Journal publications
Research Outreach Interdisciplinary Activity to classify olive oil blends integrating multicolor imaging, image processing, and machine learning
Abstract: This outreach undergraduate research project presents a low-cost method to distinguish the quality of different olive oils. The proposed method is based on an indirect measurement of the chlorophyll molecules present when a green laser diode illuminates the oil sample. Oil blends can be classified into five classes (no olive oil, light olive oil, medium olive oil, olive oil, and extra virgin olive oil) by quantifying the ratio of the red channel versus the green channel along the laser illumination path from a color image. After labeling each oil blend, a convolutional neural network has been implemented and trained to automatically classify oil blends from a color image. The trained convolutional neural network has an accuracy of 90% in identifying and categorizing oil blends. This undergraduate research project introduces students to an interdisciplinary application requiring the combination of optical spectroscopy (i.e., multicolor imaging), image processing, and machine learning. In addition, due to the simplicity of the optical apparatus and computational analysis, high school students could implement and validate their own costeffective oil-quality classification device.
Cite as: A. Abraham, K. Balachandran, and A. Doblas, “Research Outreach Interdisciplinary Activity to classify olive oil blends integrating multicolor imaging,i mage processing, and machine learning,” Undergraduate Research Journal 3(2), 6. doi:/10.58361/2766-3590.1062
In-focus quantitative phase imaging from defocused off-axis holograms: synergistic reconstruction framework
Abstract: Digital holographic microscopy (DHM) enables the three-dimensional (3D) reconstruction of quantitative phase distributions from a defocused hologram. Traditional computational algorithms follow a sequential approach in which one first reconstructs the complex amplitude distribution and later applies focusing algorithms to provide an in-focus phase map. In this work, we have developed a synergistic computational framework to compensate for the linear tilt introduced in off-axis DHM systems and autofocus the defocused holograms by minimizing a cost function, providing in-focus reconstructed phase images without phase distortions. The proposed computational tool has been validated in defocused holograms of human red blood cells and three-dimensional images of dynamic sperm cells.
Cite as: R. Castaneda, C. Trujillo, and A. Doblas, "In-focus quantitative phase imaging from defocused off-axis holograms: synergistic reconstruction framework," Opt. Letters 48(23), 6244-6247 (2023). doi: 10.1364/OL.506400
Semi-heuristic phase compensation in digital holographic microscopy for stable and accurate quantitative phase imaging of moving objects
Abstract: Digital holographic microscopy (DHM) is a cutting-edge interferometric technique to recover the complex wavefield scattered by microscopic samples from digitally recorded intensity patterns. In off-axis DHM, the challenge is digitally generating the reference wavefront replica to compensate for the tilt between the interfering waves. Current methods to estimate the reference wavefront's parameters rely on brute-force grid searches or heuristics algorithms. Whereas brute-forced searches are time-consuming and impractical for video-rate quantitative phase imaging and analysis, applying heuristics methods in holographic videos is limited since the phase background level occasionally changes between frames. A semi-heuristic phase compensation (SHPC) algorithm is proposed to address these challenges to reconstruct phase images with minimum distortion in the full field-of-view (FOV) from holograms recorded by a telecentric off-axis digital holographic microscope. The method is tested with a USAF test target, smearing red blood cells and alive human sperm. The SHPC method provides accurate phase maps as the reference brute-force method but with a 92-fold reduction in processing time. Furthermore, this method was tested for reconstructing experimental holographic videos of dynamic specimens, obtaining stable phase values and minimal differences in the background between frames. This proposed method provides state-of-the-art phase reconstructions with high accuracy and stability in holographic videos, allowing the successful XYZ tracking of single-moving sperm cells.
Cite as: S. Obando-Vasquez, A. Doblas, and C. Trujillo, “ Semi-heuristic phase compensation in digital holographic microscopy for stable and accurate quantitative phase imaging of moving objects,” Opt. Lasers Eng. 174, 107937 (2024). doi: 10.1016/j/optlaseng.2023.107937.
