Vishesh Kumar Dubey

• 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.

• 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; 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.

• 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.

• 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.

• Mann, Priyanka; Dubey, Vishesh Kumar; Ahmad, Azeem; Butola, Ankit & Mehta, Dalip Singh (2023). Synthetic wavelength scanning interferometry for 3D surface profilometry with extended range of height measurement using multi-colour LED light sources. Journal of Modern Optics. ISSN 0950-0340. doi: 10.1080/09500340.2023.2194454. Fulltekst i vitenarkiv Vis sammendrag

  We report three-dimensional surface profilometry with extended range of height measurements using synthetic wavelength scanning interferometry without tunable filters, wavelength-tuning lasers, grating elements. We have used inexpensive multiple colour light emitting diodes (LEDs) and operate them sequentially one by one or combination of two or more colours simultaneously to visualize synthetic wavelength light source. Multiple colour LED light source was synthesized and entire visible range from violet to deep red colour was covered. A wide range of synthetic wavelengths were obtained. Five step phase shifting algorithm was used to recover phase maps with Mirau type interferometer which can be further utilized for 3D height measurements. A simple phase subtraction method was used to reconstruct the phase map at synthetic wavelength. The present system provides extended range of height measurements from sub-wavelength to tens of wavelengths. Experimental results of 3D-surface profile measurements of Si-IC chip and standard step object are presented.

• 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
• 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.

• 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.

• 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.

• Juskewitz, Eric; Mischenko, Ekaterina; Dubey, Vishesh Kumar; Jenssen, Marte; Jakubec, Martin & Rainsford, Philip [Vis alle 9 forfattere av denne artikkelen] (2022). Lulworthinone: In Vitro Mode of Action Investigation of an Antibacterial Dimeric Naphthopyrone Isolated from a Marine Fungus. Marine Drugs. 20(5). doi: 10.3390/md20050277. Fulltekst i vitenarkiv Vis sammendrag

  Treatment options for infections caused by antimicrobial-resistant bacteria are rendered ineffective, and drug alternatives are needed—either from new chemical classes or drugs with new modes of action. Historically, natural products have been important contributors to drug discovery. In a recent study, the dimeric naphthopyrone lulworthinone produced by an obligate marine fungus in the family Lulworthiaceae was discovered. The observed potent antibacterial activity against Gram-positive bacteria, including several clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates, prompted this follow-up mode of action investigation. This paper aimed to characterize the antibacterial mode of action (MOA) of lulworthinone by combining in vitro assays, NMR experiments and microscopy. The results point to a MOA targeting the bacterial membrane, leading to improper cell division. Treatment with lulworthinone induced an upregulation of genes responding to cell envelope stress in Bacillus subtilis. Analysis of the membrane integrity and membrane potential indicated that lulworthinone targets the bacterial membrane without destroying it. This was supported by NMR experiments using artificial lipid bilayers. Fluorescence microscopy revealed that lulworthinone affects cell morphology and impedes the localization of the cell division protein FtsZ. Surface plasmon resonance and dynamic light scattering assays showed that this activity is linked with the compound‘s ability to form colloidal aggregates. Antibacterial agents acting at cell membranes are of special interest, as the development of bacterial resistance to such compounds is deemed more difficult to occur

• Villegas, Luis; Dubey, Vishesh Kumar; Tinguely, Jean-Claude; Coucheron, David Andre; Priyadarshi, Anish & Maldonado, Sebastian Andres Acuña [Vis alle 12 forfattere av denne artikkelen] (2021). Photonic-chip: a multimodal imaging tool for histopathology. Journal of the Optical Society of America. B, Optical physics. ISSN 0740-3224. doi: 10.1364/NTM.2021.NW3C.3. Fulltekst i vitenarkiv Vis sammendrag

  We propose the photonic-chip as a multimodal imaging platform for histopathological assessment, allowing large fields-of-view across diverse microscopy methods including total internal reflection fluorescence and single-molecule localization.

