Balpreet Singh Ahluwalia

• Afzal, Bilal; Thiyagarajan, Dhivya Borra; Ahluwalia, Balpreet Singh; Dalmo, Roy Ambli & Wolfson, Deanna (2026). Uptake of different-sized microplastic particles in skin and corneal epithelial cells from Atlantic salmon. Environmental Sciences Europe. 38(1). doi: 10.1186/s12302-026-01413-9. Fulltekst i vitenarkiv Vis sammendrag

  Background Given the growing concern over ocean-bound microplastics and their impact on wild and aquacultured aquatic species, understanding the cellular response to such pollutants is crucial. Previous research has shown that salmon keratocyte cells, which form the key physical barrier, can internalize plastic polymers in the 400–1000 nm size range. However, whether there is any size limitation of particles is not yet known. As such, the current study aims to evaluate an approximate cut-off size of particles that could be internalized by fish skin and corneal keratocytes, together with viability upon exposure. Results In the current study, we exposed Atlantic salmon keratocytes to relatively large polystyrene (PS) particles for 24 h and analyzed ingestion or cell-association of particles using deconvolution fluorescence microscopy accompanied by cell viability tests. The present study showed that individual keratocytes internalized particles, where the size limit was approximately 15 µm, while sheaths of cells collectively contained 15–30 µm particles. A single cell could accommodate 1–3 particles in the 7–10 µm range. Cells in cell-sheaths, acting collectively, can accommodate larger particles (up to 30 µm) that individual cells cannot. A cell viability assay confirmed that the cells’ membranes mostly remained intact after exposure to particles up to 30 µm. Larger particles caused nuclear deformation, though nuclear internalization remains unconfirmed and requires further study. Despite particle uptake, keratocytes maintain membrane integrity, and most cells remained viable even after prolonged exposure. Conclusion This study shows that keratocytes can internalize polystyrene particles approx. up to 15 µm in size, with smaller particles being ingested in greater numbers. Although the cells were exposed for a prolonged period, only a minor fraction of cells showed nuclear membrane ruptures. These findings shed light on keratocyte particle internalization, offering insights into cellular responses to foreign particles like nanomaterials and microplastics.

• Kamboj, Ritish; Ahluwalia, Balpreet Singh & Dubey, Satish Kumar (2026). Single-shot pixel super-resolution lensless in-line holographic microscopy using object support constraints. Applied Optics. ISSN 1559-128X. 65(18), s. 6093–6103. doi: 10.1364/AO.598994. Fulltekst i vitenarkiv Vis sammendrag

  Digital lensless in-line holographic microscopy (DLIHM) enables compact, low-cost, wide field-of-view (FoV) quantitative phase imaging, but its resolution is often limited by the detector pixel pitch because high-frequency holographic fringes are undersampled. We present support-constrained aliasing-reduction pixel super-resolution (SCAR-PSR), a single-shot reconstruction framework that explicitly trades FoV for resolution gain by enforcing a known finite object support. SCAR-PSR recovers the phase with sub-pixel resolution from a single, highly undersampled diffraction intensity measurement. Using a calibrated USAF 1951 target image, the proposed method provides stable phase recovery, demonstrating a ~5 X resolution gain relative to the native sensor sampling. We further evaluate robustness under realistic detector constraints through photon-limited Poisson noise, bit-depth quantization, and convergence stability studies. These numerical results suggest a hardware-minimal route to motion-free, single-shot super-resolution in DLIHM, with potential applicability to high-speed imaging scenarios involving rapidly evolving phase objects.

• Suski, Damian M.; Cywińska, Maria; Winnik, Julianna; Józwik, Michał; Zdańkowski, Piotr & Ahmad, Azeem [Vis alle 8 forfattere av denne artikkelen] (2026). Uncertainty-Aware Bayesian Computational Imaging for Single-Shot Widefield Interferometric Nanometrology. Laser & Photonics reviews. ISSN 1863-8880. 20(12). doi: 10.1002/lpor.202503158. Fulltekst i vitenarkiv Vis sammendrag

  Widefield interferometry offers non-destructive, scalable nanometrology for semiconductor photonics, but prevailing pipelines require multi-frame scanning (or phase-shifting) and postprocessing of reconstructed noise-limited phase, and do not provide single-shot, geometry-level uncertainties. We introduce an uncertainty-aware Bayesian computational imaging framework that estimates semiconductor waveguide geometry (e.g., height and width) directly from a single widefield interferogram, coupling an end-to-end intensity forward model with Dynamic Nested Sampling to return full posterior distributions and model evidence. Operating in the intensity domain avoids noise transfer to reconstructed topography and remains reliable under low-signal and sub-pixel fringe-shift conditions. Working in a widefield mode is a vital advantage of our Bayesian method, due to fully developed statistics over many pixels in a large field of view, significantly reducing the estimation uncertainties. We successfully validate performance in simulations showing sub-nanometer height precision and nanometric width accuracy, and in experiments on a metrologically certified 15 nm calibration step and a rib waveguide (design height 8 nm). The framework is model-agnostic and, given an appropriate forward model and priors, is in principle extendable to other nanostructures. By unifying single-shot acquisition with probabilistic inference, we establish Bayesian computational nanometrology as a potential route to widefield, uncertainty-quantified measurements for semiconductor nanophotonics and process-level monitoring.

• Afzal, Bilal; Mikkelborg, Marie Kristin; Thiyagarajan, Dhivya Borra; Wolfson, Deanna; Ahluwalia, Balpreet Singh & Dalmo, Roy Ambli [Vis alle 7 forfattere av denne artikkelen] (2026). Real-time snapping dynamics and nanoscale thickness profiling of salmon keratocyte tunneling nanotubes using partially coherent quantitative phase microscopy. Scientific Reports. 16(1). doi: 10.1038/s41598-026-46064-1. Fulltekst i vitenarkiv Vis sammendrag

  Fish skin epithelial cells, known as keratocytes, are highly migratory and exhibit distinctive morphological features, including elongated membrane protrusions called tunneling nanotubes (TNTs). In other cell types, TNTs have been reported to facilitate the intercellular transfer of various cellular cargo. Beyond cargo transport, these structures are also implicated in mediating intercellular signaling. Owing to their extremely small heights, often as low as 100 nm or less, reliable characterization of their morphology and dynamics necessitates the use of a highly sensitive quantitative phase microscopy technique. In this study, a partially spatially coherent quantitative phase microscopy (QPM) system was utilized, providing extremely high spatial sensitivity to track changes in TNT height over time, particularly during the snapping process. A five-frame phase-shifting technique was employed to recover high-resolution phase maps of the TNTs. Observations indicate that TNT height typically ranges from 100 to 900 nm. Additionally, the average height-to-width ratio indicates that the TNTs exhibit a more flattened rather than cylindrical geometry. Further, during the imaging period, diverse behaviors were observed: some TNTs remained intact and maintained structural integrity for the entire duration of the recording, whereas others exhibited rupture. Beyond morphological characterization, this work may open new avenues for understanding TNT’s potential role in the transfer of intracellular cargo, paving the way for future investigations into cellular communication mechanisms.

• Swain, Jaya Kumari; Wolfson, Deanna; Swain, Trilochan; Flaten, Gøril Eide; Skalko-Basnet, Natasa & Ahluwalia, Balpreet Singh [Vis alle 7 forfattere av denne artikkelen] (2026). Delivery and uptake of free and liposome-encapsulated cholesterol-conjugated antisense oligonucleotides in Atlantic salmon sperm: insights from high-resolution imaging. BMC Veterinary Research. 22(1), s. 1–10. doi: 10.1186/s12917-026-05465-0. Fulltekst i vitenarkiv Vis sammendrag

  The development of efficient methods for large-scale delivery of antisense molecules to Atlantic salmon (Salmo salar L.) eggs remains a significant challenge, limiting the application of antisense technologies in salmon aquaculture at an industrial scale. This study aimed to establish a proof of concept for a non-invasive, accessible method for delivering antisense oligonucleotides (ASOs) to salmon eggs using sperm cells as a delivery vehicle. Salmon spermatozoa were incubated for 24 h at 4 °C with a fluorescently labeled and cholesterol-conjugated antisense morpholino oligonucleotide (MO) in two formulations: cholesterol-conjugated antisense morpholino free in solution (F-MO) and cholesterol-conjugated antisense morpholino encapsulated into liposomes (L-MO). The binding and internalization patterns of F-MO and L-MO in spermatozoa were evaluated using fluorescence super-resolution microscopy. Both F-MO and L-MO incubations resulted in fluorescent binding in nearly 100% of the sperm cells, with distinct preferences for the head and tail regions of the sperm membrane. Notably, L-MO demonstrated superior internalization into the sperm head, as evidenced by higher fluorescence intensity within the head region compared to F-MO. Fertilization trials confirmed the successful transfer of L-MO to the egg, as indicated by visible fluorescence in the zygote. Moreover, incubation with either MO formulation did not adversely affect fertilization success or embryonic development up to the “eyed stage” under the experimental set-up conditions. In summary, high-resolution microscopy revealed enhanced uptake and internalization of L-MO compared to F-MO, enabling delivery and visualization of fluorescence in the one-cell embryo post-fertilization. These findings highlight the potential of sperm cells as a viable delivery vehicle for non-invasive transfer of MO oligonucleotides to salmon eggs. However, further research is required to optimize this approach and evaluate its scalability. Thus, this study provides a foundation for the development of cost-effective and practical ASO-based technologies for application in salmon aquaculture.

• Krysa, Mikolaj; Rogalski, Mikolaj; Arcab, Piotr; Goclowski, Pawel; Kalinowski, Kamil & Zdańkowski, Piotr [Vis alle 10 forfattere av denne artikkelen] (2026). High Space-Bandwidth Product Label-Free Examination of iPSC-Derived Brain Organoids via Fourier Ptychographic Microscopy. IEEE Journal of Selected Topics in Quantum Electronics. ISSN 1077-260X. 32(4). doi: 10.1109/JSTQE.2025.3650095. Fulltekst i vitenarkiv Vis sammendrag

  Fourier ptychographic microscopy (FPM) is a promising quantitative phase imaging technique that enables high-resolution, label-free imaging over a large field-of-view. Here, we present the first application of FPM for the quantitative analysis of human brain organoid slices, providing a powerful, cost-effective, and label-free enhancement to the current gold-standard fluorescence microscopy. Brain organoids, prepared as thin (5 μm) slices, were imaged with a custom-built FPM system consisting of a standard light microscope (4x, 0.2 NA objective) and a 7 × 7 LED array. This configuration achieved a synthetic numerical aperture of 0.54 and a spatial resolution of approximately 488 nm across an area of 2.077 × 3.65 mm. Fluorescence microscopy was used in parallel for neurons, astrocytes, and nuclei labeling, providing rich fluorescence imaging. Moreover, we designed an automated method to merge classical resolution fluorescence images to visualize the whole brain organoid and align it with the numerically increased space-bandwidth product FPM image. The provided alignment method enables rich phase-fluorescence correlative imaging. Based on the segmentation performed on the stitched fluorescence images, we devised a quantitative phase analysis revealing a higher mean optical thickness of the nuclei versus astrocytes and neurons. Notably, nuclei located in neurogenic regions consistently exhibited significantly higher phase values (optical path difference) compared to nuclei elsewhere, suggesting cell-type-specific biophysical signatures. The label-free, quantitative, and high-throughput capabilities of the FPM approach demonstrated here make it a powerful and accessible tool for future structural and functional studies of whole-section brain organoid development and disease modeling studies.