Comprehensive Tool for a Pase Compensation Reconstruction Method in Digital Holographic Microscopy Operating in Non-Telecentric Regime
Abstract: Quantitative phase imaging (QPI) via Digital Holographic microscopy (DHM) has been widely applied in material and biological applications. The performance of DHM technologies relies heavily on computational reconstruction methods to provide accurate phase measurements. Among the optical configuration of the imaging system in DHM, imaging systems operating in a non-telecentric regime are the most common ones. Nonetheless, the spherical wavefront introduced by the non-telecentric DHM system must be compensated to provide undistorted phase measurements. The proposed reconstruction approach is based on previous work from Kemper’s group. Here, we have reformulated the problem, reducing the number of required parameters needed for reconstructing phase images to the sensor pixel size and source wavelength. The developed computational algorithm can be divided into six main steps. In the first step, the selection of the +1-diffraction order in the hologram spectrum. The interference angle is obtained from the selected +1 order. Secondly, the curvature of the spherical wavefront distorting the sample’s phase map is estimated by analyzing the size of the selected +1 order in the hologram’s spectrum. The third and fourth steps are the spatial filtering of the +1 order and the compensation of the interference angle. The next step involves the estimation of the center of the spherical wavefront. An optional final optimization step has been included to fine-tune the estimated parameters and provide fully compensated phase images. Because the proper implementation of a framework is critical to achieve successful results, we have explicitly described the steps, including functions and toolboxes, required for reconstructing phase images without distortions. As a result, we have provided open-access codes and a user interface tool with minimum user input to reconstruct holograms recorded in a non-telecentric DHM system.
Cite as: B. Bogue-Jimenez, C. Trujillo, and A. Doblas, “Comprehensive Tool for a Pase Compensation Reconstruction Method in Digital Holographic Microscopy Operating in Non-Telecentric Regime,” Plos ONE 18(9), e0291103 (2023).
Global Stress Detection Framework Combining a Reduced Set of HRV Features and Random Forest Model
Abstract: Approximately 65% of the worldwide adult population has experienced stress, affecting their daily routine at least once in the past year. Stress becomes harmful when it occurs for too long or is continuous (i.e., chronic), interfering with our performance, attention, and concentration. Chronic high stress contributes to major health issues such as heart disease, high blood pressure, diabetes, depression, and anxiety. Several researchers have focused on detecting stress through combining many features with machine/deep learning models. Despite these efforts, our community has not agreed on the number of features to identify stress conditions using wearable devices. In addition, most of the reported studies have been focused on person-specific training and testing. Thanks to our community’s broad acceptance of wearable wristband devices, this work investigates a global stress detection model combining eight HRV features with a random forest (RF) algorithm. Whereas the model’s performance is evaluated for each individual, the training of the RF model contains instances of all subjects (i.e., global training). We have validated the proposed global stress model using two open-access databases (the WESAD and SWELL databases) and their combination. The eight HRV features with the highest classifying power are selected using the minimum redundancy maximum relevance (mRMR) method, reducing the training time of the global stress platform. The proposed global stress monitoring model identifies person-specific stress events with an accuracy higher than 99% after a global training framework. Future work should be focused on testing this global stress monitoring framework in real-world applications.
Cite as: K. Dahal, B. Bogue-Jimenez, A. Doblas, “Global stress detection framework combining a reduced set of HRV features and Random Forest model,” Sensors 2023, 23, 5220. https://doi.org/10.3390/s23115220
Focus Issue Introduction: 3D Image Acquisition and Display: Technology, Perception, and Applications
Abstract: This Feature Issue of Optics Express is organized in conjunction with the 2022 Optica conference on 3D Image Acquisition and Display: Technology, Perception and Applications which was held in hybrid format from 11 to 15, July 2022 as part of the Imaging and Applied Optics Congress and Optical Sensors and Sensing Congress 2022 in Vancouver, Canada. This Feature Issue presents 31 articles which cover the topics and scope of the 2022 3D Image Acquisition and Display conference. This Introduction provides a summary of these published articles that appear in this Feature Issue.
Cite as: B. Javidi, H. Hua, A. Stern, M. Martinez-Corral, O. Matoba, A. Doblas, and S. Thibault, “Focus Issue Introduction: 3D Image Acquisition and Display: Technology, Perception, and Applications,” Opt. Express 31(7), 11557-11560 (2023). doi: 10.1364/OE.487783
pyDHM: A Python library for applications in digital holographic microscopy
Abstract: pyDHM is an open-source Python library aimed at Digital Holographic Microscopy (DHM) applications. The pyDHM is a user-friendly library written in the robust programming language of Python that provides a set of numerical processing algorithms for reconstructing amplitude and phase images for a broad range of optical DHM configurations. The pyDHM implements phase-shifting approaches for in-line and slightly off-axis systems and enables phase compensation for telecentric and non-telecentric systems. In addition, pyDHM includes three propagation algorithms for numerical focusing complex amplitude distributions in DHM and digital holography (DH) setups. We have validated the library using numerical and experimental holograms.