• Priyadarshi, Anish; Dullo, Firehun Tsige; Wolfson, Deanna; Ahmad, Azeem; Jayakumar, Nikhil & Dubey, Vishesh Kumar [Vis alle 9 forfattere av denne artikkelen] (2021). A transparent waveguide chip for versatile total internal reflection fluorescence-based microscopy and nanoscopy. Communications Materials. 2. doi: 10.1038/s43246-021-00192-5. Fulltekst i vitenarkiv Vis sammendrag

  Total internal reflection fluorescence (TIRF) microscopy is an imaging technique that, in comparison to confocal microscopy, does not require a trade-off between resolution, speed, and photodamage. Here, we introduce a waveguide platform for chip-based TIRF imaging based on a transparent substrate, which is fully compatible with sample handling and imaging procedures commonly used with a standard #1.5 glass coverslip. The platform is fabricated using standard complementary metal-oxide-semiconductor techniques which can easily be scaled up for mass production. We demonstrate its performance on synthetic and biological samples using both upright and inverted microscopes, and show how it can be extended to super-resolution applications, achieving a resolution of 116 nm using super resolution radial fluctuations. These transparent chips retain the scalable field of view of opaque chip-based TIRF and the high axial resolution of TIRF, and have the versatility to be used with many different objective lenses, microscopy methods, and handling techniques. We see this as a technology primed for widespread adoption, increasing both TIRF’s accessibility to users and the range of applications that can benefit from it.

• Maldonado, Sebastian Andres Acuna; ROY, MAYANK; Villegas, Luis; Dubey, Vishesh Kumar; Ahluwalia, Balpreet Singh & Agarwal, Krishna (2021). Deriving high contrast fluorescence microscopy images through low contrast noisy image stacks. Biomedical Optics Express. 12(9), s. 5529–5543. doi: 10.1364/BOE.422747. Fulltekst i vitenarkiv Vis sammendrag

  Contrast in fluorescence microscopy images allows for the differentiation between different structures by their difference in intensities. However, factors such as point-spread function and noise may reduce it, affecting its interpretability. We identified that fluctuation of emitters in a stack of images can be exploited to achieve increased contrast when compared to the average and Richardson-Lucy deconvolution. We tested our methods on four increasingly challenging samples including tissue, in which case results were comparable to the ones obtained by structured illumination microscopy in terms of contrast.

• Saxena, Anuj; Dubey, Vishesh Kumar; Singh, Veena; Tayal, Shilpa & Mehta, Dalip Singh (2021). Field Portable Total Internal Reflection Fluorescence Microscopy. Springer Proceedings in Physics. ISSN 0930-8989. s. 293–296. doi: 10.1007/978-981-15-9259-1_66. Fulltekst i vitenarkiv
• Kumar, Anand; Ahmad, Azeem; Dubey, Vishesh Kumar; Butola, Ankit & Mehta, Dalip Singh (2021). Effect of Detector’s Noise in White Light Interferometry Based Quantitative Phase Microscopy. Springer Proceedings in Physics. ISSN 0930-8989. s. 621–624. doi: 10.1007/978-981-15-9259-1_143. Fulltekst i vitenarkiv
• Mann, Priyanka; Singh, Veena; Tayal, Shilpa; Dubey, Vishesh Kumar & Mehta, Dalip Singh (2021). White Light Interference Microscopy for Quantitative Phase Imaging of Biological Samples Using Hilbert Transform. Springer Proceedings in Physics. ISSN 0930-8989. s. 625–628. doi: 10.1007/978-981-15-9259-1_144. Fulltekst i vitenarkiv
• Bhatt, Sunil; Dubey, Vishesh Kumar & Mehta, Dalip Singh (2021). Longitudinal Spatial Coherence Gated Optical Tomography and Topography. Springer Proceedings in Physics. ISSN 0930-8989. s. 549–552. doi: 10.1007/978-981-15-9259-1_126. Fulltekst i vitenarkiv
• Ahmad, Azeem; Dubey, Vishesh Kumar; Jayakumar, Nikhil; Habib, Anowarul; Butola, Ankit & Nystad, Mona [Vis alle 10 forfattere av denne artikkelen] (2020). High throughput spatially sensitive single-shot quantitative phase microscopy. arXiv. Fulltekst i vitenarkiv
• Ahmad, Azeem; Dubey, Vishesh Kumar; Butola, Ankit; Ahluwalia, Balpreet Singh & Mehta, Dalip Singh (2020). Highly temporal stable, wavelength-independent, and scalable field-of-view common-path quantitative phase microscope. Journal of Biomedical Optics. ISSN 1083-3668. 25(11). doi: 10.1117/1.JBO.25.11.116501. Fulltekst i vitenarkiv Vis sammendrag

