Pre-processing visualization of hyperspectral fluorescent data with Spectrally Encoded Enhanced Representations

Shi, Wen; Koo, Daniel E. S.; Kitano, Masahiko; Chiang, Hsiao Ju; Turcatel, Gianluca; Steventon, Benjamin; Arnesano, Cosimo; Warburton, David; Fraser, Scott E.; Cutrale, Francesco

doi:10.1038/s41467-020-14486-8

Cited by 24 publications

(25 citation statements)

References 72 publications

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“…Hyperspectral-based imaging techniques possess the ability to capture spectral information for multiple wavelengths at each pixel in an image. 23 , 26 , 27 This capability offers the ability to discriminate, with precision, different nanomaterials and differentiate them from biological materials. 28 , 29 Nanoparticles are an excellent candidate for sensor construction due to their photophysical properties.…”

Section: Resultsmentioning

confidence: 99%

Hyperspectral Mapping for the Detection of SARS-CoV-2 Using Nanomolecular Probes with Yoctomole Sensitivity

et al. 2021

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Efficient monitoring of SARS-CoV-2 outbreak requires the use of a sensitive and rapid diagnostic test. Although SARS-CoV-2 RNA can be detected by RT-qPCR, the molecular-level quantification of the viral load is still challenging, time-consuming, and labor-intensive. Here, we report an ultrasensitive hyperspectral sensor (HyperSENSE) based on hafnium nanoparticles (HfNPs) for specific detection of COVID-19 causative virus, SARS-CoV-2. Density functional theoretical calculations reveal that HfNPs exhibit higher changes in their absorption wavelength and light scattering when bound to their target SARS-CoV-2 RNA sequence relative to the gold nanoparticles. The assay has a turnaround time of a few seconds and has a limit of detection in the yoctomolar range, which is 1 000 000-fold times higher than the currently available COVID-19 tests. We demonstrated in ∼100 COVID-19 clinical samples that the assay is highly sensitive and has a specificity of 100%. We also show that HyperSENSE can rapidly detect other viruses such as influenza A H1N1. The outstanding sensitivity indicates the potential of the current biosensor in detecting the prevailing presymptomatic and asymptomatic COVID-19 cases. Thus, integrating hyperspectral imaging with nanomaterials establishes a diagnostic platform for ultrasensitive detection of COVID-19 that can potentially be applied to any emerging infectious pathogen.

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Section: Resultsmentioning

confidence: 99%

Hyperspectral Mapping for the Detection of SARS-CoV-2 Using Nanomolecular Probes with Yoctomole Sensitivity

et al. 2021

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“…Similarly, if one uses a spectral detector, i.e., a separate detector for different spectral bands, then for each pixel, one can obtain another histogram, in this case with the number of photons arriving in each channel, i.e., at each wavelength. This curve can also be transformed to an analogous spectral phasor space to map the recorded spectra at each pixel onto the 2D spectral phasor space 32 , 33 . Combining the lifetime measurement with a spectral detector, one effectively has a 5-dimensional space in which to characterize each pixel.…”

Section: Resultsmentioning

confidence: 99%

Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis

Vallmitjana

et al. 2022

Nat Commun

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Multiplexed mRNA profiling in the spatial context provides new information enabling basic research and clinical applications. Unfortunately, existing spatial transcriptomics methods are limited due to either low multiplexing or complexity. Here, we introduce a spatialomics technology, termed Multi Omic Single-scan Assay with Integrated Combinatorial Analysis (MOSAICA), that integrates in situ labeling of mRNA and protein markers in cells or tissues with combinatorial fluorescence spectral and lifetime encoded probes, spectral and time-resolved fluorescence imaging, and machine learning-based decoding. We demonstrate MOSAICA’s multiplexing scalability in detecting 10-plex targets in fixed colorectal cancer cells using combinatorial labeling of five fluorophores with facile error-detection and removal of autofluorescence. MOSAICA’s analysis is strongly correlated with sequencing data (Pearson’s r = 0.96) and was further benchmarked using RNAscopeTM and LGC StellarisTM. We further apply MOSAICA for multiplexed analysis of clinical melanoma Formalin-Fixed Paraffin-Embedded (FFPE) tissues. We finally demonstrate simultaneous co-detection of protein and mRNA in cancer cells.

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“…In complex biological environments, the spectral components often depend on the environment presenting a challenge for traditional spectral unmixing 16 , 17 that demand a priori information. If desired, the individual spectral components can still be unmixed with conventional algorithms 18 , 19 .…”

Section: Introductionmentioning

confidence: 99%

Phasor-based hyperspectral snapshot microscopy allows fast imaging of live, three-dimensional tissues for biomedical applications

et al. 2021

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Hyperspectral imaging is highly sought after in many fields including mineralogy and geology, environment and agriculture, astronomy and, importantly, biomedical imaging and biological fluorescence. We developed ultrafast phasor-based hyperspectral snapshot microscopy based on sine/cosine interference filters for biomedical imaging not feasible with conventional hyperspectral detection methods. Current approaches rely on slow spatial or spectral scanning limiting their application in living biological tissues, while faster snapshot methods such as image mapping spectrometry and multispectral interferometry are limited in spatial and/or spectral resolution, are computationally demanding, and imaging devices are very expensive to manufacture. Leveraging light sheet microscopy, phasor-based hyperspectral snapshot microscopy improved imaging speed 10–100 fold which, combined with minimal light exposure and high detection efficiency, enabled hyperspectral metabolic imaging of live, three-dimensional mouse tissues not feasible with other methods. As a fit-free method that does not require any a priori information often unavailable in complex and evolving biological systems, the rule of linear combinations of the phasor could spectrally resolve subtle differences between cell types in the developing zebrafish retina and spectrally separate and track multiple organelles in 3D cultured cells over time. The sine/cosine snapshot method is adaptable to any microscope or imaging device thus making hyperspectral imaging and fit-free analysis based on linear combinations broadly available to researchers and the public.

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Pre-processing visualization of hyperspectral fluorescent data with Spectrally Encoded Enhanced Representations

Cited by 24 publications

References 72 publications

Hyperspectral Mapping for the Detection of SARS-CoV-2 Using Nanomolecular Probes with Yoctomole Sensitivity

Hyperspectral Mapping for the Detection of SARS-CoV-2 Using Nanomolecular Probes with Yoctomole Sensitivity

Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis

Phasor-based hyperspectral snapshot microscopy allows fast imaging of live, three-dimensional tissues for biomedical applications

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