Cite as: R. Castañeda, C. Trujillo, and A. Doblas, "pyDHM: A Python library for applications in digital holographic microscopy," PLoS ONE 17(10): e0275818 (2022) . https://doi.org/10.1371/journal.pone.0275818
Apparatus and method to recover the Mueller matrix in bright-field microscopy
Abstract: We present a simple experiment developed for undergraduate/graduate level to calculate the Mueller matrix of microscopic samples using intensity-based images by implementing a polarization-sensitive microscope. The experiment requires a brightfield microscope and standard polarizing optical components such as linear polarizers and waveplates. We provide a practical procedure for implementing the apparatus, measuring the complete Mueller matrix of linear polarizers, and discussing the possibility of analyzing biological samples using such apparatus and method. Due to the simplicity of the apparatus and method, this experiment allows students to increase their knowledge about light polarization and start their training in optical instrumentation.
Cite as: S. Obando-Vasquez, A. Doblas, and C. Trujillo, “Apparatus and method to recover the Mueller matrix in bright-field microscopy,” American Journal of Physics 90, 702 (2022). doi: 10/1119/5.0081673. Publication is available here.
Single-Shot 3D Topography of Transmissive and Reflective Samples with a Dual-Mode Telecentric-Based Digital Holographic Microscope
Abstract: Common path DHM systems are the most robust DHM systems as they are based on selfinterference and are thus less prone to external fluctuations. A common issue amongst these DHM systems is that the two replicas of the sample’s information overlay due to self-interference, making them only suitable for imaging sparse samples. This overlay has restricted the use of common-path DHM systems in material science. The overlay can be overcome by limiting the sample’s field of view to occupy only half of the imaging field of view or by using an optical spatial filter. In this work, we have implemented optical spatial filtering in a common-path DHM system using a Fresnel biprism. We have analyzed the optimal pinhole size by evaluating the frequency content of the reconstructed phase images of a star target. We have also measured the accuracy of the system and the sensitivity to noise for different pinhole sizes. Finally, we have proposed the first dual-mode common-path DHM system using a Fresnel biprism. The performance of the dual-model DHM system has been evaluated experimentally using transmissive and reflective microscopic samples.
Cite as: A.Doblas, C. Hayes-Rounds, R. Isaac, and F. Perez “Single-shot 3D topography of transmissive and reflective samples with a dual-mode telecentric-based digital holographic microscope,” Sensors, 22, 3793 (2022). Publication is available here.
Selection of Noninvasive Features in Wrist-Based Wearable Sensors to Predict Blood Glucose Concentrations Using Machine Learning Algorithms
Abstract: Glucose monitoring technologies allow users to monitor glycemic fluctuations (e.g., blood glucose levels). This is particularly important for individuals who have diabetes mellitus (DM). Traditional self-monitoring blood glucose (SMBG) devices require the user to prick their finger and extract a blood drop to measure the blood glucose based on chemical reactions with the blood. Unlike traditional glucometer devices, noninvasive continuous glucose monitoring (NICGM) devices aim to solve these issues by consistently monitoring users’ blood glucose levels (BGLs) without invasively acquiring a sample. In this work, we investigated the feasibility of a novel approach to NICGM using multiple off-the-shelf wearable sensors and learning-based models (i.e., machine learning) to predict blood glucose. Two datasets were used for this study: (1) the OhioT1DM dataset, provided by the Ohio University; and (2) the UofM dataset, created by our research team. The UofM dataset consists of fourteen features provided by six sensors for studying possible relationships between glucose and noninvasive biometric measurements. Both datasets are passed through a machine learning (ML) pipeline that tests linear and nonlinear models to predict BGLs from the set of noninvasive features. The results of this pilot study show that the combination of fourteen noninvasive biometric measurements with ML algorithms could lead to accurate BGL predictions within the clinical range; however, a larger dataset is required to make conclusions about the feasibility of this approach.
Cite as: B. Bogue-Jimenez, X. Huang, D. Powell, and A.Doblas, “Selection of Noninvasive Features in Wrist-Based Wearable Sensors to Predict Blood Glucose Concentrations Using Machine Learning Algorithms,” Sensors, 22(9), 3534 (2022). Publication is available here.
Speckle noise reduction in coherent imaging systems via Hybrid Median-Mean Filter
Abstract: Images recorded by coherent imaging systems, including laser-based photography, digital holography (DH), and digital holographic microscopy (DHM), are severely distorted by speckle noise. This work presents a single-shot image processing method to reduce the speckle noise, coined hybrid median-mean filter (HM2F). The HM2F is based on the average of conventional median-filtered images with different kernel size. The synergic combination of the median filter and mean approach provides a denoised image with reduced speckle contrast while the spatial resolution is kept up to 97% from the original value. The HM2F method is compared with the conventional median filter approach (CMF), the 3D Block Matching (BM3D) filter, the non-local means (NLM) filter, the 2D windowed Fourier transform filter (WFT2F), and the Wiener filter using different speckle-distorted images to benchmark its performance. Based on the experimental results and the simplicity of the technique, HM2F is proposed as an effective denoising tool for reducing the speckle noise in laser-based photography, DH, and DHM.