  <p><i>Significance:</i> High temporal stability, wavelength independency, and scalable field of view (FOV) are the primary requirements of a quantitative phase microscopy (QPM) system. The high temporal stability of the system provides accurate measurement of minute membrane fluctuations of the biological cells that can be an indicator of disease diagnosis. <p><i>Aim:</i> The main aim of this work is to develop a high temporal stable technique that can accurately quantify the cell’s dynamics such as membrane fluctuations of human erythrocytes. Further, the technique should be capable of acquiring scalable FOV and resolution at multiple wavelengths to make it viable for various biological applications. <p><i>Approach:</i> We developed a single-element nearly common path, wavelength-independent, and scalable resolution/FOV QPM system to obtain temporally stable holograms/interferograms of the biological specimens. <p><i>Results:</i> With the proposed system, the temporal stability is obtained ∼15  mrad without using any vibration isolation table. The capability of the proposed system is first demonstrated on USAF resolution chart and polystyrene spheres (4.5-μm diameter). Further, the system is implemented for single shot, wavelength-independent quantitative phase imaging of human red blood cells (RBCs) with scalable resolution using color CCD camera. The membrane fluctuation of healthy human RBCs is also measured and was found to be around 47 nm. <p><i>Conclusions:</i> Contrary to its optical counterparts, the present system offers an energy efficient, cost effective, and simple way of generating object and reference beam for the development of common-path QPM. The present system provides the flexibility to the user to acquire multi-wavelength quantitative phase images at scalable FOV and resolution.

• Butola, Ankit; Prasad, Dilip Kumar; Ahmad, Azeem; Dubey, Vishesh Kumar; Qaiser, Darakhshan & Srivastava, Anurag [Vis alle 9 forfattere av denne artikkelen] (2020). Deep learning architecture “LightOCT” for diagnostic decision support using optical coherence tomography images of biological samples. Biomedical Optics Express. 11(9), s. 5017–5031. doi: 10.1364/BOE.395487. Fulltekst i vitenarkiv Vis sammendrag

  Optical coherence tomography (OCT) is being increasingly adopted as a label-free and non-invasive technique for biomedical applications such as cancer and ocular disease diagnosis. Diagnostic information for these tissues is manifest in textural and geometric features of the OCT images, which are used by human expertise to interpret and triage. However, it suffers delays due to the long process of the conventional diagnostic procedure and shortage of human expertise. Here, a custom deep learning architecture, LightOCT, is proposed for the classification of OCT images into diagnostically relevant classes. LightOCT is a convolutional neural network with only two convolutional layers and a fully connected layer, but it is shown to provide excellent training and test results for diverse OCT image datasets. We show that LightOCT provides 98.9% accuracy in classifying 44 normal and 44 malignant (invasive ductal carcinoma) breast tissue volumetric OCT images. Also, >96% accuracy in classifying public datasets of ocular OCT images as normal, age-related macular degeneration and diabetic macular edema. Additionally, we show ∼96% test accuracy for classifying retinal images as belonging to choroidal neovascularization, diabetic macular edema, drusen, and normal samples on a large public dataset of more than 100,000 images. The performance of the architecture is compared with transfer learning based deep neural networks. Through this, we show that LightOCT can provide significant diagnostic support for a variety of OCT images with sufficient training and minimal hyper-parameter tuning. The trained LightOCT networks for the three-classification problem will be released online to support transfer learning on other datasets.

• Ahmad, Azeem; Dubey, Vishesh Kumar; Butola, Ankit; Tinguely, Jean-Claude; Ahluwalia, Balpreet Singh & Mehta, Dalip Singh (2020). Sub-nanometer height sensitivity by phase shifting interference microscopy under environmental fluctuations. Optics Express. 28(7), s. 9340–9358. doi: 10.1364/OE.384259. Fulltekst i vitenarkiv Vis sammendrag

  Phase shifting interferometric (PSI) techniques are among the most sensitive phase measurement methods. Owing to its high sensitivity, any minute phase change caused due to environmental instability results into, inaccurate phase measurement. Consequently, a well calibrated piezo electric transducer (PZT) and highly-stable environment is mandatory for measuring accurate phase map using PSI implementation. Here, we present an inverse approach, which can retrieve phase maps of the samples with negligible errors under environmental fluctuations. The method is implemented by recording a video of continuous temporally phase shifted interferograms and phase shifts were calculated between all the data frames using Fourier transform algorithm with a high accuracy ≤ 5.5 × 10⁻⁴ π rad. To demonstrate the robustness of the proposed method, a manual translation of the stage was employed to introduce continuous temporal phase shift between data frames. The developed algorithm is first verified by performing quantitative phase imaging of optical waveguide and red blood cells using uncalibrated PZT under the influence of vibrations/air turbulence and compared with the well calibrated PZT results. Furthermore, we demonstrated the potential of the proposed approach by acquiring the quantitative phase imaging of an optical waveguide with a rib height of only 2 nm and liver sinusoidal endothelial cells (LSECs). By using 12-bit CMOS camera the height of shallow rib waveguide is measured with a height sensitivity of 4 Å without using PZT and in presence of environmental fluctuations.