• Saxena, A.; Kumari, A.; Kumar, A.; Dhawan, S.; Kaur, H. & Dubey, S. K. [Vis alle 8 forfattere av denne artikkelen] (2026). Advancing histology with LED-based evanescent field illumination technique. Proceedings of SPIE. ISSN 0277-786X. 13849. doi: 10.1117/12.3086311. Fulltekst i vitenarkiv Vis sammendrag

  Histological analysis requires wide-field imaging to capture the spatial heterogeneity of healthy and diseased tissue. We present a compact LED-based total internal reflection fluorescence (LED-TIRF) microscopy platform that enables highcontrast, surface-selective fluorescence imaging over large fields of view. The system is integrated with conventional bright-field and epi-fluorescence modalities, providing a multimodal framework for comprehensive tissue evaluation. The platform was validated using formalin-fixed paraffin-embedded (FFPE) human lung tissue sections, including canceraffected regions. LED-TIRF imaging enhanced membrane-associated and fine structural features while effectively suppressing tissue and paraffin-induced autofluorescence compared to conventional fluorescence imaging. Bright-field and epi-fluorescence imaging complemented the TIRF modality, allowing for correlated structural and fluorescence-based assessments. The underlying optical design was systematically examined, demonstrating the feasibility of using standard histological glass slides as planar waveguides for generating evanescent fields under LED illumination. This framework supports accessible, slide-based fluorescence imaging with potential for scalable clinical histopathology applications.

• Jayakumar, Nikhil & Ahluwalia, Balpreet Singh (2025). From superior contrast to super resolution label free optical microscopy. NPJ Imaging. 3(1). doi: 10.1038/s44303-024-00064-w. Fulltekst i vitenarkiv Vis sammendrag

  Label-free optical microscopy utilizes the information encoded in light scattered off unlabeled particles to generate the images. This review article starts off with a discussion on how this light matter interaction gives rise to the issues of poor-contrast and diffraction-limited spatial resolution. Then, this article reviews the various far-field label-free optical microscopy techniques that have been developed, with an emphasis on the physical mechanisms behind the image formation processes in such techniques. Thus the article aims to elucidate the various state-of-the-art label-free techniques and their current applications.

• Villegas-Hernández, Luis Enrique; Dubey, Vishesh Kumar; Acharya, Ganesh & Ahluwalia, Balpreet Singh (2025). Optical super-resolution histology of formalin-fixed paraffin-embedded tissue samples: challenges and opportunities. Nature Communications. 16(1). doi: 10.1038/s41467-025-64626-1. Fulltekst i vitenarkiv
• Habib, Anowarul; Mateos, Paula Casasano; Dubey, Vishesh Kumar; Ahmad, Azeem; Acharya, Ganesh & Ahluwalia, Balpreet Singh [Vis alle 8 forfattere av denne artikkelen] (2025). Non-invasive quantitative acoustic imaging of intact brain organoids for structural assessment in drug discovery. Materials Today Advances. 28. doi: 10.1016/j.mtadv.2025.100651. Fulltekst i vitenarkiv Vis sammendrag

  Quantitative characterization of microstructural variations in human brain organoids is essential for advancing both fundamental neuroscience and translational applications, such as drug discovery and understanding tissue development and pathology. In this study, intact human brain organoids were developed and imaged using high-frequency Scanning Acoustic Microscopy (SAM) with 40 MHz and 60 MHz transducers. Both transducers were experimentally characterized and numerically simulated to assess their performance and confirm their suitability for high-resolution acoustic imaging. The statistical distribution of the scattering amplitude was analyzed using the Rayleigh and Nakagami models to infer tissue heterogeneity. Multiple regions of interest (ROIs) within the organoid structures were examined, revealing that the Nakagami distribution–with its additional shape parameter–provided a better fit to experimental data, capturing subtle microstructural differences not evident in conventional B-mode images. Across all ROIs, the Nakagami shape parameter 𝑚 ranged from 0.62 to 0.99, corresponding to uniform neuroproliferative zones and heterogeneous differentiated regions, respectively, demonstrating the method’s ability to distinguish developmental compartments. These findings demonstrate hat statistical acoustic imaging, supported by transducer performance validation, provides a non-invasive and quantitative method for examining brain organoid architecture, facilitating enhanced evaluation of tissue response in preclinical drug development and studies of tissue growth and disease progression.

• Saxena, Anuj; Bhatt, Sunil; Das, Sathi; Mao, Hong; Tinguely, Jean-Claude & Dubey, Satish Kumar [Vis alle 8 forfattere av denne artikkelen] (2025). Coverslip-guided total internal reflection fluorescence microscopy for super-resolved bio-imaging. Optics and Laser Technology. ISSN 0030-3992. 192. doi: 10.1016/j.optlastec.2025.113729. Fulltekst i vitenarkiv
• Sharma, Sahil; Tiwari, Anupriya; Ahluwalia, Balpreet Singh & Joseph, Joby (2025). Absorption modulation-based non-linear structured illumination microscopy. Journal of Optics. ISSN 2040-8978. 27(9). doi: 10.1088/2040-8986/ae06b1. Fulltekst i vitenarkiv Vis sammendrag

  We propose a novel super-resolution microscopy technique, named absorption modulation-based non-linear structured illumination microscopy (AM-NLSIM), by utilizing the photochromic properties of a material, specifically azobenzene chain polymers. In the proposed technique, dual-wavelength sinusoidal illumination interacts with a layer of photochromic molecules, referred to as an absorption modulation layer. This interaction generates a non-linear illumination pattern encoding additional high-frequency components within the system’s passband. We present the theoretical foundation of AM-NLSIM, supported by numerical simulations. Simulations are performed on different samples, where the captured Moiré frames undergo a blind reconstruction approach tailored for non-linear SIM. The simulations demonstrate the utility of AM-NLSIM to achieve sub-50 nm resolution based on computer-generated images while maintaining the practicality of conventional linear SIM, i.e. using low-intensity, continuous-wave lasers and standard fluorophores.

• Jayakumar, Nikhil; Villegas-Hernández, Luis Enrique; Zhao, Weisong; Mao, Hong; Dullo, Firehun Tsige & Tinguely, Jean-Claude [Vis alle 9 forfattere av denne artikkelen] (2025). Chip-based label-free incoherent super-resolution optical microscopy. Light: Science & Applications (LSA). ISSN 2095-5545. 14(1). doi: 10.1038/s41377-025-01914-x. Fulltekst i vitenarkiv Vis sammendrag

  The photo-kinetics of fluorescent molecules have enabled the circumvention of the far-field optical diffraction limit. Despite its enormous potential, the necessity to label the sample may adversely influence the delicate biology under investigation. Thus, continued development efforts are needed to surpass the far-field label-free diffraction barrier. The statistical similarity or finite coherence of the scattered light off the sample in label-free mode hinders the application of existing super-resolution methods based on incoherent fluorescence imaging. In this article, we present physics and propose a methodology to circumvent this challenge by exploiting the photoluminescence (PL) of silicon nitride waveguides for near-field illumination of unlabeled samples. The technique is abbreviated EPSLON, Evanescently decaying Photoluminescence Scattering enables Label-free Optical Nanoscopy. We demonstrate that such an illumination has properties that mimic the photo-kinetics of nano-sized fluorescent molecules, i.e., such an illumination permits incoherence between the scattered fields from various locations on the sample plane. Thus, the illumination scheme enables the development of a far-field label-free incoherent imaging system that is linear in intensity and stable over time, thereby permitting the application of techniques like structured illumination microscopy (SIM) and intensity-fluctuation-based optical nanoscopy (IFON) in label-free mode to circumvent the diffraction limit. In this proof-of-concept work, we observed a two-point resolution of $$\sim$$ ~ 180 nm on super-resolved nanobeads and resolution improvements between 1.9× to 2.8× over the diffraction limit, as quantified using Fourier Ring Correlation (FRC), on various biological samples. We believe EPSLON is a step forward within the field of incoherent far-field label-free super-resolution microscopy that holds a key to investigating biological systems in their natural state without the need for exogenous labels.

• Winnik, Julianna; Zdańkowski, Piotr; Stefaniuk, Marzena; Ahmad, Azeem; Zuo, Chao & Ahluwalia, Balpreet Singh [Vis alle 7 forfattere av denne artikkelen] (2025). Gradient optical diffraction tomography. Communications Physics. 8(1). doi: 10.1038/s42005-025-02416-3. Fulltekst i vitenarkiv
• Cywińska, Maria; Józwik, Michał; Patorski, Krzysztof; Ahmad, Azeem; Ahluwalia, Balpreet Singh & Kemper, Björn [Vis alle 7 forfattere av denne artikkelen] (2025). DeepQuadrature: universal convolutional neural network enlarging space-bandwidth product in single-shot fringe pattern optical metrology. JPhys Photonics. 7(2). doi: 10.1088/2515-7647/adc219. Fulltekst i vitenarkiv
• Mirza, Sarfaraj; Bohane, Vivek; Ahluwalia, Balpreet Singh & John, Renu (2025). A hybrid model for structured illumination microscopy reconstruction using attention mechanism and deep Laplacian pyramid network with Fourier loss. Journal of Microscopy. ISSN 0022-2720. doi: 10.1111/jmi.70057. Fulltekst i vitenarkiv
• Bhatt, Sunil; Verma, Ashwani Kumar; Dastidar, Prabir G.; Kumar, Punit; Thapa, Pramila & Jacob, Tony George [Vis alle 11 forfattere av denne artikkelen] (2025). Investigation on morphological and molecular fingerprints of penguin brain using label-free optical imaging and spectroscopic techniques. Scientific Reports. 15(1). doi: 10.1038/s41598-024-76127-0. Fulltekst i vitenarkiv
• Dullo, Firehun Tsige; Jayakumar, Nikhil; Getz, Michael Norderhaug; Herbjørnrød, Aina Kristin; Dirdal, Christopher Andrew & Wright, Daniel Nilsen [Vis alle 10 forfattere av denne artikkelen] (2025). Low-loss, low-background aluminum oxide waveguide platform for broad-spectrum on-chip microscopy. Optics Letters. ISSN 0146-9592. 50(7), s. 2159–2162. doi: 10.1364/OL.551736. Fulltekst i vitenarkiv Vis sammendrag

  A versatile wide-spectrum photonic integrated circuit (PIC) platform, spanning from ultraviolet (UV) to infrared (IR) wavelengths, is essential for advancing on-chip optical microscopy and spectroscopy applications. The key desirable requirements for PICs are low-loss, low-autofluorescence background signals, and high-refractive index contrast (HIC) to enable compact designs. Here, we present a low-loss, low-autofluorescence aluminum oxide (Al2O3) waveguide platform developed using atomic layer deposition (ALD). At 405 nm, the Al2O3 strip waveguide exhibits an autofluorescence background approximately 200 times lower than silicon nitride (Si3N4) and a propagation loss of less than 0.5 dB/cm. We demonstrate the suitability of the Al2O3 platform for multicolor on-chip total internal reflection fluorescence (TIRF) and super-resolution optical microscopy. The proposed Al2O3 platform offers a promising solution for highly sensitive on-chip bioimaging and spectroscopy applications.