Cite as: R. Castaneda, J. Garcia-Sucerquia, and A.Doblas, “Speckle noise reduction in coherent imaging systems via Hybrid Median-Mean Filter,” Opt. Engineering 60(12), 123107 (2021). Publication is available here.
Video-Rate Quantitative Phase Imaging Using a Digital Holographic Microscope and a Generative Adversarial Network
Abstract: The conventional reconstruction method in off-axis Digital Holographic Microscopy (DHM) relies on computational processing, which involves the spatial filtering of the sample spectrum and the tilt compensation between the interfering waves to reconstruct the phase of the biological sample accurately. Additional computational procedures such as numerical focusing may be needed to re-construct free-of-distortion quantitative phase images based on the optical configuration of the DHM system. Regardless of the implementation, any DHM computational processing leads to long processing times, hampering the use of DHM to video-rate renderings of dynamic biological processes. In this work, a conditional generative adversarial network (cGAN) for robust and fast quantitative phase imaging in DHM is reported. The reconstructed phase images provided by the GAN model present stable background levels, enhancing the visualization of the specimens for different experimental conditions in which the conventional approach often fails. The proposed learning-based method has been trained and validated using human red blood cells recorded on an off-axis Mach-Zehnder DHM system. After proper training, the proposed GAN yields a computationally efficient method, reconstructing DHM images 7X faster than conventional computational approaches.
Cite as: R. Castaneda, C. Trujillo, and A. Doblas, “Video-Rate Quantitative Phase Imaging Using a Digital Holographic Microscope and a Generative Adversarial Network,” Sensors 21(23), 8021 (2021). Publication is available here.
Fast-iterative automatic reconstruction method for quantitative phase image with reduced phase perturbations in off-axis digital holographic microscopy
Abstract: This works presents a reconstruction algorithm to recover the complex object information for an off-axis digital holographic microscope (DHM) operating in the telecentric regimen. We introduce an automatic and fast method to minimize a cost function that finds the best numerical conjugated reference beam to compensate the filtered object information, eliminating any undesired phase perturbation due to the tilt between the reference and object waves. The novelties of the proposed approach, to the best of our knowledge, are a precise estimation of the interference angle between the object and reference waves, reconstructed phase images without phase perturbations, and reduced processing time. The method has been validated using a manufactured phase target and biological samples.
Cite as: R. Castaneda and A.Doblas, "Fast-iterative automatic reconstruction method for quantitative phase image with reduced phase perturbations in off-axis digital holographic microscopy,” Appl. Opt. 60(32), 10214-10220 (2021). Publication is available here.
Fast-iterative blind phase-shifting digital holographic microscopy using two images
Abstract: Digital holographic microscopy (DHM) has consolidated as a tool for diagnosis and measuring in life sciences, thanks to its capability to perform quantitative phase imaging. The reduction of the acquisition and computation time has driven the development of diverse reconstruction methodologies using a single-shot and two-frame approach. Methods based on the Fourier transform, the Hilbert transform, and the phase derivative are counted among the most utilized. The sensitivity of those methods is highly dependent on the compensation of the phase step, which requires the accurate knowledge of the phase shift between the two recorded holograms. Here, an alternative fast-iterative method based on the demodulation of the different components of the recorded interferograms is presented. The novelties of the proposed two-frame approach are: minimum number of images, since it requires 2 recorded holograms; a minimum phase error of the order of 0.005% independently of the phase step ranging from 0 to 180 deg.; a maximum correlation coefficient equal to 1 between the phase and the retrieved phase image; and, finally, a reduced processing time compared with the previous three-frame approach. Experimental results demonstrate the goodness and feasibility of the proposed technique.
Cite as: R. Castaneda, C. Buitrago-Duque, J. Garcia-Sucerquia, and A.Doblas, “Fast-iterative blind phase-shifting digital holographic microscopy using two images,” Appl. Opt. 59(24) 7469-7476 (2020). Publication available is here.
Advantages of Fresnel biprism-based Digital Holographic Microscopy in Quantitative Phase Imaging
Abstract: The hallmarks of digital holographic microscopy (DHM) compared with other quantitative phase imaging (QPI) methods are high speed, accuracy, spatial resolution, temporal stability, and polarization-sensitivity (PS) capability. The above features make DHM suitable for real-time quantitative PS phase imaging in a broad number of biological applications aimed at understanding cell growth and dynamic changes occurring during physiological processes and/or in response to pharmaceutical agents.