• Butola, Ankit; Kanade, Sheetal Raosaheb; Bhatt, Sunil; Dubey, Vishesh Kumar; Kumar, Anand & Ahmad, Azeem [Vis alle 10 forfattere av denne artikkelen] (2020). High space-bandwidth in quantitative phase imaging using partially spatially coherent digital holographic microscopy and a deep neural network. Optics Express. 28(24), s. 36229–36244. doi: 10.1364/OE.402666. Fulltekst i vitenarkiv Vis sammendrag

  Quantitative phase microscopy (QPM) is a label-free technique that enables monitoring of morphological changes at the subcellular level. The performance of the QPM system in terms of spatial sensitivity and resolution depends on the coherence properties of the light source and the numerical aperture (NA) of objective lenses. Here, we propose high space-bandwidth quantitative phase imaging using partially spatially coherent digital holographic microscopy (PSC-DHM) assisted with a deep neural network. The PSC source synthesized to improve the spatial sensitivity of the reconstructed phase map from the interferometric images. Further, compatible generative adversarial network (GAN) is used and trained with paired low-resolution (LR) and high-resolution (HR) datasets acquired from the PSC-DHM system. The training of the network is performed on two different types of samples, i.e. mostly homogenous human red blood cells (RBC), and on highly heterogeneous macrophages. The performance is evaluated by predicting the HR images from the datasets captured with a low NA lens and compared with the actual HR phase images. An improvement of 9× in the space-bandwidth product is demonstrated for both RBC and macrophages datasets. We believe that the PSC-DHM + GAN approach would be applicable in single-shot label free tissue imaging, disease classification and other high-resolution tomography applications by utilizing the longitudinal spatial coherence properties of the light source.

• Ahmad, Azeem; Kumar, Anand; Dubey, Vishesh Kumar; Butola, Ankit; Ahluwalia, Balpreet Singh & Mehta, Dalip Singh (2019). Characterization of color cross-talk of CCD detectors and its influence in multispectral quantitative phase imaging. Optics Express. 27(4), s. 4572–4589. doi: 10.1364/OE.27.004572. Fulltekst i vitenarkiv Vis sammendrag

  Multi-spectral quantitative phase imaging (QPI) is an emerging imaging modality for wavelength dependent studies of several biological and industrial specimens. Simultaneous multi-spectral QPI is generally performed with color CCD cameras. Here, we present a new approach for accurately measuring the color crosstalk of 2D area detectors, without needing prior information about camera specifications. Color crosstalk is systematically studied and compared using compact interference microscopy on two different cameras commonly used in QPI, single chip CCD (1-CCD) and three chip CCD (3-CCD). The influence of color crosstalk on the fringe width and the visibility of the monochromatic constituents corresponding to three color channels of white light interferogram are studied both through simulations and experiments. It is observed that presence of color crosstalk changes the fringe width and visibility over the imaging field of view. This leads to an unwanted non-uniform background error in the multi-spectral phase imaging of the specimens. The color crosstalk of the detector is observed to be the limiting factor for phase measurement accuracy of simultaneous multi-spectral QPI systems.

• Dubey, Vishesh Kumar; Ahmad, Azeem; Butola, Ankit; Qaiser, Darakhshan; Srivastava, Anurag & Mehta, Dalip Singh (2019). Low coherence quantitative phase microscopy with machine learning model and Raman spectroscopy for the study of breast cancer cells and their classification. Applied Optics. ISSN 1559-128X. 58(5), s. A112–A119. doi: 10.1364/AO.58.00A112. Fulltekst i vitenarkiv
• Butola, Ankit; Ahmad, Azeem; Dubey, Vishesh Kumar; Srivastava, Vishal; Qaiser, Darakhshan & Srivastava, Anurag [Vis alle 8 forfattere av denne artikkelen] (2019). Volumetric analysis of breast cancer tissues using machine learning and swept-source optical coherence tomography. Applied Optics. ISSN 1559-128X. 58(5), s. A135–A141. doi: 10.1364/AO.58.00A135. Fulltekst i vitenarkiv
• Dubey, Vishesh Kumar; Popova, Daria; Ahmad, Azeem; Acharya, Ganesh; Basnet, Purusotam & Mehta, Dalip Singh [Vis alle 7 forfattere av denne artikkelen] (2019). Partially spatially coherent digital holographic microscopy and machine learning for quantitative analysis of human spermatozoa under oxidative stress condition. Scientific Reports. 9:3564, s. 1–10. doi: 10.1038/s41598-019-39523-5. Fulltekst i vitenarkiv Vis sammendrag