• Tiwari, Anupriya; Samanta, Krishnendu; Devinder, Shital; Ahluwalia, Balpreet Singh & Joseph, Joby (2025). Co-linear Hexa-Mirror-Based Multi-Periodic Structured Illumination Microscopy. Nano Letters. ISSN 1530-6984. 25(6), s. 2133–2140. doi: 10.1021/acs.nanolett.4c04799. Fulltekst i vitenarkiv
• Mao, Hong; Kruse, Larissa Dorothea; Li, Ruomei; Oteiza, Ana; Struck, Eike Christopher & Schürstedt, Jasmin [Vis alle 14 forfattere av denne artikkelen] (2024). Impact of oxidized low-density lipoprotein on rat liver sinusoidal endothelial cell morphology and function. npj Gut and Liver. 1(9). doi: 10.1038/s44355-024-00009-5. Fulltekst i vitenarkiv Vis sammendrag

  Atherogenesis is associated with elevated plasma levels of oxidized low-density lipoproteins (oxLDL). In vivo, oxLDL causes liver endothelial swelling, and disrupts liver sinusoidal endothelial cell (LSECs) fenestrations. We mapped the nanoscale kinetics of these changes in vitro in isolated rat LSECs challenged with oxLDL and monitored viability with endocytosis and cytotoxicity assays. OxLDL disrupted LSEC ultrastructure – increasing oxLDL concentrations and oxidation levels caused sieve plate loss, fenestration fusion, and gap formation. Importantly, these effects were not uniform across all LSECs. LSECs retained the ability to endocytose ligands irrespective of the presence of oxLDL. However, increasing oxidation levels and concentrations of oxLDL inhibited LSEC mediated degradation of endocytosed ligands. Viability was unaffected by any oxLDL challenge. In conclusion, oxLDL disrupts LSEC ultrastructural morphology in vitro but LSECs remain viable and mostly maintain the scavenging function during oxLDL challenge.

• Thiyagarajan, Dhivya Borra; Stette, Marie; Afzal, Muhammad Bilal; Ahluwalia, Balpreet Singh; Agarwal, Krishna & Dalmo, Roy Ambli [Vis alle 7 forfattere av denne artikkelen] (2024). 3D imaging shows nano- and microparticles are internalized by salmon skin and corneal epithelial cells. Frontiers in Marine Science. 11. doi: 10.3389/fmars.2024.1422748. Fulltekst i vitenarkiv Vis sammendrag

  The rising problem of plastic pollution is becoming one of the major environmental issues for the world. In the ocean, plastics undergo degradation into smaller microplastics (MPs) and nanoplastics (NPs). Wild fish and farmed salmon would likely be exposed to these NPs and MPs both through skin and through skin wounds. Keratocyte cells, located in the skin epithelial layer, are scavenger cells which may remove foreign materials and maintain the salmon’s health. They are therefore first in line to handle and to suffer from MP and NP exposure. While the impacts of MPs have been well studied in many different organisms, much less is known about the effects of NP exposure, particularly at the subcellular level. Here, we have used holotomographic and fluorescence microscopy to show that both skin and corneal salmon keratocyte cells fully internalize 500–1000 nm polystyrene particles, as well as inorganic 500 nm silica particles. The fact that corneal epithelial cells also take up particles is novel. Furthermore, some of these particles likely end up in lysosomal compartments within 2 hours of exposure. Here, we show that both conventional and new modalities of microscopy have a role to play to understand how micro- and nano particles affect epithelial cells.

• Saxena, Anuj; Ahmad, Azeem; Dubey, Vishesh Kumar; Mao, Hong; Kumar, Anand & Habib, Anowarul [Vis alle 9 forfattere av denne artikkelen] (2024). Single-shot quantitative differential phase contrast microscope using a single calcite beam displacer. Applied Optics. ISSN 1559-128X. 63(32), s. 8350–8358. doi: 10.1364/AO.536593. Fulltekst i vitenarkiv Vis sammendrag

  This paper presents the development of a single-shot, partially spatially coherent quantitative differential phase contrast microscopy (Q-DPCM) system. The optical scheme comprises a polarizer, lenses, calcite beam displacer, and analyzer, which can be seamlessly integrated to an existing bright-field microscopy system, transforming it into a Q-DPCM system. It utilizes a partially spatially coherent light source, enabling single-shot quantitative differential phase recovery of the specimens with high spatial phase sensitivity. It generates highly sensitive quantitative differential phase images of the specimens along one direction, like a gradient light interference microscopy (GLIM) system, using only a single interferogram. First, we validated the differential phase measurement capability of the system through experiments on polystyrene spheres (diameter 5.2 µm) and HeLa cells. Next, the system is utilized to generate quantitative phase maps of human red blood cells using two orthogonal differential interferograms recorded at two orientations of the calcite beam displacer. Further, the Q-DPCM system is implemented for 1-h time-lapse live cell monitoring, revealing the dynamics of intracellular granules such as nucleolus and lipids in U2OS cells.

• Das, Sathi; Tinguely, Jean-Claude; Kundu, Vrishty; Saxena, Kanchan; Ahluwalia, Balpreet Singh & Mehta, Dalip Singh (2024). Sculptured silicon nanopillars bridging face to face nanogaps with metal-insulator-metal coating for surface enhanced Raman spectroscopy. Surfaces and Interfaces. 44. doi: 10.1016/j.surfin.2023.103836. Fulltekst i vitenarkiv Vis sammendrag

  A multilayer structure of metal-insulator-metal (MIM) thin film on a sculptured silicon nanopillar (Si NP) is designed and optimized for surface-enhanced Raman spectroscopy (SERS) applications. A facile fabrication method of large-area periodic nanopillars was developed by combining reactive ion etching and monolayer polystyrene (PS) beads on a Si wafer to fabricate a regular array of Si NPs. The MIM-coated Si NP showed better Raman signal enhancement than a single metal layer-coated Si NP due to multidimensional coupled plasmonic enhancement at metal-dielectric interface. Further, the MIM-coated Si NPs showed better SERS activity than the MIM-coated unprocessed PS beads due to increased surface area for hotspot generation and coupling of plasmonic modes induced by the formation of closely located branches in sculpture pillar morphology. The shape- and size-dependent SERS activity of fabricated NPs and the dielectric gap layer variation for tuning plasmonic properties were investigated using rhodamine 6 G as a probe molecule. The investigation of plasmonic enhancement using finite difference time domain (FDTD) simulation provided insight into the distribution of hotspots and the amount of local electric field enhancement. Furthermore, the developed pillar exhibited distinct and enhanced peak of R6G up to 10⁻¹⁵ M concentrations.

• Rosen, Joseph; Alford, Simon; Allan, Blake; Anand, Vijayakumar; Arnon, Shlomi & Arockiaraj, Francis Gracy [Vis alle 83 forfattere av denne artikkelen] (2024). Roadmap on computational methods in optical imaging and holography [invited]. Applied physics B. ISSN 0946-2171. 130(9). doi: 10.1007/s00340-024-08280-3. Fulltekst i vitenarkiv Vis sammendrag

  Computational methods have been established as cornerstones in optical imaging and holography in recent years. Every year, the dependence of optical imaging and holography on computational methods is increasing significantly to the extent that optical methods and components are being completely and efficiently replaced with computational methods at low cost. This roadmap reviews the current scenario in four major areas namely incoherent digital holography, quantitative phase imaging, imaging through scattering layers, and super-resolution imaging. In addition to registering the perspectives of the modern-day architects of the above research areas, the roadmap also reports some of the latest studies on the topic. Computational codes and pseudocodes are presented for computational methods in a plug-and-play fashion for readers to not only read and understand but also practice the latest algorithms with their data. We believe that this roadmap will be a valuable tool for analyzing the current trends in computational methods to predict and prepare the future of computational methods in optical imaging and holography.

• Ahmad, Azeem; Goclowski, Pawel Piotr; Dubey, Vishesh Kumar; Trusiak, Maciej & Ahluwalia, Balpreet Singh (2024). High space–time bandwidth product imaging in low coherence quantitative phase microscopy. Scientific Reports. 14(1). doi: 10.1038/s41598-024-59874-y. Fulltekst i vitenarkiv Vis sammendrag

  Current low coherence quantitative phase microscopy (LC-QPM) systems suffer from either reduced field of view (FoV) or reduced temporal resolution due to the short temporal coherence (TC) length of the light source. Here, we propose a hybrid, experimental and numerical approach to address this core problem associated with LC-QPM. We demonstrate high spatial resolution and high phase sensitivity in LC-QPM at high temporal resolution. High space–time bandwidth product is achieved by employing incoherent light source for sample illumination in QPM to increase the spatial resolution and single-shot Hilbert spiral transform (HST) based phase recovery algorithm to enhance the temporal resolution without sacrificing spatial resolution during the reconstruction steps. The high spatial phase sensitivity comes by default due to the use of incoherent light source in QPM which has low temporal coherence length and does not generate speckle noise and coherent noise. The spatial resolution achieved by the HST is slightly inferior to the temporal phase-shifting (TPS) method when tested on a specimen but surpasses that of the single-shot Fourier transform (FT) based phase recovery method. Contrary to HST method, FT method requires high density fringes for lossless phase recovery, which is difficult to achieve in LC-QPM over entire FoV. Consequently, integration of HST algorithm with LC-QPM system makes an attractive route. Here, we demonstrate scalable FoV and resolution in single-shot LC-QPM and experimentally corroborate it on a test object and on both live and fixed biological specimen such as MEF, U2OS and human red blood cells (RBCs). LC-QPM system with HST reconstruction offer high-speed single-shot QPM imaging at high phase sensitivity and high spatial resolution enabling us to study sub-cellular dynamic inside U2OS for extended duration (3 h) and observe high-speed (50 fps) dynamics of human RBCs. The experimental results validate the effectiveness of the present approach and will open new avenues in the domain of biomedical imaging in the future.

