Fluorescence Interference Contrast-enabled structures improve the microarrays performance

Dobroiu, Serban; Delft, F.C.M.J.M. van; Aveyard, Jenny; Shetty, Prasad; Nicolau, Dan V.

doi:10.1016/j.bios.2018.09.009

Cited by 3 publications

(8 citation statements)

References 47 publications

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“…The diagram showing a simplified optical setup valid for the substrates presented in this paper is shown in Figure S1. For the microterraces with identical heights, a brighter fluorescence was observed on structures having a larger footprint (in Figure S2, for 25 μm 2 versus 9 μm 2 and 4 μm 2 microterraces, respectively), as also reported before Figure S2 also provides intensity results for much smaller areas, namely, 1 μm 2 , 1.56 μm 2 , and 2.25 μm 2 areas for the terraces.…”

Section: Resultssupporting

confidence: 82%

“…This uneven lateral distribution of fluorescence and its complex relationship with the size of the footprint of the microterraces (presented in more detail in the Supporting Information and the Supporting Information reported previously 24 ) led to the quantification of fluorescence signal dependent on the size of the spot. Also, the lack of flexibility in accounting for the actual vertical position of the fluorophores suggested that a different FLIC geometry needed to be used.…”

Section: ■ Materials and Methodsmentioning

confidence: 78%

“…For each fluorophore tested there was at least one position along the side wall of the structure where fluorescence intensity is maximum. The theoretical fluorescence intensity (Figure B) was computed as the product between the square of the electric field intensities at the excitation and emission wavelengths of each fluorophore using an iterative procedure described elsewhere. , …”

Section: Resultsmentioning

confidence: 99%

“…Subsequently, SiO 2 layers with thicknesses of 20, 40, 60, 80, and 100 nm, respectively, were deposited onto all the wafers. All sputter deposition processes were carried out using a Veeco Nexus 800 sputter deposition tool (process parameters detailed elsewhere ,, ). Next, a 1.5 μm thick HPR504 resist layer was spin coated on the wafers, soft-baked at 95 °C for 2 min, exposed on an ASML i-line stepper using a standard “lines and spaces” test reticule, and developed for 2 min at 21 °C in Tetramethylammonium hydroxide (TMAOH).…”

Section: Methodsmentioning

confidence: 99%

“…For the microterraces with identical heights, a brighter fluorescence was observed on structures having a larger footprint (in Figure S2, for 25 μm 2 versus 9 μm 2 and 4 μm 2 microterraces, respectively), as also reported before. 24 Figure S2 also provides intensity results for much smaller areas, namely, 1 μm 2 , 1.56 μm 2 , and 2.25 μm 2 areas for the terraces. The use of FLIC was also reported before, 14 where CVD deposited polymeric steps, resulting in the amplification of the fluorescence signal in the region of interest and its quenching outside.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

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Spatially Addressable Multiplex Biodetection by Calibrated Micro/Nanostructured Surfaces

et al. 2023

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A challenge of any biosensing technology is the detection of very low concentrations of analytes. The fluorescence interference contrast (FLIC) technique improves the fluorescence-based sensitivity by selectively amplifying, or suppressing, the emission of a fluorophore-labeled biomolecule immobilized on a transparent layer placed on top of a mirror basal surface. The standing wave of the reflected emission light means that the height of the transparent layer operates as a surface-embedded optical filter for the fluorescence signal. FLIC extreme sensitivity to wavelength is also its main problem: small, e.g., 10 nm range, variations of the vertical position of the fluorophore can translate in unwanted suppression of the detection signal. Herein, we introduce the concept of quasi-circular lenticular microstructured domes operating as continuous-mode optical filters, generating fluorescent concentric rings, with diameters determined by the wavelengths of the fluorescence light, in turn modulated by FLIC. The critical component of the lenticular structures was the shallow sloping side wall, which allowed the simultaneous separation of fluorescent patterns for virtually any fluorophore wavelength. Purposefully designed microstructures with either stepwise or continuous-slope dome geometries were fabricated to modulate the intensity and the lateral position of a fluorescence signal. The simulation of FLIC effects induced by the lenticular microstructures was confirmed by the measurement of the fluorescence profile for three fluorescent dyes, as well as high-resolution fluorescence scanning using stimulated emission depletion (STED) microscopy. The high sensitivity of the spatially addressable FLIC technology was further validated on a diagnostically important target, i.e., the receptor-binding domain (RBD) of the SARS-Cov2 via the detection of RBD:anti-S1-antibody.

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Section: Resultssupporting

confidence: 82%

Section: ■ Materials and Methodsmentioning

confidence: 78%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: ■ Materials and Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Spatially Addressable Multiplex Biodetection by Calibrated Micro/Nanostructured Surfaces

et al. 2023

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Single-Molecule Detection on Nanoparticles-on-Nanoposts

Dobroiu,

van Delft,

Wilson

et al. 2023

2023 IEEE 23rd International Conference on Nanotechnology (NANO)

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Hexagonal-Grid-Layout Image Segmentation Using Shock Filters: Computational Complexity Case Study for Microarray Image Analysis Related to Machine Learning Approaches

Baloi

Costea

Gutt

et al. 2023

Sensors

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Hexagonal grid layouts are advantageous in microarray technology; however, hexagonal grids appear in many fields, especially given the rise of new nanostructures and metamaterials, leading to the need for image analysis on such structures. This work proposes a shock-filter-based approach driven by mathematical morphology for the segmentation of image objects disposed in a hexagonal grid. The original image is decomposed into a pair of rectangular grids, such that their superposition generates the initial image. Within each rectangular grid, the shock-filters are once again used to confine the foreground information for each image object into an area of interest. The proposed methodology was successfully applied for microarray spot segmentation, whereas its character of generality is underlined by the segmentation results obtained for two other types of hexagonal grid layouts. Considering the segmentation accuracy through specific quality measures for microarray images, such as the mean absolute error and the coefficient of variation, high correlations of our computed spot intensity features with the annotated reference values were found, indicating the reliability of the proposed approach. Moreover, taking into account that the shock-filter PDE formalism is targeting the one-dimensional luminance profile function, the computational complexity to determine the grid is minimized. The order of growth for the computational complexity of our approach is at least one order of magnitude lower when compared with state-of-the-art microarray segmentation approaches, ranging from classical to machine learning ones.

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Fluorescence Interference Contrast-enabled structures improve the microarrays performance

Cited by 3 publications

References 47 publications

Spatially Addressable Multiplex Biodetection by Calibrated Micro/Nanostructured Surfaces

Spatially Addressable Multiplex Biodetection by Calibrated Micro/Nanostructured Surfaces

Single-Molecule Detection on Nanoparticles-on-Nanoposts

Hexagonal-Grid-Layout Image Segmentation Using Shock Filters: Computational Complexity Case Study for Microarray Image Analysis Related to Machine Learning Approaches

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