Cite as: C. Hayes-Round, B. Bogue-Jimenez, J. Garcia-Sucerquia, O. Skalli, and A. Doblas, “Advantages of Fresnel biprism-based Digital Holographic Microscopy in Quantitative Phase Imaging,” J. Biomed. Opt. 25(8), 086501 (2020), doi: 10.1117/1.JBO.25.8.086501. Publication is available here.
Phase-Shifting Digital Holographic Microscopy with iterative blind reconstruction algorithm
Abstract: In phase-shifting digital holographic microscopy (PS-DHM), the reconstructed phase map is obtained after processing several holograms of the same scene with a phase shift between them. Most of the reconstruction algorithms in PS-DHM require an accurate and known phase shift between the recorded holograms. This requirement limits the applicability of the method. To ease the use of PS-DHM, this paper presents an iterative-blind phase shift extraction method based on demodulation of the different components of the recorded holograms. The method uses a DHM system operating in a slightly off-axis architecture. The proposed method uses three-frame holograms with arbitrary and unequal phase shifts between them and therefore eases the use of the PS-DHM. We believe both simulated and experimental results demonstrate the goodness and feasibility of the proposed technique.
Cite as: A. Doblas, C. Buitrago-Duque, A. Robinson, J. Garcia-Sucerquia, and, “Phase-Shifting Digital Holographic Microscopy with iterative blind reconstruction algorithm,” Appl. Opt., 58(34), G311-G317 (2019). Publication is available here.
Structured illumination in compact and field-portable 3D-printed shearing digital holographic microscopy for resolution enhancement
Abstract: A compact and field-portable three-dimensional (3D)-printed structured illumination (SI) digital holographic microscope based on shearing geometry is presented. By illuminating the sample using a SI pattern, the lateral resolution in both reconstructed phase and amplitude images can be improved up to twice the resolution provided by conventional illumination. The use of a 3D-printed system and shearing geometry reduces the complexity of the system while providing high temporal stability. The experimental results for the USAF resolution target show a resolution improvement of a factor of two which corroborates the theoretical prediction. Resolution enhancement in phase imaging is also demonstrated by imaging a biological sample. To the best of our knowledge, this is the first report of a compact and field-portable SI digital holographic system based on shearing geometry.
Cite as: T. O’Connor, A. Doblas, and B. Javidi, “Structured illumination in compact and field-portable 3D-printed shearing digital holographic microscopy for resolution enhancement,” Opt. Letters 44(9), 2326-2329 (2019). Publication is available here.
Common-path, single-shot phase-shifting digital holographic microscopy using a Ronchi ruling
Abstract: Phase-shifting digital holography is widely considered to be a groundbreaking method to quantitatively investigate the phase distribution of specimens, such as living cells. The main flaws of this method, however, are that the requirement for several sequential phase-shifted holograms eliminates the possibility of single-shot imaging and complex configurations would also increase the temporal noise. The present paper aims to validate a single-shot, common-path, phase-shifting digital holographic microscopy, employing a self-referencing geometry. A Ronchi ruling, located in the Fourier plane of a standard microscopic imaging system, produces multiple replicas of sample information in the image plane. The phase retrieval algorithm is performed by superposition of the sample-free portion of each replica with the object information and requires at least three adjacent diffraction orders. To evaluate the performance of the proposed method, the phase distribution of silica microspheres as a test sample and the morphology of red blood cells as a biological specimen are determined. This configuration offers improved temporal stability in comparison with previously reported Mach–Zehnder interferometers and may serve as an alternative for real-time surveying of nanometric and sub-nanometric fluctuations of living microscopic specimens
Cite as: S. Hossein, S. Yaghoubi, S. Ebrahimi, M. Dashtdar, A. Doblas, and B. Javidi, “Common-path, single-shot phase-shifting digital holographic microscopy using a Ronchi ruling,” Appl. Phys. Letter 114, 183701 (2019). Publication is available here.
Optical transfer function engineering using a tunable 3D structured illumination microscope
Abstract: Two important features of three-dimensional structured illumination microscopy (3D-SIM) are its optical sectioning (OS) and super-resolution (SR) capabilities. Previous works on 3D-SIM systems show that these features are coupled. We demonstrate that a 3D-SIM system using a Fresnel biprism illuminated by multiple linear incoherent sources provides a structured illumination pattern whose lateral and axial modulation frequencies can be tuned separately. Therefore, the compact support of the synthetic optical transfer function (OTF) can be engineered to achieve the highest OS and SR capabilities for a particular imaging application. The theoretical performance of our engineered system based on the OTF support is compared to that achieved by other well-known SIM systems.
Cite as: H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “Optical transfer function engineering using a tunable 3D structured illumination microscope,” Opt. Letters 44(7), 1560-1563 (2019). Cite as: S. Hossein, S. Yaghoubi, S. Publication is available here.