• Haputhanthri, Udith; Herath, Kithmini; Hettiarachchi, Ramith; Kariyawasam, Hasindu; Ahmad, Azeem & Ahluwalia, Balpreet Singh [Vis alle 9 forfattere av denne artikkelen] (2024). Towards ultrafast quantitative phase imaging via differentiable microscopy [Invited]. Biomedical Optics Express. 15(3), s. 1798–1812. doi: 10.1364/BOE.504954. Fulltekst i vitenarkiv Vis sammendrag

  With applications ranging from metabolomics to histopathology, quantitative phase microscopy (QPM) is a powerful label-free imaging modality. Despite significant advances in fast multiplexed imaging sensors and deep-learning-based inverse solvers, the throughput of QPM is currently limited by the pixel-rate of the image sensors. Complementarily, to improve throughput further, here we propose to acquire images in a compressed form so that more information can be transferred beyond the existing hardware bottleneck of the image sensor. To this end, we present a numerical simulation of a learnable optical compression-decompression framework that learns content-specific features. The proposed differentiable quantitative phase microscopy (∂-QPM) first uses learnable optical processors as image compressors. The intensity representations produced by these optical processors are then captured by the imaging sensor. Finally, a reconstruction network running on a computer decompresses the QPM images post aquisition. In numerical experiments, the proposed system achieves compression of × 64 while maintaining the SSIM of ∼0.90 and PSNR of ∼30 dB on cells. The results demonstrated by our experiments open up a new pathway to QPM systems that may provide unprecedented throughput improvements.

• Das, Sathi; Tinguely, Jean-Claude; Obuobi, Sybil Akua Okyerewa; Basnet, Natasa Skalko; Saxena, Kanchan & Ahluwalia, Balpreet Singh [Vis alle 7 forfattere av denne artikkelen] (2024). Plasmonic nano-bowls for monitoring intra-membrane changes in liposomes, and DNA-based nanocarriers in suspension. Biomedical Optics Express. 15(4), s. 2293–2307. doi: 10.1364/BOE.517471. Fulltekst i vitenarkiv Vis sammendrag

  Programmable nanoscale carriers, such as liposomes and DNA, are readily being explored for personalized medicine or disease prediction and diagnostics. The characterization of these nanocarriers is limited and challenging due to their complex chemical composition. Here, we demonstrate the utilization of surface-enhanced Raman spectroscopy (SERS), which provides a unique molecular fingerprint of the analytes while reducing the detection limit. In this paper, we utilize a silver coated nano-bowl shaped polydimethylsiloxane (PDMS) SERS substrate. The utilization of nano-bowl surface topology enabled the passive trapping of particles by reducing mobility, which results in reproducible SERS signal enhancement. The biological nanoparticles’ dwell time in the nano-trap was in the order of minutes, thus allowing SERS spectra to remain in their natural aqueous medium without the need for drying. First, the geometry of the nano-traps was designed considering nanosized bioparticles of 50-150 nm diameter. Further, the systematic investigation of maximum SERS activity was performed using rhodamine 6 G as a probe molecule. The potential of the optimized SERS nano-bowl is shown through distinct spectral features following surface- (polyethylene glycol) and bilayer- (cholesterol) modification of empty liposomes of around 140 nm diameter. Apart from liposomes, the characterization of the highly crosslinked DNA specimens of only 60 nm in diameter was performed. The modification of DNA gel by liposome coating exhibited unique signatures for nitrogenous bases, sugar, and phosphate groups. Further, the unique sensitivity of the proposed SERS substrate displayed distinct spectral signatures for DNA micelles and drug-loaded DNA micelles, carrying valuable information to monitor drug release. In conclusion, the findings of the spectral signatures of a wide range of molecular complexes and chemical morphology of intra-membranes in their natural state highlight the possibilities of using SERS as a sensitive and instantaneous characterization alternative.

• Ranjan, Abhishek; Swain, Jaya Kumari; Ahluwalia, Balpreet Singh & Melandsø, Frank (2024). 3-D Visualization of Atlantic salmon skin through Ultrasound and Photoacoustic Microscopy. PLoS Computational Biology. ISSN 1553-734X. 20(10). doi: 10.1371/journal.pcbi.1011709. Fulltekst i vitenarkiv Vis sammendrag

  Significance Three-dimensional photoacoustic imaging (PAM) has emerged as a promising technique for non-invasive label-free visualization and characterization of biological tissues with high spatial resolution and functional contrast.<p> <p>Aim The application of PAM and ultrasound as a microscopy technique of study for Atlantic salmon skin is presented here. <p>Approach A custom ultrasound and photoacoustic experimental setup was used for conducting this experiment with a sample preparation method where the salmon skin is embedded in aga rose and lifted from the bottom of the petridish. <p>Results The results of C-scan, B-scan, and overlayed images of ultrasound and photoacoustic are presented. The results are then analyzed for understanding the pigment map and its relation to salmon behavior to external stimuli. The photoacoustic images are compared with the optical images and analyzed further. A custom colormap and alpha map is designed and the matrices responsible for PAM and ultrasound are inserted together to overlay the ultrasound image and PAM image on top of each other. <p>Conclusions In this study, we propose an approach that combines scanning acoustic microscopy (SAM) images with PAM images for providing a comprehensive understanding of the salmon skin tissue. Overlaying acoustic and photoacoustic images enabled unique visualization of tissue morphology, with respect to identification of structural features in the context of their pigment distribution.

• Das, Sathi; Saxena, Kanchan; Khezri, Abdolrahman; Dubey, Vishesh Kumar; Ahmad, Azeem & Tinguely, Jean-Claude [Vis alle 9 forfattere av denne artikkelen] (2023). Rapid identification of antimicrobial drug resistance strains of E-coli using SERS nanowire chip. Proceedings of SPIE, the International Society for Optical Engineering. ISSN 0277-786X. 12396. doi: 10.1117/12.2650578. Fulltekst i vitenarkiv Vis sammendrag

  We have investigated the enhanced Raman spectra of AMR bacteria strains of E. coli using silver coated silicon nanowires SERS assay. Three different E. coli strains, E. coli CCUG17620, NCTC 13441, and A239, were detected using two different excitation laser wavelengths. We found stable and enhanced SERS spectrum using 785 nm laser as opposed to 532 nm. Future development of SERS-chip could offer a reliable platform for direct identification of the pathogen in bio-fluid samples at strains level.

• Ströhl, Florian; Wolfson, Deanna; Opstad, Ida Sundvor; Hansen, Daniel Henry; Mao, Hong & Ahluwalia, Balpreet Singh (2023). Label-free superior contrast with c-band ultra-violet extinction microscopy. Light: Science & Applications (LSA). ISSN 2095-5545. 12(1). doi: 10.1038/s41377-023-01105-6. Fulltekst i vitenarkiv Vis sammendrag

  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 caused by the sample. Most cells are transparent at visible wavelengths, which means the imaginary component of their complex refractive index, also known as extinction coefficient k, is close to zero. Here, we explore the use of c-band ultra-violet (UVC) light for high-contrast high-resolution label-free microscopy, as k is naturally substantially higher in the UVC than at visible wavelengths. Using differential phase contrast illumination and associated processing, we achieve a 7- to 300-fold improvement in contrast compared to visible-wavelength and UVA differential interference contrast microscopy or holotomography, and quantify the extinction coefficient distribution within liver sinusoidal endothelial cells. With a resolution down to 215 nm, we are, for the first time in a far-field label-free method, able to image individual fenestrations within their sieve plates which normally requires electron or fluorescence superresolution microscopy. UVC illumination also matches the excitation peak of intrinsically fluorescent proteins and amino acids and thus allows us to utilize autofluorescence as an independent imaging modality on the same setup.

• Krishnendu, Samanta; Ahmad, Azeem; Tinguely, Jean-Claude; Ahluwalia, Balpreet Singh & Joseph, Joby (2023). Transmission structured illumination microscopy with tunable frequency illumination using tilt mirror assembly. Scientific Reports. 13(1). doi: 10.1038/s41598-023-27814-x. Fulltekst i vitenarkiv Vis sammendrag

  We present experimental demonstration of tilt-mirror assisted transmission structured illumination microscopy (tSIM) that offers a large field of view super resolution imaging. An assembly of custom-designed tilt-mirrors are employed as the illumination module where the sample is excited with the interference of two beams reflected from the opposite pair of mirror facets. Tunable frequency structured patterns are generated by changing the mirror-tilt angle and the hexagonal-symmetric arrangement is considered for the isotropic resolution in three orientations. Utilizing high numerical aperture (NA) objective in standard SIM provides super-resolution compromising with the field-of-view (FOV). Employing low NA (20X/0.4) objective lens detection, we experimentally demonstrate ∼ (0.56 mm× 0.35 mm) size single FOV image with ∼ 1.7- and ∼ 2.4-fold resolution improvement (exploiting various illumination by tuning tilt-mirrors) over the diffraction limit. The results are verified both for the fluorescent beads as well as biological samples. The tSIM geometry decouples the illumination and the collection light paths consequently enabling free change of the imaging objective lens without influencing the spatial frequency of the illumination pattern that are defined by the tilt-mirrors. The large and scalable FOV supported by tSIM will find usage for applications where scanning large areas are necessary as in pathology and applications where images must be correlated both in space and time.

