A rigorous forward model solver for conventional coherent microscope is presented. The forward model is derived from Maxwell’s equations and models the wave behaviour of light matter interaction. Vectorial waves and multiple-scattering effect are considered in this model. Scattered field can be calculated with given distribution of the refractive index of the biological sample. Bright field images ...

In this work we have explored the live-cell friendly nanoscopy method Multiple Signal Classification Algorithm (MUSICAL) for multi-colour imaging of various organelles and sub-cellular structures in the cardiomyoblast cell line H2c9. We have tested MUSICAL for fast (up to 230Hz), multi-colour time-lapse sequences of various sub-cellular structures (mitochondria, endoplasmic reticulum, microtubules, ...

The quantitative analysis of subcellular organelles such as mitochondria in cell fluorescence microscopy images is a demanding task because of the inherent challenges in the segmentation of these small and morphologically diverse structures. In this article, we demonstrate the use of a machine learning-aided segmentation and analysis pipeline for the quantification of mitochondrial morphology in ...

Streaming classification methods assume the number of input features is fixed and always received. But in many real-world scenarios, some features are reliable while others are unreliable or inconsistent. We propose a novel online deep learning-based model called Auxiliary Network (Aux-Net), which is scalable and agile and can handle any number of inputs at each time instance. The Aux-Net model is ...

Histology involves the observation of structural features in tissues using a microscope. While diffraction-limited optical microscopes are commonly used in histological investigations, their resolving capabilities are insufficient to visualize details at subcellular level. Although a novel set of super-resolution optical microscopy techniques can fulfill the resolution demands in such cases, the ...

Contrast in fluorescence microscopy images allows for the differentiation between different structures by their difference in intensities. However, factors such as point-spread function and noise may reduce it, affecting its interpretability. We identified that fluctuation of emitters in a stack of images can be exploited to achieve increased contrast when compared to the average and Richardson-Lucy ...

Photonic chip-based total internal reflection fluorescence microscopy (c-TIRFM) is an emerging technology enabling a large TIRF excitation area decoupled from the detection objective. Additionally, due to the inherent multimodal nature of wide waveguides, it is a convenient platform for introducing temporal fluctuations in the illumination pattern. The fluorescence fluctuation-based nanoscopy technique ...

The multiple signal classification algorithm (MUSICAL) is a statistical super-resolution technique for wide-field fluorescence microscopy. Although MUSICAL has several advantages, such as its high resolution, its low computational performance has limited its exploitation. This paper aims to analyze the performance and scalability of MUSICAL for improving its low computational performance. We first ...

Scanning Acoustic Microscopy (SAM) uses high-frequency acoustic waves to generate non-ionizing, label-free images of the surface and internal structures of industrial objects and biological specimens. The resolution of SAM images is limited by several factors such as the frequency of excitation signals, the signal-to-noise ratio, and the pixel size. We propose to use a hypergraphs image inpainting ...

Chip-based Evanescent Light Scattering (cELS) utilizes the multiple modes of a high-index contrast optical waveguide for near-field illumination of unlabeled samples, thereby repositioning the highest spatial frequencies of the sample into the far-field. The multiple modes scattering off the sample with different phase differences is engineered to have random spatial distributions within the integration ...