad RMS using 297 frames of blinking molecules, thereby enabling robust SMLM at 50 m depth and even up to 80 m depth when pre-correcting spherical aberration.Aberrations alter the points spread function (PSF), which decreases contrast and the spatial frequency support (see Figure 1a-d). The key for intensity-based AO is to find a relevant metric, a quality measure computed from the acquisitions, in combination with an optimization algorithm to efficiently and robustly optimize the metric [10]. To reduce the effect of strongly fluctuating signal levels of the acquisitions, all existing methods propose a weighted sum of the Fourier transform of the acquisition as metric, while differing in the specific weighting of the spatial frequencies and in normalization (see insert Figure 1d). We termed these metrics M1, M2 and M3, corresponding to Burke et al. [7], Tehrani et al. [8], and Mlodzianoski et al. [9], respectively. Because SMLM acquisitions are comprised of pseudo-random point sources, these methods effectively ...

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“…WS technology has previously shown that 2-photon imaging through intact skull of juvenile mouse skull is possible [19]. By engineering the wavefront and restoring the diffraction-limited PSF, WS can correct for low and high order aberrations, and enhance both the peak and width of the PSF deep inside of a sample [4,[20][21][22][23][24][25][26][27][28][29][30], which has many applications in the musculoskeletal system [31] and nervous system [32] imaging.…”

Section: Introductionmentioning

confidence: 99%

In situ measurement of the isoplanatic patch for imaging through intact bone

Tehrani

Koukourakis

Czarske

et al. 2020

Preprint

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Wavefront-shaping (WS) enables imaging through scattering tissues like bone, which is important for neuroscience and bone-regeneration research. WS corrects for the optical aberrations at a given depth and field-of-view (FOV) within the sample; the extent of the validity of which is limited to a region known as the isoplanatic patch (IP). Knowing this parameter helps to estimate the number of corrections needed for WS imaging over a given FOV. In this paper, we first present direct transmissive measurement of murine skull IP using digital optical phase conjugation (DOPC) based focusing. Second, we extend our previously reported Phase Accumulation Ray Tracing (PART) method to provide in-situ in-silico estimation of IP, called correlative PART (cPART). Our results show an IP range of 1-3 μm for mice within an age range of 8-14 days old and 1.00+/-0.25 μm in a 12-week old adult skull. Consistency between the two measurement approaches indicates that cPART can be used to approximate the IP before a WS experiment, which can be used to calculate the number of corrections required within a given field of view.

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Adaptive optics stochastic optical reconstruction microscopy (AO-STORM) by particle swarm optimization

Cited by 43 publications

References 38 publications

PGC-1α overexpression partially rescues impaired oxidative and contractile pathophysiology following volumetric muscle loss injury

PGC-1α overexpression partially rescues impaired oxidative and contractile pathophysiology following volumetric muscle loss injury

REALM: AO-based localization microscopy deep in complex tissue

In situ measurement of the isoplanatic patch for imaging through intact bone

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