Wollaston prism-based structured illumination microscope with tunable-frequency
Abstract: This work proposes an alternative structured illumination (SI) system based on a Wollaston prism (WP) illuminated by the diffracted field of an incoherent linear source. The proposed WP-based SI system presents several advantages. First, the generated fringes can be approximated by a pure sinusoidal pattern; thereby, computational methods developed for sinusoidal SI can be used without the need for additional processing. Second, the SI pattern’s period can be continuously varied up to the cutoff frequency of the native widefield system. Most significantly, the phase shifting of the SI pattern required for demodulation in SI microscopy can be easily accomplished using a de Sénarmont compensator, which provides accurate lateral displacement of the fringes independently of the lateral modulation frequency. Experimental verifications confirm the presented theoretical predictions.
Cite as: A. Doblas, S. Bedoya, and C. Preza, “Wollaston prism-based structured illumination microscope with tunable-frequency,” Appl. Opt. 58(7), B1-B8(2019). Publication is available here.
Tunable-frequency three-dimensional structured illumination microscopy with reduced data-acquisition
Abstract: The performance of a tunable three-dimensional (3D) structured illumination microscope (SIM) system and its ability to provide simultaneously super-resolution (SR) and optical-sectioning (OS) capabilities are investigated. Numerical results show that the performance of our 3D-SIM system is comparable with the one provided by a three-wave interference SIM, while requiring 40% fewer images for the reconstruction and providing frequency tunability in a cost-effective implementation. The performance of the system has been validated experimentally with images from test samples, which were also imaged with a commercial SIM based on incoherent-grid projection for comparison. Restored images from data acquired from an axially-thin fluorescent layer show a 1.6× improvement in OS capability compared to the commercial instrument while results from a fluorescent tilted USAF target show the OS and SR capabilities achieved by our system.
Cite as: A. Doblas, H. Shabani, G. Saavedra, and C. Preza, “Tunable-frequency three-dimensional structured illumination microscopy with reduced data-acquisition,” Opt. Express 26(23), 30492-30505 (2018). Publication is available here.
Image restoration approach to address reduced modulation contrast in structured illumination microscopy
Abstract: The performance of structured illumination microscopy (SIM) is hampered in many biological applications due to the inability to modulate the light when imaging deep into the sample. This is in part because sample-induced aberration reduces the modulation contrast of the structured pattern. In this paper, we present an image restoration approach suitable for processing raw incoherent-grid-projection SIM data with a low fringe contrast. Restoration results from simulated and experimental ApoTome SIM data show results with an improved signal-to-noise ratio (SNR) and optical sectioning compared to the results obtained from existing methods, such as 2D demodulation and 3D SIM deconvolution. Our proposed method provides satisfactory results (quantified by the achieved SNR and normalized mean square error) even when the modulation contrast of the illumination pattern is as low as 7%.
Cite as: N. Patwary, A. Doblas, and C. Preza, “Image restoration approach to address reduced modulation contrast in structured illumination microscopy,” Biomed. Opt. Express 9(4), 1630-1647 (2018). Publication is available here.
Improvement of two-dimensional structured illumination microscopy with an incoherent illumination pattern
Abstract: In two-dimensional structured illumination microscopy (2D-SIM), high-resolution images with optimal optical sectioning (OS) cannot be obtained simultaneously. This tradeoff can be overcome by using a tunable-frequency 2D-SIM system and a proper reconstruction method. The goal of this work is twofold. First, we present a computational approach to reconstruct optical-sectioned images with super-resolution enhancement (OS-SR) by using a tunable SIM system. Second, we propose an incoherent tunable-frequency 2D-SIM system based on a Fresnel biprism implementation. Integration of the proposed computational method with this tunable structured illumination (SI) system results in a new 2D-SIM system that is advantageous compared to other 2D-SIM systems with comparable complexity, because it provides high-resolution OS images independent of the objective lens used, without the presence of coherent noise and without reducing the contrast of the structured pattern, as in other incoherent implementations. Evaluation of our proposed system is demonstrated with comparative studies of simulated and experimental reconstructed images to validate our theoretical findings. Our experimental results show a simultaneous improvement of the lateral resolution by a factor of 1.8x with the desired OS capability achieved in the resulting OS-SR combination image. Our experimental results also verify that our system can provide better OS capability than the commercial Zeiss ApoTome-SIM system in the investigated study.
Cite as: H. Shabani, A. Doblas, G. Saavedra, E. Sanchez-Ortiga and C. Preza, “Improvement of two-dimensional structured illumination microscopy with an incoherent illumination pattern” Appl. Optics 57(7), B92-B101 (2018). Publication is available here.