• Saxena, Anuj; Ahmad, Azeem; Dubey, Vishesh Kumar; Habib, Anowarul; Dubey, Satish Kumar & Ahluwalia, Balpreet Singh [Vis alle 7 forfattere av denne artikkelen] (2023). Dynamic quantitative phase imaging using calcite crystal-based temporally stable interferometer. Journal of Modern Optics. ISSN 0950-0340. 70(19-21), s. 973–982. doi: 10.1080/09500340.2024.2365772. Fulltekst i vitenarkiv
• Ahmad, Azeem; Hettiarachchi, Ramith; Khezri, Abdolrahman; Ahluwalia, Balpreet Singh; Wadduwage, Dushan & Ahmad, Rafi (2023). Highly sensitive quantitative phase microscopy and deep learning aided with whole genome sequencing for rapid detection of infection and antimicrobial resistance. Frontiers in Microbiology. 14. doi: 10.3389/fmicb.2023.1154620. Fulltekst i vitenarkiv Vis sammendrag

  Current state-of-the-art infection and antimicrobial resistance (AMR) diagnostics are based on culture-based methods with a detection time of 48–96 h. Therefore, it is essential to develop novel methods that can do real-time diagnoses. Here, we demonstrate that the complimentary use of label-free optical assay with whole-genome sequencing (WGS) can enable rapid diagnosis of infection and AMR. Our assay is based on microscopy methods exploiting label-free, highly sensitive quantitative phase microscopy (QPM) followed by deep convolutional neural networks-based classification. The workflow was benchmarked on 21 clinical isolates from four WHO priority pathogens that were antibiotic susceptibility tested, and their AMR profile was determined by WGS. The proposed optical assay was in good agreement with the WGS characterization. Accurate classification based on the gram staining (100% recall for gram-negative and 83.4% for gram-positive), species (98.6%), and resistant/susceptible type (96.4%), as well as at the individual strain level (100% sensitivity in predicting 19 out of the 21 strains, with an overall accuracy of 95.45%). The results from this initial proof-of-concept study demonstrate the potential of the QPM assay as a rapid and first-stage tool for species, strain-level classification, and the presence or absence of AMR, which WGS can follow up for confirmation. Overall, a combined workflow with QPM and WGS complemented with deep learning data analyses could, in the future, be transformative for detecting and identifying pathogens and characterization of the AMR profile and antibiotic susceptibility.

• Ranjan, Abhishek; Ahmad, Azeem; Ahluwalia, Balpreet Singh & Melandsø, Frank (2023). Laser-Generated Scholte Waves in Floating Microparticles. Sensors. 23(4). doi: 10.3390/s23041776. Fulltekst i vitenarkiv Vis sammendrag

  This study aims to demonstrate the generation and detection of Scholte waves inside polystyrene microparticles. This was proven using both experimental analysis and COMSOL simulation. Microspheres of different sizes were excited optically with a pulsed laser (532 nm), and the acoustic signals were detected using a transducer (40 MHz). On analyzing the laser-generated ultrasound signals, the results obtained experimentally and from COMSOL are in close agreement both in the time and frequency domain. A simplified analysis of Scholte wave generation by laser irradiation for homogeneous, isotropic microspheres is presented. The theoretical wave velocity of the Scholte wave was calculated and found close to our experimental results. A representation of pressure wave motion showing the Scholte wave generation is presented at different times.

• Mao, Hong; Szafranska, Karolina; Kruse, Larissa Dorothea; Holte, Christopher Florian; Wolfson, Deanna & Ahluwalia, Balpreet Singh [Vis alle 13 forfattere av denne artikkelen] (2023). Effect of caffeine and other xanthines on liver sinusoidal endothelial cell ultrastructure. Scientific Reports. 13(1). doi: 10.1038/s41598-023-40227-0. Fulltekst i vitenarkiv Vis sammendrag

  Xanthines such as caffeine and theobromine are among the most consumed psychoactive stimulants in the world, either as natural components of cofee, tea and chocolate, or as added ingredients. The present study assessed if xanthines affect liver sinusoidal endothelial cells (LSEC). Cultured primary rat LSEC were challenged with xanthines at concentrations typically obtained from normal consumption of xanthine-containing beverages, food or medicines; and at higher concentrations below the in vitro toxic limit. The fenestrated morphology of LSEC were examined with scanning electron and structured illumination microscopy. All xanthine challenges had no toxic effects on LSEC ultrastructure as judged by LSEC fenestration morphology, or function as determined by endocytosis studies. All xanthines in high concentrations (150 μg/mL) increased fenestration frequency but at physiologically relevant concentrations, only theobromine (8 μg/mL) showed an effect. LSEC porosity was influenced only by high caffeine doses which also shifted the fenestration distribution towards smaller pores. Moreover, a dose-dependent increase in fenestration number was observed after caffeine treatment. If these compounds induce similar changes in vivo, age-related reduction of LSEC porosity can be reversed by oral treatment with theobromine or with other xanthines using targeted delivery.

• Das, Sathi; Saxena, Kanchan; Tinguely, Jean-Claude; Pal, Arijit; Wickramasinghe, Nima L. & Khezri, Abdolrahman [Vis alle 13 forfattere av denne artikkelen] (2023). SERS Nanowire Chip and Machine Learning-Enabled Classification of Wild-Type and Antibiotic-Resistant Bacteria at Species and Strain Levels. ACS Applied Materials & Interfaces. ISSN 1944-8244. 15(20), s. 24047–24058. doi: 10.1021/acsami.3c00612. Fulltekst i vitenarkiv Vis sammendrag

  Antimicrobial resistance (AMR) is a major health threat worldwide and the culture-based bacterial detection methods are slow. Surface-enhanced Raman spectroscopy (SERS) can be used to identify target analytes in real time with sensitivity down to the single-molecule level, providing a promising solution for the culture-free bacterial detection. We report the fabrication of SERS substrates having tightly packed silver (Ag) nanoparticles loaded onto long silicon nanowires (Si NWs) grown by the metal-assisted chemical etching (MACE) method for the detection of bacteria. The optimized SERS chips exhibited sensitivity down to 10–12 M concentration of R6G molecules and detected reproducible Raman spectra of bacteria down to a concentration of 100 colony forming units (CFU)/mL, which is a thousand times lower than the clinical threshold of bacterial infections like UTI (105 CFU/mL). A Siamese neural network model was used to classify SERS spectra from bacteria specimens. The trained model identified 12 different bacterial species, including those which are causative agents for tuberculosis and urinary tract infection (UTI). Next, the SERS chips and another Siamese neural network model were used to differentiate AMR strains from susceptible strains of Escherichia coli (E. coli). The enhancement offered by SERS chip-enabled acquisitions of Raman spectra of bacteria directly in the synthetic urine by spiking the sample with only 103 CFU/mL E. coli. Thus, the present study lays the ground for the identification and quantification of bacteria on SERS chips, thereby offering a potential future use for rapid, reproducible, label-free, and low limit detection of clinical pathogens.

• Arguello, Henry; Bacca, Jorge; Kariyawasam, Hasindu; Vargas, Edwin; Marquez, Miguel & Hettiarachchi, Ramith [Vis alle 13 forfattere av denne artikkelen] (2023). Deep Optical Coding Design in Computational Imaging: A data-driven framework. IEEE Signal Processing Magazine. ISSN 1053-5888. 40(2), s. 75–88. doi: 10.1109/MSP.2022.3200173. Fulltekst i vitenarkiv Vis sammendrag

  Computational optical imaging (COI) systems leverage optical coding elements (CEs) in their setups to encode a high-dimensional scene in a single or in multiple snapshots and decode it by using computational algorithms. The performance of COI systems highly depends on the design of its main components: the CE pattern and the computational method used to perform a given task. Conventional approaches rely on random patterns or analytical designs to set distribution of the CE. However, the available data and algorithm capabilities of deep neural networks (DNNs) have opened a new horizon in CE data-driven designs that jointly consider the optical and computational decoders. Specifically, by modeling the COI measurements through a fully differentiable image-formation model that considers the physics-based propagation of light and its interaction with the CEs, the parameters that define the CE and the computational decoder can be optimized in an end-to-end (E2E) manner. Moreover, by optimizing just CEs in the same framework, inference tasks can be performed from pure optics. This work surveys the recent advances in CE data-driven design and provides guidelines on how to parameterize different optical elements to include them in the E2E framework. As the E2E framework can handle different inference applications by changing the loss function and the DNN, we present low-level tasks such as spectral imaging reconstruction or high-level tasks such as pose estimation with privacy preservation enhanced by using optimal task-based optical architectures. Finally, we illustrate classification and 3D object-recognition applications performed at the speed of the light using all-optics DNNs.

• Ströhl, Florian; Bruggeman, Ezra; Rowlands, Christopher; Wolfson, Deanna & Ahluwalia, Balpreet Singh (2022). Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations. Microscopy research and technique (Print). ISSN 1059-910X. 85(5), s. 2016–2022. doi: 10.1002/jemt.24060. Fulltekst i vitenarkiv Vis sammendrag

  Vectorial diffraction simulations show that the PSF of a z-polarised emitter changes shape above a 0.7 NA of the image-forming lens and can thus impact novel microscopy techniques like OPM in single molecule studies.

• Somani, Ayush; Sekh, Arif Ahmed; Opstad, Ida Sundvor; Birgisdottir, Åsa birna; Myrmel, Truls & Ahluwalia, Balpreet Singh [Vis alle 9 forfattere av denne artikkelen] (2022). Virtual labeling of mitochondria in living cells using correlative imaging and physics-guided deep learning. Biomedical Optics Express. 13(10), s. 5495–5516. doi: 10.1364/BOE.464177. Fulltekst i vitenarkiv Vis sammendrag

  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 spread function in the learning of an adversarial neural network for improving virtual labeling. We show results (average Pearson correlation 0.86) significantly better than what was achieved by state-of-the-art (0.71) for virtual labeling of mitochondria. We also provide new insights into the virtual labeling problem and suggest additional metrics for quality assessment. The results show that our virtual labeling approach is a powerful way of segmenting and tracking individual mitochondria in bright-field images, results previously achievable only for fluorescently labeled mitochondria.

• Piccardo, Marco; Ginis, Vincent; Forbes, Andrew; Mahler, Simon; Friesem, Asher A. & Davidson, Nir [Vis alle 38 forfattere av denne artikkelen] (2022). Roadmap on multimode light shaping. Journal of Optics. ISSN 2040-8978. 24(1). doi: 10.1088/2040-8986/ac3a9d. Fulltekst i vitenarkiv
• Ahmad, Azeem; Jayakumar, Nikhil & Ahluwalia, Balpreet Singh (2022). Demystifying speckle field interference microscopy. Scientific Reports. 12(1). doi: 10.1038/s41598-022-14739-0. Fulltekst i vitenarkiv Vis sammendrag

  Dynamic speckle illumination (DSI) has recently attracted strong attention in the feld of biomedical imaging as it pushes the limits of interference microscopy (IM) in terms of phase sensitivity, and spatial and temporal resolution compared to conventional light source illumination. To date, despite conspicuous advantages, it has not been extensively implemented in the feld of phase imaging due to inadequate understanding of interference fringe formation, which is challenging to obtain in dynamic speckle illumination interference microscopy (DSI-IM). The present article provides the basic understanding of DSI through both simulation and experiments that is essential to build interference microscopy systems such as quantitative phase microscopy, digital holographic microscopy and optical coherence tomography. Using the developed understanding of DSI, we demonstrated its capabilities which enables the use of non-identical objective lenses in both arms of the interferometer and opens the fexibility to use user-defned microscope objective lens for scalable feld of view and resolution phase imaging. It is contrary to the present understanding which forces us to use identical objective lenses in conventional IM system and limits the applicability of the system for fxed objective lens. In addition, it is also demonstrated that the interference fringes are not washed out over a large range of optical path diference (OPD) between the object and the reference arm providing competitive edge over low temporal coherence light source based IM system. The theory and explanation developed here would enable wider penetration of DSI-IM for applications in biology and material sciences.

