3D imaging in volumetric scattering media using phase-space measurements

Liu, Hsiou-Yuan; Jonas, Eric; Tian, Lei; Zhong, Jingshan; Recht, Benjamin; Waller, Laura

doi:10.1364/oe.23.014461

Cited by 79 publications

(87 citation statements)

References 43 publications

(33 reference statements)

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“…In biology this tool has revolutionized imaging of subcellular features [16,41]. A variant of this framework allows imaging through scattering media [31]. In §6.1, we show that our algorithm improves upon the current state of the art for localizing point sources in a fluorescence microscopy challenge dataset.…”

Section: Example Applicationsmentioning

confidence: 92%

The Alternating Descent Conditional Gradient Method for Sparse Inverse Problems

Boyd¹,

Schiebinger²,

Recht³

2017

SIAM J. Optim.

Self Cite

145

191

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We propose a variant of the classical conditional gradient method (CGM) for sparse inverse problems with differentiable measurement models. Such models arise in many practical problems including superresolution, time-series modeling, and matrix completion. Our algorithm combines nonconvex and convex optimization techniques: we propose global conditional gradient steps alternating with nonconvex local search exploiting the differentiable measurement model. This hybridization gives the theoretical global optimality guarantees and stopping conditions of convex optimization along with the performance and modeling flexibility associated with nonconvex optimization. Our experiments demonstrate that our technique achieves state-of-the-art results in several applications.

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Section: Example Applicationsmentioning

confidence: 92%

The Alternating Descent Conditional Gradient Method for Sparse Inverse Problems

Boyd¹,

Schiebinger²,

Recht³

2017

SIAM J. Optim.

Self Cite

145

191

View full text Add to dashboard Cite

show abstract

“…4D phase-space measurements, as done by LFM, contain a high redundancy in the information on the 3D location of an object, resulting in a strong robustness against scattering compared to other camera-based wide-field techniques (Liu et al 2015). By using a computational approach termed Seeded Iterative De-mixing (SID), our laboratory could extend the capabilities of LFM to mammalian cortex and show large-volume functional recording in awake, behaving mice (Nöbauer et al 2017) reaching 30 vol/s at single cell resolution for volumes as large as 900 x 900 x 260 μ m and at depths down to ~380 μ m. It is noteworthy that the signal extraction using SID considerably reduces crosstalk between voxels compared to frame-by-frame image reconstructions.…”

Section: Categorization Of Current Microscopy Methods Used For Ca2mentioning

confidence: 99%

A Guide to Emerging Technologies for Large-Scale and Whole-Brain Optical Imaging of Neuronal Activity

Weisenburger

Vaziri

2018

Annu. Rev. Neurosci.

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The mammalian brain is a densely interconnected network that consists of millions to billions of neurons. Decoding how information is represented and processed by this neural circuitry requires the ability to capture and manipulate the dynamics of large populations at high speed and resolution over a large area of the brain. While there has been a rapid increase in use of optical approaches in the neuroscience community over the last two decades, most microscopy approaches lack the ability to record the activity of all neurons comprising a functional network across the mammalian brain at relevant temporal and spatial resolution. In this review, we survey the recent development in the optical calcium imaging technologies in this regard and provide an overview of the strengths and limitations of each modality and their potential for scalability. We provide a guidance from a biological user perspective that is driven by the typical biological applications and sample conditions. We also discuss the potential for future advances and synergies that could be obtained through hybrid approaches or other modalities.

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“…Whilst the redundancy of a light field measurement due to a point source is recognized [15], this geometric approach combines information from these redundant measurements in order 6 to determine the three-dimensional position of a point source with unprecedented precision as compared with existing light field methods. Instead of trading spatial resolution for angular information, this approach is capable of three-dimensional point source localization with a precision far smaller than the diffraction limited spot of the corresponding widefield microscope.…”

Section: Localizing Points In Light Fieldsmentioning

confidence: 99%

“…It is anticipated that this technique will find application for imaging in ballistic scattering regimes such as biological tissue since previous studies have exploited the redundancy of the light field measurement to mitigate the effects of volumetric scattering [15,23]. Identifying the appropriate balance between measurement redundancy and signal-to-noise ratio will be the subject of future work.…”

Section: Simulating Light Fieldsmentioning

confidence: 99%

Super-resolving light fields in microscopy: depth from disparity

Rehman

Lenz

et al. 2019

Preprint

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Single molecule localisation microscopy (SMLM) has opened a new window for imaging fluorescently labelled biological specimens. Common 3D SMLM techniques enable data collection across an axial range of 1 − 5µm with high precision. Despite the success of 3D single molecule imaging there is a real need to image larger volumes. Here we demonstrate, through simulation and experiment, the potential of Single Molecule Light Field Microscopy (SMLFM) for extended depthof-field super-resolution imaging, extracting 3D point source position by measuring the disparity between localizations of a point emitter in multiple perspective views.

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3D imaging in volumetric scattering media using phase-space measurements

Cited by 79 publications

References 43 publications

The Alternating Descent Conditional Gradient Method for Sparse Inverse Problems

The Alternating Descent Conditional Gradient Method for Sparse Inverse Problems

A Guide to Emerging Technologies for Large-Scale and Whole-Brain Optical Imaging of Neuronal Activity

Super-resolving light fields in microscopy: depth from disparity

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