Experimental validation of a customized phase mask designed to enable efficient computational optical sectioning microscopy through wavefront encoding
Abstract: In this paper, wavefront-encoded (WFE) computational optical sectioning microscopy (COSM) using a fabricated square cubic (SQUBIC) phase mask, designed to render the system less sensitive to depth-induced aberration, is investigated. The WFE-COSM system is characterized by a point spread function (PSF) that does not vary as rapidly with imaging depth compared to the conventional system. Thus, in WFE-COSM, image restoration from large volumes can be achieved using computationally efficient space-invariant (SI) algorithms, thereby avoiding the use of depth-variant algorithms. The fabricated SQUBIC phase mask was first evaluated and found to have a 75% fidelity compared to the theoretical design; it was then integrated in a commercial wide-field microscope to implement a WFE-COSM system. Evaluation of the WFE-COSM system is demonstrated with comparative studies of theoretical and experimental PSFs and simulated and measured images of spherical shells located at different depths in a test sample. These comparisons show that PSF and imaging models capture major trends in experimental data with a 99% correlation between forward image intensity distribution in experimental and simulated images of spherical shells. Our experimental SI restoration results demonstrate that the WFE-COSM system achieves more than a twofold performance improvement over the conventional system of up to a 65 μm depth below the coverslip investigated in this study.
Cite as: N. Patwary, H. Shabani, A. Doblas, G. Saavedra, and C. Preza, “Experimental validation of a customized phase mask designed to enable efficient computational optical sectioning microscopy through wavefront encoding” Appl. Optics 56(9), D14-D23 (2017). Publication is available here.
High-speed and high-sensitivity parallel spectral-domain optical coherence tomography using a supercontinuum light source
Abstract: The three most important metrics in optical coherence tomography (OCT) are resolution, speed, and sensitivity. Because there is a complex interplay between these metrics, no previous work has obtained the best performance in all three metrics simultaneously. We demonstrate that a high-power supercontinuum source, in combination with parallel spectral-domain OCT, achieves an unparalleled combination of resolution, speed, and sensitivity. This system captures cross-sectional images spanning 4 mm×0.5 mm at 1,024,000 lines/s with 2×14 μm resolution (axial x transverse) at a sensitivity of 113 dB. Imaging using the proposed system is demonstrated on highly differentiated human bronchial epithelial cells to capture and spatially localize ciliary dynamics.
Cite as: J. Barrick, A. Doblas, M. R. Gardner, P. R. Sears, L. E. Ostrowski, and A. L. Oldenburg, “High-speed and high-sensitivity parallel spectral-domain optical coherence tomography using a supercontinuum light source,” Opt. Lett., 41(24), 5620-5623 (2016). Publication is available here.
Older works
Phase-shifting by means of an electronically tunable lens: quantitative phase imaging of biological specimens with digital holographic microscopy
Cite as: C. Trujillo, A. Doblas, G. Saavedra, M. Martinez-Corral and J. Garcia-Sucerquia, “Phase-shifting by means of an electronically tunable lens: quantitative phase imaging of biological specimens with digital holographic microscopy,” Opt. Lett., 41(7), 1416-1419 (2016). Publication is available here.
Diabetes screening by telecentric digital holographic microscopy
Cite as: A. Doblas, E. Roche, F. J. Ampudia-Blasco, M. Martínez-Corral, G. Saavedra and J. Garcia-Sucerquia, “Diabetes screening by telecentric digital holographic microscopy,” J. Microsc., 261(3), 285-290 (2016). doi: 10.1111/jmi.12331. Publication is available here.
Digital holographic microscopy for diabetes screening
Cite as: A. Doblas, M. Martínez-Corral, G. Saavedra, and J. Garcia-Sucerquia “Digital holographic microscopy for diabetes screening,” SPIE Newsroom (2016). doi: 10.1117/2.1201604.006435. Publication is available here.
Spatial light modulator phase mask implementation of wavefront encoded 3D computational-optical microscopy
Cite as: S. V. King, A. Doblas, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Spatial light modulator phase mask implementation of wavefront encoded 3D computational-optical microscopy,” Appl. Optics 54, 8587-8595 (2015). Publication is available here.
Physical compensation of phase curvature in digital holographic microscopy by use of programmable liquid lens
Cite as: A. Doblas, D. Hincapie-Zuluaga, G. Saavedra, M. Martínez-Corral and J. Garcia-Sucerquia, “Physical compensation of phase curvature in digital holographic microscopy by use of programmable liquid lens,” Appl. Opt., 54, 5229-5233 (2015). Publication is available here.
