Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging

Cutrale, Francesco; Trivedi, Vikas; Trinh, Le A.; Chiu, Charles B.; Choi, Joonhee; Artiga, M. S.; Fraser, Scott E.

doi:10.1038/nmeth.4134

Cited by 134 publications

(122 citation statements)

References 25 publications

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“…Future experiments using novel faster imaging techniques, like lattice light sheet imaging, that image fast endosomal dynamics along with technologies that can image multiple components simultaneously, such as hyper spectral imaging, might answer the plethora of questions that this fantastic biological system poses. It will be imperative to continue mapping the various lipids and protein machineries and their effectors at the endosome in the context of cargoes, and to measure their spatiotemporal distribution and dynamics by using modern technologies …”

Section: Discussionmentioning

confidence: 99%

The Lipids of the Early Endosomes: Making Multimodality Work

Arumugam

Kaur

2017

ChemBioChem

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Early endosomes are dynamic intracellular compartments that fuse with incoming endocytic carrier vesicles and associated cargoes from the plasma membrane. It has been long known that the chemical structures of lipids confer striking properties and rich biochemistry on bilayers. Although the organisational principles of the plasma membrane are relatively better understood, understanding endosomal membranes has been challenging. It has become increasingly apparent that endosomal membranes, because of their lipid compositions and interactions, use distinct lipid chemistries. We discuss the biochemical and biophysical phenomena in play at the early endosomal membrane. We focus on cholesterol, phosphoinositides, and phosphatidylserine and their clear roles in endosome functions. We discuss the various principles and mechanisms underpinning how these lipids are implicated at the functional level in the working of endosomes, and we summarise early endosomes as a multimodal organelle employing distinct lipid-specific mechanisms.

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Section: Discussionmentioning

confidence: 99%

The Lipids of the Early Endosomes: Making Multimodality Work

Arumugam

Kaur

2017

ChemBioChem

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“…The process can be computing intense and sensitive to noise. Faster and more robust algorithms are being developed for fluorescent hyperspectral imaging [25].…”

Section: Retaining the Ability Of Removing Out-of-focus And Scatteredmentioning

confidence: 99%

Three-dimensional live multi-label light-sheet imaging with synchronous excitation-multiplexed structured illumination

Zhou

Peng

2017

Opt. Express

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Multiplexed imaging is a powerful tool for studying complex interactions inside biological systems. Spectral imaging methods that capture multiple fluorescent markers synchronously without sacrificing the imaging speed or resolution are most suitable for live imaging. We describe spectral-encoded structured illumination (spectral-SIM) light-sheet microscopy, which enables parallel multi-excitation-channel imaging in 3D. Spectral-SIM encodes the excitation wavelength as the phase of the illumination pattern, and allows synchronous image capture over multiple excitation channels at the same speed and spatial resolution as mono-channel structured light-sheet imaging. The technique retains structured light-sheet microscopy's ability in removing out-of-focus and scattered emission background, and generates clear 3D multiplexed images in thick tissue. The capability of this technique was demonstrated by the imaging of live triple-labeled transgenic zebrafish to over 300 µm deep with 0.5µm-by-2µm (lateral-by-axial) resolution. two-photon Bessel light-sheet nonlinear structured illumination microscopy," Biomed.

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“…Here we address this task for imaging studies of developing tissues, where patterns of cell fates are established by complex regulatory networks [6][7][8]. Advances in live imaging continue to provide new insights into the dynamics of individual components in these networks, but imaging more than three reporters at the same time is still challenging and limited to model genetic organisms [9,10]. Furthermore, in the absence of reliable live reporters, dynamics of some state variables can only be inferred from fixed tissues.…”

Section: Introductionmentioning

confidence: 99%

Synthesizing developmental trajectories

Villoutreix

Andén

Lim

et al. 2017

Preprint

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Dynamical processes in biology are studied using an ever-increasing number of techniques, each of which brings out unique features of the system. One of the current challenges is to develop systematic approaches for fusing heterogeneous datasets into an integrated view of multivariable dynamics. We demonstrate that heterogeneous data fusion can be successfully implemented within a semi-supervised learning framework that exploits the intrinsic geometry of high-dimensional datasets. We illustrate our approach using a dataset from studies of pattern formation in Drosophila. The result is a continuous trajectory that reveals the joint dynamics of gene expression, subcellular protein localization, protein phosphorylation, and tissue morphogenesis. Our approach can be readily adapted to other imaging modalities and forms a starting point for further steps of data analytics and modeling of biological dynamics. Author summaryA wide range of problems in biology require analysis of multivariable dynamics in space and time. As a rule, the multiscale nature and complexity of real systems precludes simultaneous monitoring of all the relevant variables, and multivariable dynamics must be synthesized from partial views provided by different experimental techniques. We present a formal framework for accomplishing this task in the context of imaging studies of pattern formation in developing tissues.

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Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging

Cited by 134 publications

References 25 publications

The Lipids of the Early Endosomes: Making Multimodality Work

The Lipids of the Early Endosomes: Making Multimodality Work

Three-dimensional live multi-label light-sheet imaging with synchronous excitation-multiplexed structured illumination

Synthesizing developmental trajectories

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