  Semen quality assessed by sperm count and sperm cell characteristics such as morphology and motility, is considered to be the main determinant of men’s reproductive health. Therefore, sperm cell selection is vital in assisted reproductive technology (ART) used for the treatment of infertility. Conventional bright field optical microscopy is widely utilized for the imaging and selection of sperm cells based on the qualitative analysis by experienced clinicians. In this study, we report the development of a highly sensitive quantitative phase microscopy (QPM) using partially spatially coherent light source, which is a label-free, non-invasive and high-resolution technique to quantify various biophysical parameters. The partial spatial coherence nature of light source provides a significant improvement in spatial phase sensitivity and hence reconstruction of the phase of the entire sperm cell is demonstrated, which was otherwise not possible using highly spatially coherent light source. High sensitivity of the system enables quantitative phase imaging of the specimens having very low refractive index contrast with respect to the medium like tail of the sperm cells. Further, it also benefits with accurate quantification of 3D-morphological parameters of sperm cells which might be helpful in the infertility treatment. The quantitative analysis of more than 2500 sperm cells under hydrogen peroxide (H2O2) induced oxidative stress condition is demonstrated. It is further correlated with motility of sperm cell to study the effect of oxidative stress on healthy sperm cells. The results exhibit a decrease in the maximum phase values of the sperm head as well as decrease in the sperm cell’s motility with increasing oxidative stress, i.e., H2O2 concentration. Various morphological and texture parameters were extracted from the phase maps and subsequently support vector machine (SVM) based machine learning algorithm is employed for the classification of the control and the stressed sperms cells. The algorithm achieves an area under the receiver operator characteristic (ROC) curve of 89.93% based on the all morphological and texture parameters with a sensitivity of 91.18%. The proposed approach can be implemented for live sperm cells selection in ART procedure for the treatment of infertility.

• Usmani, Kashif; Ahmad, Azeem; Joshi, Rakesh; Dubey, Vishesh Kumar; Butola, Ankit & Mehta, Dalip Singh (2019). Relationship between the source size at the diffuser plane and the longitudinal spatial coherence function of the optical coherence microscopy system. Optical Society of America. Journal A: Optics, Image Science, and Vision (JOSA A). ISSN 1084-7529. 36(12), s. D41–D46. doi: 10.1364/JOSAA.36.000D41. Fulltekst i vitenarkiv Vis sammendrag

  Coherence properties of light sources are indispensable for optical coherence microscopy/tomography as they greatly influence the signal-to-noise ratio, axial resolution, and penetration depth of the system. In the present paper, we report the investigation of longitudinal spatial coherence properties of a pseudothermal light source (PTS) as a function of the laser spot size at the rotating diffuser plate. The laser spot size is varied by translating a microscope objective lens toward or away from the diffuser plate. The longitudinal spatial coherence length, which governs the axial resolution of the coherence microscope, is found to be minimum for the beam spot size of 3.5 mm at the diffuser plate. The axial resolution of the system is found to be equal to an ∼13µm at 3.5 mm beam spot size. The change in the axial resolution of the system is confirmed by performing the experiments on standard gauge blocks of a height difference of 15 µm by varying the spot size at the diffuser plate. Thus, by appropriately choosing the beam spot size at the diffuser plane, any monochromatic laser light source can be utilized to obtain high axial resolution irrespective of the source’s temporal coherence length. It can provide speckle-free tomographic images of multilayered biological specimens with large penetration depth. In addition, a PTS avoids the use of any chromatic-aberration-corrected optics and dispersion-compensation mechanism unlike conventional setups.