• Opstad, Ida Sundvor; Godtliebsen, Gustav; Ströhl, Florian; Myrmel, Truls; Ahluwalia, Balpreet Singh & Agarwal, Krishna [Vis alle 7 forfattere av denne artikkelen] (2022). Three-dimensional structured illumination microscopy data of mitochondria and lysosomes in cardiomyoblasts under normal and galactose-adapted conditions. Scientific Data. 9(1). doi: 10.1038/s41597-022-01207-7. Fulltekst i vitenarkiv Vis sammendrag

  This three-dimensional structured illumination microscopy (3DSIM) dataset was generated to highlight the suitability of 3DSIM to investigate mitochondria-derived vesicles (MDVs) in H9c2 cardiomyoblasts in living or fxed cells. MDVs act as a mitochondria quality control mechanism. The cells were stably expressing the tandem-tag eGFP-mCherry-OMP25-TM (outer mitochondrial membrane) which can be used as a sensor for acidity. A part of the dataset is showing correlative imaging of lysosomes labeled using LysoTracker in fxed and living cells. The cells were cultivated in either normal or glucose-deprived medium containing galactose. The resulting 3DSIM data were of high quality and can be used to undertake a variety of studies. Interestingly, many dynamic tubules derived from mitochondria are visible in the 3DSIM videos under both glucose and galactose-adapted growth conditions. As the raw 3DSIM data, optical parameters, and reconstructed 3DSIM images are provided, the data is especially suitable for use in the development of SIM reconstruction algorithms, bioimage analysis methods, and for biological studies of mitochondria.

• Shukla, Kaushik; Ahmad, Azeem; Ahluwalia, Balpreet Singh; Melandsø, Frank & Habib, Anowarul (2022). Finite element simulation of transmission and reflection of acoustic waves in the ultrasonic transducer. Japanese Journal of Applied Physics (JJAP). ISSN 0021-4922. 61. doi: 10.35848/1347-4065/ac5db1. Fulltekst i vitenarkiv Vis sammendrag

  In scanning acoustic microscopy (SAM), the image quality depends on several factors such as noise level, resolution, and interaction of the waves with sample boundaries. The theoretical equations for the reflection coefficient and transmission coefficient are suitable for plane boundaries but fail for curved/rough boundaries. We presented a finite element method-based modeling for the loss coefficients in SAM. A focused and unfocused lens with a flat object, furthermore a focused lens with a curved object was selected for loss coefficients calculation. The loss calculation in terms of energy for defining the acoustic reflection and transmission losses and its dependence on the radius of curvature of the test object has also been presented.

• Jayakumar, Nikhil; Dullo, Firehun Tsige; Dubey, Vishesh Kumar; Ahmad, Azeem; Ströhl, Florian & Cauzzo, Jennifer [Vis alle 11 forfattere av denne artikkelen] (2022). Multi-moded high-index contrast optical waveguide for super-contrast high-resolution label-free microscopy. Nanophotonics. ISSN 2192-8606. 11(15), s. 3421–3436. doi: 10.1515/nanoph-2022-0100. Fulltekst i vitenarkiv Vis sammendrag

  The article elucidates the physical mechanism behind the generation of superior-contrast and highresolution label-free images using an optical waveguide. Imaging is realized by employing a high index contrast multi-moded waveguide as a partially coherent light source. The modes provide near-field illumination of unlabeled samples, thereby repositioning the higher spatial frequencies of the sample into the far-field. These modes coherently scatter off the sample with different phases and are engineered to have random spatial distributions within the integration time of the camera. This mitigates the coherent speckle noise and enhances the contrast (2–10) × as opposed to other imaging techniques. Besides, the coherent scattering of the different modes gives rise to fluctuations in intensity. The technique demonstrated here is named chip-based Evanescent Light Scattering (cELS). The concepts introduced through this work are described mathematically and the high-contrast image generation process using a multi-moded waveguide as the light source is explained. The article then explores the feasibility of utilizing fluctuations in the captured images along with fluorescence-based techniques, like intensity-fluctuation algorithms, to mitigate poor-contrast and diffraction-limited resolution in the coherent imaging regime. Furthermore, a straight waveguide is demonstrated to have limited angular diversity between its multiple modes and therefore, for isotropic sample illumination, a multiple-arms waveguide geometry is used. The concepts introduced are validated experimentally via high-contrast label-free imaging of weakly scattering nanosized specimens such as extra-cellular vesicles (EVs), liposomes, nanobeads and biological cells such as fixed and live HeLa cells.

• Villegas, Luis; Dubey, Vishesh Kumar; Nystad, Mona; Tinguely, Jean-Claude; Coucheron, David Andre & Dullo, Firehun Tsige [Vis alle 18 forfattere av denne artikkelen] (2022). Chip-based multimodal super-resolution microscopy for histological investigations of cryopreserved tissue sections. Light: Science & Applications (LSA). ISSN 2095-5545. doi: 10.1038/s41377-022-00731-w. Fulltekst i vitenarkiv Vis sammendrag

  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 system complexity, high operating cost, lack of multi-modality, and lowthroughput imaging of these methods limit their wide adoption for histological analysis. In this study, we introduce the photonic chip as a feasible high-throughput microscopy platform for super-resolution imaging of histological samples. Using cryopreserved ultrathin tissue sections of human placenta, mouse kidney, pig heart, and zebrafish eye retina prepared by the Tokuyasu method, we demonstrate diverse imaging capabilities of the photonic chip including total internal reflection fluorescence microscopy, intensity fluctuation-based optical nanoscopy, single-molecule localization microscopy, and correlative light-electron microscopy. Our results validate the photonic chip as a feasible imaging platform for tissue sections and pave the way for the adoption of super-resolution high-throughput multimodal analysis of cryopreserved tissue samples both in research and clinical settings.

• Szafranska, Karolina; Neuman, Tanja; Baster, Zbigniew; Rajfur, Zenon; Szelest, Oskar & Holte, Christopher Florian [Vis alle 15 forfattere av denne artikkelen] (2022). From fixed-dried to wet-fixed to live-comparative super-resolution microscopy of liver sinusoidal endothelial cell fenestrations. Nanophotonics. ISSN 2192-8606. 11(10), s. 2253–2270. doi: 10.1515/nanoph-2021-0818. Fulltekst i vitenarkiv Vis sammendrag

  Fenestrations in liver sinusoidal endothelial cells (LSEC) are transcellular nanopores of 50–350 nm diameter that facilitate bidirectional transport of solutes and macromolecules between the bloodstream and the parenchyma of the liver. Liver diseases, ageing, and various substances such as nicotine or ethanol can negatively influence LSECs fenestrations and lead to defenestration. Over the years, the diameter of fenestrations remained the main challenge for imaging of LSEC in vitro. Several microscopy, or rather nanoscopy, approaches have been used to quantify fenestrations in LSEC to assess the effect of drugs and, and toxins in different biological models. All techniques have their limitations, and measurements of the “true” size of fenestrations are hampered because of this. In this study, we approach the comparison of different types of microscopy in a correlative manner. We combine scanning electron microscopy (SEM) with optical nanoscopy methods such as structured illumination microscopy (SIM) or stimulated emission depletion (STED) microscopy. In addition, we combined atomic force microscopy (AFM) with SEM and STED, all to better understand the previously reported differences between the reports of fenestration dimensions. We conclude that sample dehydration alters fenestration diameters. Finally, we propose the combination of AFM with conventional microscopy that allows for easy super-resolution observation of the cell dynamics with additional chemical information that can be traced back for the whole experiment. Overall, by pairing the various types of imaging techniques that provide topological 2D/3D/label-free/chemical information we get a deeper insight into both limitations and strengths of each type microscopy when applied to fenestration analysis.

• Rogalski, Mikołaj; Cywińska, Maria; Ahmad, Azeem; Patorski, Krzysztof; Micó, Vicente & Ahluwalia, Balpreet Singh [Vis alle 7 forfattere av denne artikkelen] (2022). Hilbert phase microscopy based on pseudo thermal illumination in the Linnik configuration. Optics Letters. ISSN 0146-9592. 47(22), s. 5793–5796. doi: 10.1364/OL.471858. Fulltekst i vitenarkiv
• Zapotoczny, Barlomiej; Szafranska, Karolina; Lekka, Malgorzata; Ahluwalia, Balpreet Singh & McCourt, Peter Anthony (2022). Tuning of Liver Sieve: The Interplay between Actin and Myosin Regulatory Light Chain Regulates Fenestration Size and Number in Murine Liver Sinusoidal Endothelial Cells. International Journal of Molecular Sciences. ISSN 1661-6596. 23(17). doi: 10.3390/ijms23179850. Fulltekst i vitenarkiv Vis sammendrag

  Liver sinusoidal endothelial cells (LSECs) facilitate the efficient transport of macromolecules and solutes between the blood and hepatocytes. The efficiency of this transport is realized via transcellular nanopores, called fenestrations. The mean fenestration size is 140 ± 20 nm, with the range from 50 nm to 350 nm being mostly below the limits of diffraction of visible light. The cellular mechanisms controlling fenestrations are still poorly understood. In this study, we tested a hypothesis that both Rho kinase (ROCK) and myosin light chain (MLC) kinase (MLCK)-dependent phosphorylation of MLC regulates fenestrations. We verified the hypothesis using a combination of several molecular inhibitors and by applying two high-resolution microscopy modalities: structured illumination microscopy (SIM) and scanning electron microscopy (SEM). We demonstrated precise, dose-dependent, and reversible regulation of the mean fenestration diameter within a wide range from 120 nm to 220 nm and the fine-tuning of the porosity in a range from ~0% up to 12% using the ROCK pathway. Moreover, our findings indicate that MLCK is involved in the formation of new fenestrations—after inhibiting MLCK, closed fenestrations cannot be reopened with other agents. We, therefore, conclude that the Rho-ROCK pathway is responsible for the control of the fenestration diameter, while the inhibition of MLCK prevents the formation of new fenestrations.

