Dataset Information

DeepBlink: threshold-independent detection and localization of diffraction-limited spots.

ABSTRACT: Detection of diffraction-limited spots in single-molecule microscopy images is traditionally performed with mathematical operators designed for idealized spots. This process requires manual tuning of parameters that is time-consuming and not always reliable. We have developed deepBlink, a neural network-based method to detect and localize spots automatically. We demonstrate that deepBlink outperforms other state-of-the-art methods across six publicly available datasets containing synthetic and experimental data.

SUBMITTER: Eichenberger BT

PROVIDER: S-EPMC8287908 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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Publications

deepBlink: threshold-independent detection and localization of diffraction-limited spots.

Eichenberger Bastian Th BT Zhan YinXiu Y Rempfler Markus M Giorgetti Luca L Chao Jeffrey A JA

Nucleic acids research 20210701 13

Detection of diffraction-limited spots in single-molecule microscopy images is traditionally performed with mathematical operators designed for idealized spots. This process requires manual tuning of parameters that is time-consuming and not always reliable. We have developed deepBlink, a neural network-based method to detect and localize spots automatically. We demonstrate that deepBlink outperforms other state-of-the-art methods across six publicly available datasets containing synthetic and e ...[more]

PMID: 34197605

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Project description:In this contribution, we demonstrate a wide-field hyperspectral mid-infrared (MIR) microscope based on multidimensional single-pixel imaging (SPI). The microscope employs a high brightness MIR supercontinuum source for broadband (1.55 [Formula: see text]-4.5 [Formula: see text]) sample illumination. Hyperspectral imaging capability is achieved by a single micro-opto-electro-mechanical digital micromirror device (DMD), which provides both spatial and spectral differentiation. For that purpose the operational spectral bandwidth of the DMD was significantly extended into the MIR spectral region. In the presented design, the DMD fulfills two essential tasks. On the one hand, as standard for the SPI approach, the DMD sequentially masks captured scenes enabling diffraction-limited imaging in the tens of millisecond time-regime. On the other hand, the diffraction at the micromirrors leads to dispersion of the projected field and thus allows for wavelength selection without the application of additional dispersive optical elements, such as gratings or prisms. In the experimental part, first of all, the imaging and spectral capabilities of the hyperspectral microscope are characterized. The spatial and spectral resolution is assessed by means of test targets and linear variable filters, respectively. At a wavelength of 4.15 [Formula: see text] a spatial resolution of 4.92 [Formula: see text] is achieved with a native spectral resolution better than 118.1 nm. Further, a post-processing method for drastic enhancement of the spectral resolution is proposed and discussed. The performance of the MIR hyperspectral microsopce is demonstrated for label-free chemical imaging and examination of polymer compounds and red blood cells. The acquisition and reconstruction of Hadamard sampled 64 [Formula: see text] 64 images is achieved in 450 ms and 162 ms, respectively. Thus, combined with an unprecedented intrinsic flexibiliy gained by a tunable field of view and adjustable spatial resolution, the demonstrated design drastically improves the sample throughput in MIR chemical and biomedical imaging.

Dataset Information

DeepBlink: threshold-independent detection and localization of diffraction-limited spots.

Publications

deepBlink: threshold-independent detection and localization of diffraction-limited spots.

Similar Datasets

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