Rapid image deconvolution and multiview fusion for optical microscopy

Guo, Min; Li, Yue; Su, Yijun; Lambert, Talley J.; Nogare, Damian Dalle; Moyle, Mark W.; Duncan, Leighton H.; Ikegami, Richard; Santella, Anthony; Rey-Suarez, Ivan; Green, Daniel; Beiriger, Anastasia; Chen, Jiji; Vishwasrao, Harshad D.; Ganesan, Sundar; Prince, Victoria; Waters, Jennifer; Annunziata, Christina M.; Hafner, Markus; Mohler, William A.; Chitnis, Ajay B.; Upadhyaya, Arpita; Usdin, Ted B.; Bao, Zhirong; Colón-Ramos, Daniel A.; Rivière, Patrick La; Liu, Huafeng; Wu, Yicong; Shroff, Hari

doi:10.1038/s41587-020-0560-x

Cited by 134 publications

(164 citation statements)

References 60 publications

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“…The new genetically encoded neuromodulatory sensors, fortuitously, emit a large amount of photons with their fluorescence responses being largely independent of the expression levels [29,[32][33][34]. The welcoming properties, when combined with the recent advances of superresolution and/or deconvolution microscopy [44,45], make it possible to quantify transmission properties of neuromodulation [11], which is essential for demarcating the physiology of behaviors and the pathogenesis of diseases [1][2][3][4]. Initial experiments demonstrated that top-performing sensors could resolve synaptic properties of neuromodulatory transmission [29,[32][33][34].…”

Section: A New Sensor-based Analysis Methodsmentioning

confidence: 99%

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Genetically encoded sensors enable micro- and nano-scopic decoding of transmission in healthy and diseased brains

et al. 2020

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Neural communication orchestrates a variety of behaviors, yet despite impressive effort, delineating transmission properties of neuromodulatory communication remains a daunting task due to limitations of available monitoring tools. Recently developed genetically encoded neurotransmitter sensors, when combined with superresolution and deconvolution microscopic techniques, enable the first micro- and nano-scopic visualization of neuromodulatory transmission. Here we introduce this image analysis method by presenting its biophysical foundation, practical solutions, biological validation, and broad applicability. The presentation illustrates how the method resolves fundamental synaptic properties of neuromodulatory transmission, and the new data unveil unexpected fine control and precision of rodent and human neuromodulation. The findings raise the prospect of rapid advances in the understanding of neuromodulatory transmission essential for resolving the physiology or pathogenesis of various behaviors and diseases.

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Section: A New Sensor-based Analysis Methodsmentioning

confidence: 99%

“…It is important to note that deconvolving large datasets of imaging episodes of neuromodulatory transmissions is computationally intensive tasks, taking hours, if not days [ 32 ]. Hence, it is wise to employ the optimized and deep learning analysis algorithms to carry out these tasks [ 44 ].…”

Section: Introductionmentioning

confidence: 99%

Genetically encoded sensors enable micro- and nano-scopic decoding of transmission in healthy and diseased brains

et al. 2020

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“…Currently, speckle reduction is implemented with shaking an inserted section of multimode fiber with a coin vibrator (15000 rpm), which performs well (Figure 8 B-E) but can also be further improved, especially for the more coherent 561 nm line. As an example application, we imaged two CODEX-processed samples (Figure 8 F-G, Supplementary Video 3), where z-stacks (17 planes, 1.5 m spacing) were taken and the results are deconvolved with an unmatched back projector [77].…”

Section: Multicolor Epifluorescence Illumination and Patterned Illumimentioning

confidence: 99%

“…Multiple LEDs can be combined with light delivered . Deconvolution is done with an unmatched back projector [77] to the microscope in free space or through a liquid light guide (many customizable off-the-shelf solutions are already available, e.g. from Prizmatix and bluebox optics).…”

Section: Multicolor Epifluorescence Illumination and Patterned Illumimentioning

confidence: 99%

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Squid: Simplifying Quantitative Imaging Platform Development and Deployment

Krishnamurthy

et al. 2020

Preprint

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With rapid developments in microscopy methods, highly versatile, robust and affordable implementations are needed to enable rapid and wide adoption by the biological sciences community. Here we report Squid, a quantitative imaging platform with a full suite of hardware and software components and configurations for deploying facility-grade widefield microscopes with advanced features like flat field fluorescence excitation, patterned illumination and tracking microscopy, at a fraction of the cost of commercial solutions. The open and modular nature (both in hardware and in software) lowers the barrier for deployment, and importantly, simplifies development, making the system highly configurable and experiments that can run on the system easily programmable. Developed with the goal of helping translate the rapid advances in the field of microscopy and microscopy-enabled methods, including those powered by deep learning, we envision Squid will simplify roll-out of microscopy-based applications - including at point of care and in low resource settings, make adoption of new or otherwise advanced techniques easier, and significantly increase the available microscope-hours to labs.

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Distribution changes of non‐self‐test cells and self‐tunic cells surrounding the outer body during Ciona metamorphosis

Totsuka,

Kuwana,

Sawai

et al. 2023

Developmental Dynamics

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Background: Ascidians significantly change their body structure through metamorphosis, but the spatio‐temporal cell dynamics in the early metamorphosis stage has not been clarified. A natural Ciona embryo is surrounded by maternally derived non‐self‐test cells before metamorphosis. However, after metamorphosis, the juvenile is surrounded by self‐tunic cells derived from mesenchymal cell lineages. Both test cells and tunic cells are thought to be changed their distributions during metamorphosis, but the precise timing is unknown.Results: Using a metamorphosis induction by mechanical stimulation, we investigated the dynamics of mesenchymal cells during metamorphosis in a precise time course. After the stimulation, two‐round Ca2+ transients were observed. Migrating mesenchymal cells came out through the epidermis within 10 min after the second phase. We named this event “cell extravasation.” The cell extravasation occurred at the same time as the backward movement of posterior trunk epidermal cells. Timelapse imaging of transgenic‐line larva revealed that non‐self‐test cells and self‐tunic cells temporarily coexist outside the body until the test cells are eliminated. At the juvenile stage, only extravasated self‐tunic cells remained outside the body.Conclusions: We found that mesenchymal cells extravasated following two‐round Ca2+ transients, and distributions of test cells and tunic cells changed in the outer body after tail regression.

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Rapid image deconvolution and multiview fusion for optical microscopy

Cited by 134 publications

References 60 publications

Genetically encoded sensors enable micro- and nano-scopic decoding of transmission in healthy and diseased brains

Genetically encoded sensors enable micro- and nano-scopic decoding of transmission in healthy and diseased brains

Squid: Simplifying Quantitative Imaging Platform Development and Deployment

Distribution changes of non‐self‐test cells and self‐tunic cells surrounding the outer body during Ciona metamorphosis

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