• Ahmad, Azeem; Habib, Anowarul; Dubey, Vishesh Kumar & Ahluwalia, Balpreet Singh (2022). Unbalanced low coherence interference microscopy. Optics and lasers in engineering. ISSN 0143-8166. 151. doi: 10.1016/j.optlaseng.2021.106932. Fulltekst i vitenarkiv Vis sammendrag

  Low coherence interference microscopy (LCIM) provides high spatial phase sensitivity, i.e., speckle free and coherent noise free quantitative phase images of the test specimens. Due to low temporal coherence (TC) length of the light source, LCIM requires precise adjustment of the optical path difference (OPD) between the object and the reference arm, which is only a few micrometers. Consequently, previously demonstrated LCIM systems are implemented with the use of identical objective lenses in both the arms and also known as balanced interferometric configuration. The use of identical objective lens hinders both the use of high numerical aperture objective lens and also the swift change of the objective lens during imaging. In the present work, LCIM is implemented with non-identical objective lenses in the object and the reference arm also called unbalanced optical configuration. A range of objective lenses 10 × /0.25NA, 20 × /0.45NA and 60 × /1.2NA are employed in the object arm of the system while keeping single objective lens 10 × /0.25NA in the reference arm. To resolve the challenges associated with unbalanced configuration, advanced iterative algorithm (AIA) and principal component analysis (PCA) algorithms are integrated to recover quadratic phase error free phase images of the test specimens. The capabilities of the proposed method are exhibited on various specimens like USAF resolution, step-like test object and for the biological cells, HeLa cells. The proposed approach enables scalable magnification and resolution by simply rotating the imaging objective turret without the need of changing objective lens in the reference arm.

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• Naqvi, Tania; Ahluwalia, Balpreet Singh & Ahmad, Rafi (2026). MBA/Ag-rGO SERS immunosensing Platform for Sensitive and Selective E.coli Detection in Complex Biological Medium. Fulltekst i vitenarkiv
• Naqvi, Tania; Ahluwalia, Balpreet Singh & Ahmad, Rafi (2025). Fabrication of SERS substrates for pathogen detection. Fulltekst i vitenarkiv
• Awasthi, Vimarsh & Ahluwalia, Balpreet Singh (2025). Raman Spectroscopy based Pathogen Detection. Fulltekst i vitenarkiv Vis sammendrag

  Raman Spectroscopy based classification among different species of pathogens and thereafter classifying among different strains of the same species.

• Ahluwalia, Balpreet Singh (2023). Advanced optical microscopy for bio-imaging application. Fulltekst i vitenarkiv
• Ahluwalia, Balpreet Singh (2023). Overview of optical microscopy activities at UiT. Fulltekst i vitenarkiv
• Ahluwalia, Balpreet Singh (2023). Super-resolution optical microscopy for life science. Fulltekst i vitenarkiv
• Ahluwalia, Balpreet Singh (2023). Development of advanced optical microscopy for bio-imaging application. Fulltekst i vitenarkiv
• Ahluwalia, Balpreet Singh (2023). Overview of the INTPART project. Fulltekst i vitenarkiv
• Hernandez, Luis Enrique Villegas; Dubey, Vishesh Kumar; Maldonado, Sebastian Andres Acuna; Mao, Hong; Tinguely, Jean-Claude & Agarwal, Krishna [Vis alle 7 forfattere av denne artikkelen] (2023). Photonic chip: a high-throughput multimodal nanoscopy platform for histopathology. Fulltekst i vitenarkiv
• Maldonado, Sebastian Andres Acuna; Opstad, Ida Sundvor; Hernandez, Luis Enrique Villegas; Ahluwalia, Balpreet Singh & Agarwal, Krishna (2023). MUSICAL: a family of computational techniques for fluorescence nanoscopy. Fulltekst i vitenarkiv
• Ahluwalia, Balpreet Singh (2023). Overview of fluorescence based advanced optical microscopy methods. Fulltekst i vitenarkiv
• Ahluwalia, Balpreet Singh (2023). Impact of Photons: Internet, security, space and beyond. Fulltekst i vitenarkiv
• Ahluwalia, Balpreet Singh (2023). Development of highly sensitive and high throughput Quantitative phase microscopy for life science and diagnosis. Fulltekst i vitenarkiv
• Ahluwalia, Balpreet Singh (2023). Development and Application of Highly Sensitive and High Throughput Quantitative Phase Microscopy for Life Sciences. Fulltekst i vitenarkiv
• Dubey, Vishesh Kumar; Ahmad, Azeem & Ahluwalia, Balpreet Singh (2023). Highly sensitive quantitative phase microscopy for biomedical imaging. Fulltekst i vitenarkiv
• Mehta, Dalip Singh; Tayal, Shilpa; Ahmad, Azeem; Bhatt, Sunil; Dubey, Vishesh Kumar & Butola, Ankit [Vis alle 7 forfattere av denne artikkelen] (2023). Effect of partial spatial coherence of light on quantitative phase microscopy of biological samples: improved spatial phase sensitivity, space-bandwidth product, and high accuracy in phase measurement. Fulltekst i vitenarkiv
• Jayakumar, Nikhil; Dubey, Vishesh Kumar; Ahluwalia, Balpreet Singh & Ahmad, Azeem (2023). Deciphering dynamic speckle illumination interference microscopy. Fulltekst i vitenarkiv
• Opstad, Ida Sundvor; Maldonado, Sebastian Andres Acuna; Ströhl, Stefan; Ströhl, Florian; Ahluwalia, Balpreet Singh & Agarwal, Krishna (2023). Blind reconstruction of challenging raw data outperforms commercial 3DSIM. Fulltekst i vitenarkiv
• Opstad, Ida Sundvor; Maldonado, Sebastian Andres Acuna; Ströhl, Stefan; Ströhl, Florian; Ahluwalia, Balpreet Singh & Agarwal, Krishna (2023). Blind reconstruction of challenging raw data outperforms commercial 3DSIM. Fulltekst i vitenarkiv Vis sammendrag

  Flash poster presentation

• Opstad, Ida Sundvor; Maldonado, Sebastian Andres Acuna; Birgisdottir, Åsa birna; Ahluwalia, Balpreet Singh & Agarwal, Krishna (2023). From super-resolution imaging to cellular dynamics. Fulltekst i vitenarkiv
• Ahluwalia, Balpreet Singh (2023). Development of highly sensitive and high throughput Quantitative phase microscopy for life science and diagnosis. Fulltekst i vitenarkiv
• Ahluwalia, Balpreet Singh (2023). Development of Photonics sensors for pathogen detection. Fulltekst i vitenarkiv
• Ahluwalia, Balpreet Singh (2023). Development of high-throughput on-chip optical nanoscopy and quantitative phase microscopy for life science. Fulltekst i vitenarkiv
• Maldonado, Sebastian Andres Acuna; Hernandez, Luis Enrique Villegas; Opstad, Ida Sundvor; Tinguely, Jean-Claude; Ahluwalia, Balpreet Singh & Agarwal, Krishna (2023). MUSICAL: results on chip nanoscopy. Fulltekst i vitenarkiv
• Tinguely, Jean-Claude; Dubey, Vishesh Kumar; Maldonado, Sebastian Andres Acuna; Opstad, Ida Sundvor; Hernandez, Luis Enrique Villegas & Ströhl, Florian [Vis alle 8 forfattere av denne artikkelen] (2023). Integrated optical circuits for multimodal super-resolution microscopy. Fulltekst i vitenarkiv
• Myhr, Anne Ingeborg; Wolfson, Deanna; Opstad, Ida Sundvor; Ahluwalia, Balpreet Singh; Thiyagarajan, Dhivya Borra & Blix, Torill Pauline Bakkelund [Vis alle 7 forfattere av denne artikkelen] (2023). Nano- and micro-plastics and fish: Novel methods for detection and the role of RRI in such research. Fulltekst i vitenarkiv Vis sammendrag

  Plastic production and use continues to grow, and after use most of it resides in landfills or is dispersed in the environment including oceans. Focus has recently turned towards the potential threat of degradation products – action from sunlight, wind, rain, waves and microbiota – potentially yielding e.g., nano- and microplastics (NPs and MPs, respectively). These degradation products are so-called secondary microplastics. The arctic marine environment is vulnerable to anthropogenic microplastics impact – where microplastics have been found abundant in many animal phyla as fragments larger than 0.25 mm. Due to methodological difficulties, the abundance of nanoparticles is more difficult to assess, thus the effects of the tiniest nanoplastics/particles on e.g., the skin cells of fish are largely unknown This project addresses the impact of NPs and MPs on Atlantic salmon skin health by introducing a systems biology approach. In this project we aim to develop new methods, including advanced microscopy and -omics technologies to answer fundamental questions: a) Whether the skin cells of salmon actively take up tiny plastic particles, b) Presence of any plastic polymer-specific biological effects, and c) Whether wounded fish (e.g., sea lice infected fish) especially suffer from uptake of NPs and MPs. This will be investigated by studying: 1) Uptake mechanism in fish keratocytes (skin cells) by advanced superresolution nanoscopy, 2) Transcriptomic and proteomic response, 3) Aberration of metabolism by cells exposed to NPs and MPs, and to find 4) Correlation between plastic type and impacts. In the presentation we will present our novel methodological approach (advanced microscopy to study uptake of nanoparticles) and how we apply RRI (responsible research and innovation) concepts to guide the development of our methodological approach. RRI is a science policy framework, which seeks to align scientific research and technological innovation with broader social values and can help to consider effects and potential impacts on the environment and society by such projects. The findings will be of crucial importance with respect to management on how environmental NPs and MPs affect fish, and this connects with agenda of RRI, where anticipation is one of the key dimensions. Anticipation can include a diversity of activities, and here we aim to identify uncertainties and knowledge gaps of relevance for risk assessments of NPs and MPs. As inclusion of stakeholders is a key objective in RRI, the project will engage several stakeholders including citizens, government, agencies and authorities, NGOs, and industries both with regard to the approach chosen in the project and about plastic degradation products in oceans. This project is in line with UN Sustainable Development Goals: No. 14 – Conserve and sustainably use the ocean, seas and marine resources, and No. 12 - Ensure sustainable consumption and production patterns.

