Ida Opstad

UiT The Arctic University of Norway · Department of Physics and Technology

In 1934, Frits Zernike demonstrated that it is possible to exploit the sample’s refractive index to obtain superior contrast images of biological cells. The refractive index contrast of a cell surrounded by media yields a change in the phase and intensity of the transmitted light wave. This change can be due to either scattering or absorption cause...

Mitochondria play a crucial role in cellular metabolism. This paper presents a novel method to visualize mitochondria in living cells without the use of fluorescent markers. We propose a physics-guided deep learning approach for obtaining virtually labeled micrographs of mitochondria from bright-field images. We integrate a microscope’s point sprea...

Intact skin is of uttermost importance for fish welfare. The fish skin provides an environmental barrier and protects against invading pathogens. However, both pathogens and physical insults cause skin wounds that are of major concern in modern fish farming. The behavior and interactions between keratocyte cells and sheets of cells are not well und...

Optical waveguide chips are shown as an alternative to far-field optics for the excitation of biological microscopy samples, with high refractive index materials and photonic circuits pushing the boundaries of conventional super-resolution optical microscopy implementations.

Segmenting subcellular structures in living cells from fluorescence microscope images is a ground truth (GT)-deficient problem. The microscopes’ three-dimensional blurring function, finite optical resolution due to light diffraction, finite pixel resolution and the complex morphological manifestations of the structures all contribute to GT-hardness...

Mitochondria are essential energy-providing organelles of particular importance in energy-demanding tissue such as the heart. The production of mitochondria-derived vesicles (MDVs) is a cellular mechanism by which cells ensure a healthy pool of mitochondria. These vesicles are small and fast-moving objects not easily captured by imaging. In this wo...

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....

Examining specific sub-cellular structures while minimizing cell perturbation is important in the life sciences. Fluorescence labeling and imaging is widely used for introducing specificity despite its perturbative and photo-toxic nature. With the advancement of deep learning, digital staining routines for label-free analysis have emerged as a repl...

Image denoising or artefact removal using deep learning is possible in the availability of supervised training dataset acquired in real experiments or synthesized using known noise models. Neither of the conditions can be fulfilled for nanoscopy (super-resolution optical microscopy) images that are generated from microscopy videos through statistic...

Multiple signal classification algorithm (MUSICAL) exploits temporal fluctuations in fluorescence intensity to perform super-resolution microscopy by computing the value of a super-resolving indicator function across a fine sample grid. A key step in the algorithm is the separation of the measurements into signal and noise subspaces, based on a sin...

Multiple signal classification algorithm (MUSICAL) exploits temporal fluctuations in fluorescence intensity to perform super-resolution microscopy by computing the value of a super-resolving indicator function across a fine sample grid. A key step in the algorithm is the separation of the measurements into signal and noise subspaces, based on a sin...

In many real-world scientific problems, generating ground truth (GT) for supervised learning is almost impossible. The causes include limitations imposed by scientific instrument, physical phenomenon itself, or the complexity of modeling. Performing artificial intelligence (AI) tasks such as segmentation, tracking, and analytics of small sub-cellul...

Fluorescence fluctuations-based super-resolution microscopy (FF-SRM) is an emerging field promising low-cost and live-cell compatible imaging beyond the resolution of conventional optical microscopy. A comprehensive overview on how the nature of fluctuations, label density, out-of-focus light, sub-cellular dynamics, and the sample itself influence...

Detecting and analyzing nanoscale motion patterns of vesicles, smaller than the microscope resolution (∼ 250 nm), inside living biological cells is a challenging problem. State-of-the-art CV approaches based on detection, tracking, optical flow or deep learning perform poorly on this problem. We propose an integrative approach built upon physics-ba...

We present an open-source implementation of the fluctuation-based nanoscopy method MUSICAL for ImageJ. This implementation improves the algorithm’s computational efficiency and takes advantage of multi-threading to provide orders of magnitude faster reconstructions than the original MATLAB implementation. In addition, the plugin is capable of gener...

Large fields of view (FOVs) in total internal reflection fluorescence microscopy (TIRFM) via waveguides have been shown to be highly beneficial for single molecule localisation microscopy on fixed cells [1,2] and have also been demonstrated for short‐term live‐imaging of robust cell types [3‐5], but not yet for delicate primary neurons nor over ext...

Large fields of view (FOVs) in total internal reflection fluorescence microscopy (TIRFM) via waveguides have been shown to be highly beneficial for single molecule localisation microscopy on fixed cells [1, 2] and have also been demonstrated for short-term live-imaging of robust cell types [3–5], but not yet for delicate primary neurons nor over ex...

Labelfree nanoscopy encompasses optical imaging with resolution in the 100 nm range using visible wavelengths. Here, we present a labelfree nanoscopy method that combines coherent imaging techniques with waveguide microscopy to realize a super-condenser featuring maximally inclined coherent darkfield illumination with artificially stretched wave ve...

Labelfree nanoscopy encompasses optical imaging with resolution in the 100 nm range using visible wavelengths. Here, we present a labelfree nanoscopy method that combines Fourier ptychography with waveguide microscopy to realize a 'super-condenser' featuring maximally inclined coherent darkfield illumination with artificially stretched wave vectors...

Structural details of spermatozoa are interesting from the perspectives of fundamental biology and growing reproductive health problems. Studies of nanostructural details of these extremely motile cells have been limited to fixed cells, largely using electron microscopy. Here we provide the protocols for and demonstrate live-cell multi-color super-...

The dimensions of mitochondria are close to the diffraction limit of conventional light microscopy techniques, making the complex internal structures of mitochondria unresolvable. In recent years, new fluorescence-based optical imaging techniques have emerged, which allow for optical imaging below the conventional limit, enabling super-resolution (...