Study of spatial lateral resolution in off-axis digital holographic microscopy
Cite as: A. Doblas, E. Sánchez-Ortiga, M. Martínez-Corral and J. Garcia-Surcerquia, “Study of spatial lateral resolution in off-axis digital holographic microscopy,” Opt. Commun. 352, 63-69 (2015). Publication is available here.
Static axial scanning in 3D microscopy through electrically controlled liquid lens
Cite as: M. Martínez-Corral, A. Doblas, E. Sánchez-Ortiga, J. Sola-Pikabea and G. Saavedra, “Static axial scanning in 3D microscopy through electrically controlled liquid lens,” SPIE Newsroom (2015). doi: 10.1117/2.1201503.005832.
Fast axial-scanning widefield microscopy with constant magnification and resolution
Cite as: M. Martínez-Corral, P.-Y. Hsieh, A. Doblas, E. Sánchez-Ortiga, G. Saavedra and Y.-P. Huang, “Fast axial-scanning widefield microscopy with constant magnification and resolution,” J. Display Technol 11, 913-920 (2015). doi: 10.1109/JDT.2015.2404347. Publication is available here.
Accurate single-shot quantitative phase imaging of biological specimens with telecentric digital holographic microscopy
Cite as: A. Doblas, E. Sánchez-Ortiga, M. Martínez-Corral, G. Saavedra and J. Garcia-Surcerquia, “Accurate single-shot quantitative phase imaging of biological specimens with telecentric digital holographic microscopy,” J. Biomed. Opt. 19(4), 046022- (2014). Publication is available here.
Off-axis Digital Holographic Microscopy: practical design parameters for operating at diffraction limit
Cite as: E. Sánchez-Ortiga, A. Doblas, G. Saavedra, M. Martínez-Corral and J. Garcia-Sucerquia, “Off-axis Digital Holographic Microscopy: practical design parameters for operating at diffraction limit,” Appl. Opt. 53(10), 2058-2066 (2014). Publication is available here.
Axial resonance of periodic patterns by using a Fresnel biprism
Cite as: A. Doblas, G. Saavedra, M. Martínez-Corral, J. C. Barreiro, E. Sánchez-Ortiga and A. Llavador, “Axial resonance of periodic patterns by using a Fresnel biprism,” J. Opt. Soc. Am. A 30(1), 140-148 (2013). Publication is available here.
Shift-variant digital holographic microscopy: innacuracies in quantitative phase imaging
Cite as: A. Doblas, E. Sánchez-Ortiga, M. Martínez-Corral, G. Saavedra, P. Andres, and J. Garcia-Sucerquia, “Shift-variant digital holographic microscopy: innacuracies in quantitative phase imaging,” Opt. Lett. 38(8), 1352-1354 (2013). Publication is available here.
Scanning microscopy with spatial sampling of the detector plane
Cite as: E. Sánchez-Ortiga, G. Saavedra, C. J. R. Sheppard, A. Doblas and M. Martínez-Corral, “Scanning microscopy with spatial sampling of the detector plane,” Opt. Pur. Apl. 46(2), 137-146 (2013). Publication is available here.
Shaded-Mask Filtering for Extended Depth-of-Field Microscopy
Cite as: I. Escobar, G. Saavedra, M. Martínez-Corral, A. Calatayud and A. Doblas, “Shaded-Mask Filtering for Extended Depth-of-Field Microscopy,” J. Inf. Commun. Converg. Eng 11(2), 139-146, (2013). Publication is available here.
Aberration compensation for objective phase curvature in phase holographic microscopy: comment
Cite as: E. Sánchez-Ortiga, A. Doblas, M. Martínez-Corral, G. Saavedra and J. Garcia-Surcerquia, “Aberration compensation for objective phase curvature in phase holographic microscopy: comment,” Opt. Lett. 39(3), 417-417 (2013). Publication is available here.
Subtractive imaging in confocal scanning microscope using a CCD camera as a detector
Cite as: E. Sánchez-Ortiga, C.J.R. Sheppard, G. Saavedra, M. Martínez-Corral, A. Doblas and A. Calatayud, “Subtractive imaging in confocal scanning microscope using a CCD camera as a detector”, Optics Letters, 37(7), 1280-1282(2012). Publication is available here.
Digital holographic microscopy with pure-optical spherical phase compensation
Cite as: E. Sánchez-Ortiga, Pietro Ferraro, M. Martínez-Corral, G. Saavedra and A. Doblas, “Digital holographic microscopy with pure-optical spherical phase compensation”, J. Opt. Soc. Am. A 28(7), 1410-1417(2011). Publication is available here.
Cite as: R. Castaneda, J. Garcia-Sucerquia, and A.Doblas, “Speckle noise reduction in coherent imaging systems via Hybrid Median-Mean Filter,” Opt. Engineering 60(12), 123107 (2021). Publication is available here.