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• 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
• Dubey, Vishesh Kumar (2023). Super-resolution fluorescence and quantitative phase imaging of biological samples. 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
• 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
• 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
• Ahluwalia, Balpreet Singh; Ahmad, Azeem; Dubey, Vishesh Kumar & Butola, Ankit (2023). Quantitative phase microscopy for life science and diagnosis (Conference Presentation). 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
• 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
• 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
• Villegas, Luis; Dubey, Vishesh Kumar; Ahluwalia, Balpreet Singh & Ahmad, Azeem (2021). Photonic-chip: a multimodal super-resolution imaging tool for histopathology. Fulltekst i vitenarkiv
• Jayakumar, Nikhil; Dullo, Firehun Tsige; Dubey, Vishesh Kumar; Ahmad, Azeem; Cauzzo, Jennifer & Guerreiro, Eduarda Mazagao [Vis alle 10 forfattere av denne artikkelen] (2021). Label-free imaging on waveguide platform with enhanced resolution and contrast. Fulltekst i vitenarkiv Vis sammendrag

  Chip-based Evanescent Light Scattering (cELS) utilizes the multiple modes of a high-index contrast optical waveguide for near-field illumination of unlabeled samples, thereby repositioning the highest spatial frequencies of the sample into the far-field. The multiple modes scattering off the sample with different phase differences is engineered to have random spatial distributions within the integration time of the camera, mitigating the coherent speckle noise. This enables label-free superior-contrast imaging of weakly scattering nanosized specimens such as extra-cellular vesicles (EVs) and liposomes, dynamics of living HeLa cells etc. We demonstrate a multi-moded straight waveguide as a partially coherent light source. For isotropic super-resolution, spatially incoherent light engineered via multiple-arms waveguide chip and intensity-fluctuation based algorithms are used. The proof-of-concept results are demonstrated on 100 nm polystyrene beads and resolution improvement of close to 2× is shown. cELS also realizes (2-10)× more contrast as opposed to conventional imaging techniques.

• Dubey, Vishesh Kumar; Hernández, Luis Enrique Villegas; Nystad, Mona; Tinguely, Jean-Claude; Coucheron, David Andre & Dullo, Firehun Tsige [Vis alle 18 forfattere av denne artikkelen] (2021). Photonic-chip for multimodal super-resolution imaging in histopathology applications. Fulltekst i vitenarkiv
• Dubey, Vishesh Kumar; Hernández, Luis Enrique Villegas; Tinguely, Jean-Claude; Coucheron, David Andre; Priyadarshi, Anish & Acuña, Sebastian [Vis alle 12 forfattere av denne artikkelen] (2021). Multimodal super-resolution imaging for histopathology applications. Fulltekst i vitenarkiv
• Hernandez, Luis Enrique Villegas; Dubey, Vishesh Kumar; Ströhl, Florian; Nystad, Mona; Basnet, Purusotam & Acharya, Ganesh [Vis alle 7 forfattere av denne artikkelen] (2020). NanoPath. High-throughput and high-resolution pathology using chip-based nanoscopy. Fulltekst i vitenarkiv
• Dubey, Vishesh Kumar (2020). Optical Nanoscopy at UiT The Arctic University of Norway. Fulltekst i vitenarkiv
• Dubey, Vishesh Kumar; Popova, Daria; Ahmad, Azeem; Acharya, Ganesh; Basnet, Purusotam & Mehta, Dalip Singh [Vis alle 7 forfattere av denne artikkelen] (2019). Author Correction: Partially spatially coherent digital holographic microscopy and machine learning for quantitative analysis of human spermatozoa under oxidative stress condition (Scientific Reports, (2019), 9, 1, (3564), 10.1038/s41598-019-39523-5). Scientific Reports. 9(1). doi: 10.1038/s41598-019-42490-6. Fulltekst i vitenarkiv
• Dubey, Vishesh Kumar; Ahmad, Azeem; Singh, Rajwinder; Mehta, Dalip Singh & Ahluwalia, Balpreet Singh (2019). Digital holographic microscopy and machine learning approach for the classification of inflammation in macrophages. Fulltekst i vitenarkiv
• Ahmad, Azeem; Jayakumar, Nikhil; Butola, Ankit; Dubey, Vishesh Kumar; Mehta, Dalip Singh & Ahluwalia, Balpreet Singh (2019). High space-bandwidth product with high spatial phase sensitivity in single-shot digital holographic microscopy. Fulltekst i vitenarkiv
• Butola, Ankit; Popova, Daria; Ahmad, Azeem; Dubey, Vishesh Kumar; Acharya, Ganesh & Basnet, Purusotam [Vis alle 9 forfattere av denne artikkelen] (2019). Classification of human spermatozoa using quantitative phase imaging and machine learning. Fulltekst i vitenarkiv
• Ahmad, Azeem; Dubey, Vishesh Kumar; Butola, Ankit; Mehta, Dalip Singh & Ahluwalia, Balpreet Singh (2019). Novel highly stable wavelength independent quantitative phase microscope. Fulltekst i vitenarkiv

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