• Bhatt, Sunil; Butola, Ankit; Maldonado, Sebastian Andres Acuna; Hansen, Daniel Henry; Tinguely, Jean-Claude & Mehta, Dalip Singh [Vis alle 8 forfattere av denne artikkelen] (2023). Quantitative phase imaging for tracing the motion of waveguide trapped bead particle. Fulltekst i vitenarkiv
• Dubey, Vishesh Kumar; Ahmad, Azeem; Hernandez, Luis Enrique Villegas; Mao, Hong; Nystad, Mona & Acharya, Ganesh Prasad [Vis alle 7 forfattere av denne artikkelen] (2023). Photonic-chip based multimodal optical imaging of formalin-fixed paraffin-embedded tissue sections (Conference Presentation). Fulltekst i vitenarkiv
• Haputhanthri, Udith; Herath, Kithmini; Hettiarachchi, Ramith; Kariyawasam, Hasindu; Ahmad, Azeem & Ahluwalia, Balpreet Singh [Vis alle 8 forfattere av denne artikkelen] (2023). From hours to seconds: towards 100x faster quantitative phase imaging via differentiable microscopy (Conference Presentation). Fulltekst i vitenarkiv
• Ahluwalia, Balpreet Singh; Ahmad, Azeem; Dubey, Vishesh Kumar & Butola, Ankit (2023). Quantitative phase microscopy for life science and diagnosis (Conference Presentation). Fulltekst i vitenarkiv
• Vanderpoorten, Oliver & Ahluwalia, Balpreet Singh (2022). Nanofluidic chips for sizing of single molecules and nanoparticles in solution. Fulltekst i vitenarkiv
• Vanderpoorten, Oliver & Ahluwalia, Balpreet Singh (2022). Nanolithography, Nanoscopy, Nanofluidics: Hybrid 2-photon lithography for wafer-scale nanofluidic chip fabrication and single molecule sizing in solution. Fulltekst i vitenarkiv
• Vanderpoorten, Oliver & Ahluwalia, Balpreet Singh (2022). “N3: Hybrid 2-photon lithography for wafer-scale nanofluidic chip fabrication”. Fulltekst i vitenarkiv
• Marco, Laia Hernandez; Vanderpoorten, Oliver & Ahluwalia, Balpreet Singh (2022). Nanofluidics as new analysis method in neurodegeneration and protein misfolding disease research. Fulltekst i vitenarkiv
• Villegas, Luis; Dubey, Vishesh Kumar; Nystad, Mona; Fenton, Kristin Andreassen; Acharya, Ganesh & Mateos, Jose M. [Vis alle 8 forfattere av denne artikkelen] (2022). Chip-based multimodal microscopy for histological investigations of cryopreserved tissue sections. Fulltekst i vitenarkiv
• Hutmacher, Felix; Opstad, Ida Sundvor; Ahluwalia, Balpreet Singh & Fuchshofer, Rudolf (2022). Super-resolution imaging of Schlemm’s canal using 3D SIM. Fulltekst i vitenarkiv
• Tinguely, Jean-Claude; Opstad, Ida Sundvor; Acuña, Sebastian; Villegas-Hernandez, Luis E.; Dubey, Vishesh & Ströhl, Florian [Vis alle 8 forfattere av denne artikkelen] (2022). Integrated photonics for super-resolution microscopy. Fulltekst i vitenarkiv
• Opstad, Ida Sundvor; Wolfson, Deanna; Ahluwalia, Balpreet Singh; Agarwal, Krishna; Seternes, Tore & Dalmo, Roy Ambli (2022). Diving into fish skin: understanding cell avalanches and migrating keratocytes. Fulltekst i vitenarkiv
• Opstad, Ida Sundvor; Hansen, Daniel Henry; Maldonado, Sebastian Andres Acuna; Ströhl, Florian; Priyadarshi, Anish & Tinguely, Jean-Claude [Vis alle 11 forfattere av denne artikkelen] (2022). Large area super-resolution TIRFM of arctic fish species. Fulltekst i vitenarkiv
• Opstad, Ida Sundvor; Godtliebsen, Gustav; Ahluwalia, Balpreet Singh; Myrmel, Truls; Agarwal, Krishna & Birgisdottir, Åsa birna (2022). Mitochondrial dynamics and quantification of mitochondria-derived vesicles (MDVs) in cardiomyoblasts using 3DSIM. Fulltekst i vitenarkiv
• Jayakumar, Nikhil; Dullo, Firehun Tsige; Dubey, Vishesh Kumar; Ahmad, Azeem; Ströhl, Florian & Cauzzo, Jennifer [Vis alle 11 forfattere av denne artikkelen] (2022). Erratum: Multi-moded high-index contrast optical waveguide for super-contrast high-resolution label-free microscopy (Nanophotonics DOI: 10.1515/nanoph-2022-0500.pdf). Nanophotonics. ISSN 2192-8606. doi: 10.1515/nanoph-2022-0500. Fulltekst i vitenarkiv
• Villegas, Luis; Dubey, Vishesh Kumar & Ahluwalia, Balpreet Singh (2022). Photonic chip: a versatile nanoscopy platform for histopathology. Fulltekst i vitenarkiv
• Butola, Ankit; Coucheron, David Andre; Szafranska, Karolina; Ahmad, Azeem; Mao, Hong & Tinguely, Jean-Claude [Vis alle 11 forfattere av denne artikkelen] (2022). Quantitative phase imaging and on-chip nanoscopy for 3D imaging of liver sinusoidal endothelial cells. Fulltekst i vitenarkiv
• Villegas, Luis; Dubey, Vishesh Kumar & Ahluwalia, Balpreet Singh (2022). Super-resolution histopathology on a photonic chip. Fulltekst i vitenarkiv
• Villegas, Luis; Dubey, Vishesh Kumar & Ahluwalia, Balpreet Singh (2022). Towards high-resolution histopathology via evanescent-field excitation. Fulltekst i vitenarkiv
• Villegas, Luis; Dubey, Vishesh Kumar & Ahluwalia, Balpreet Singh (2022). Photonic chip: a versatile nanoscopy platform for histopathology. Fulltekst i vitenarkiv
• Ahmad, Azeem; Dubey, Vishesh Kumar; Jayakumar, Nikhil; Nystad, Mona & Ahluwalia, Balpreet Singh (2022). Deciphering dynamic speckle illumination interference microscopy and its applications. Spie Bios. Fulltekst i vitenarkiv
• Dubey, Vishesh Kumar; Ahmad, Azeem; Villegas-Hernández, Luis Enrique; Mao, Hong; Nystad, Mona & Acharya, Ganesh [Vis alle 7 forfattere av denne artikkelen] (2022). Photonic-chip based multimodal optical imaging of formalin-fixed paraffin-embedded tissue sections. Spie Bios. Fulltekst i vitenarkiv
• Opstad, Ida Sundvor; Godtliebsen, Gustav; Ahluwalia, Balpreet Singh; Myrmel, Truls; Agarwal, Krishna & Birgisdottir, Åsa birna (2022). Quantification of mitochondria‐derived vesicles in cardiomyoblasts using 3DSIM & machine learning-based segmentation. Fulltekst i vitenarkiv
• Bellankimath, Anurag Basavaraj; Ahmad, Rafi; Wilson, Robert Charles; Ahluwalia, Balpreet Singh & Johansen, Truls Erik Bjerklund (2026). Transforming urinary tract infection diagnostics: Clinical metagenomics for rapid pathogen identification and antimicrobial resistance profiling. Universitetet i Innlandet. ISSN 9788283806229. Fulltekst i vitenarkiv Vis sammendrag

  Urinary tract infections (UTIs) are among the most common bacterial infections world wide, impacting 405 million people and resulting in significant morbidity and healthcare costs. The routine diagnostic test, urine culture, takes 2-4 days to identify the pathogen and determine an appropriate antibiotic. This approach can lead to suboptimal clinical management, high antibiotic prescription rates, and improper use, which in turn foster antimicrobial resistance (AMR). Clinical metagenomics, which involves DNA sequencing of patient samples, offers a promising opportunity to revolutionize UTI diagnosis and treatment. Using Oxford Nanopore Technology (ONT), sequencing and data analysis can be performed in real-time. However, a crucial step for clinical application is the depletion of abundant human DNA, which dominates microbial DNA, as well as the removal of impurities and inhibitors present in the urine sample. Existing DNA extraction methods are not suitable for real-time sequencing because of their lengthy turnaround times, high costs, and challenges in managing clinical samples. The thesis aimed to develop, evaluate, and optimize DNA extraction methods for rapid pathogen identification and antibiotic susceptibility profiling in UTI diagnostics. We developed a culture-independent DNA extraction method that selectively removes human DNA and enriches microbial DNA. This method is accurate, fast, and cost-effective for clinical samples. In a proof-of-concept (PoC) study, urine samples from 78 patients with complicated UTI (cUTI) were evaluated using 11 different DNA extraction methods. The methods encompassed combinations of HL-SAN and M-SAN endonucleases, enzymatic and mechanical lysis strategies, and column and magnetic bead based DNA extraction techniques. Compared with routine culture-based diagnostic assays, the optimized method yielded the best pathogen identification performance (accuracy 99%, sensitivity 99%, specificity 100%) and antibiotic-susceptibility predictions (accuracy 90%, sensitivity 68%, specificity 95%). The method is also rapid, with a turnaround time of approximately 4 hours and a per sample cost of $36. Following modifications, a prospective validation study was carried out on an additional 296 cUTI samples, confirming pathogen identification performance consistent with the PoC study and slightly improved antibiotic susceptibility predictions. The limit of detection was 9.3 × 103 CFU/mL. The modifications also enabled the detection of Candida species, indicating the potential for comprehensive pathogen identification. The developed method’s usefulness extends beyond cUTI samples, as shown by the PoC study on blood cultures for diagnosing bloodstream infections. In this study, key parameters like saponin, endonucleases, and salt concentrations were fine tuned for the blood cultures. The optimized approach successfully depleted host material in blood cultures. In conclusion, the culture-independent sample preparation methods tackle the crucial challenge of DNA extraction from clinical samples. They provide a comprehensive and practical strategy to improve the diagnosis and management of UTIs and bloodstream infections, and to promote prudent antibiotic use and AMR stewardship. While additional validation is necessary, these findings show strong potential for broad clinical application and the potential to improve patient care.

• Goclowski, Pawel Piotr & Ahluwalia, Balpreet Singh (2026). Optical Diffraction Tomography for life sciences. UiT Norges arktiske universitet. ISSN 9788282366953. Fulltekst i vitenarkiv Vis sammendrag

  Quantitative phase microscopy (QPM) enables label-free measurement of local optical path length variations, providing critical insight into the structure and dynamics of transparent biological specimens. Optical diffraction tomography (ODT) merges principles of QPM with collecting angular projections to measure the three-dimensional refractive index (RI) distribution of the object. In this thesis a new versatile microscopy system is proposed, based on a novel double Sagnac common-path interferometric configuration combined with pseudo-thermal illumination. The system can be quickly switched between the two modalities: lateral shearing QPM (LS-QPM) for phase imaging of highly motile cells and lateral shearing ODT (LS-ODT) for refractive index reconstruction of heterogeneous thick samples. Proposed approach merges a few unique advantages, which contribute to the versatility of the system. Phase microscopy is by default a label-free, bio-friendly technique which provides quantitative information about the sample. Common-path configuration ensures temporal stability and high contrast interference fringes immune to multiple scattering. Single shot phase reconstruction enables high framerate imaging, while reduced coherence of the light provides superior spatial phase sensitivity. The approach is tested on large variety of specimens, including calibration objects (beads, cell phantoms), live cells, tissue sections and organoids.

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