Publications

High-speed optical imaging with sCMOS pixel reassignment

Published in Nature communications, 2024

Fluorescence microscopy has undergone rapid advancements, offering unprecedented visualization of biological events and shedding light on the intricate mechanisms governing living organisms. However, the exploration of rapid biological dynamics still poses a significant challenge due to the limitations of current digital camera architectures and the inherent compromise between imaging speed and other capabilities. Here, we introduce sHAPR, a high-speed acquisition technique that leverages the operating principles of sCMOS cameras to capture fast cellular and subcellular processes. sHAPR harnesses custom fiber optics to convert microscopy images into one-dimensional recordings, enabling acquisition at the maximum camera readout rate, typically between 25 and 250 kHz. We have demonstrated the utility of sHAPR with a variety of phantom and dynamic systems, including high-throughput flow cytometry, cardiomyocyte contraction, and neuronal calcium waves, using a standard epi-fluorescence microscope. sHAPR is highly adaptable and can be integrated into existing microscopy systems without requiring extensive platform modifications. This method pushes the boundaries of current fluorescence imaging capabilities, opening up new avenues for investigating high-speed biological phenomena.

Light-field flow cytometry for high-resolution, volumetric and multiparametric 3D single-cell analysis

Published in Nature Communications, 2024

Imaging flow cytometry (IFC) combines flow cytometry and fluorescence microscopy to enable high-throughput, multiparametric single-cell analysis with rich spatial details. However, current IFC techniques remain limited in their ability to reveal subcellular information with a high 3D resolution, throughput, sensitivity, and instrumental simplicity. In this study, we introduce a light-field flow cytometer (LFC), an IFC system capable of high-content, single-shot, and multi-color acquisition of up to 5,750 cells per second with a near-diffraction-limited resolution of 400-600 nm in all three dimensions. The LFC system integrates optical, microfluidic, and computational strategies to facilitate the volumetric visualization of various 3D subcellular characteristics through convenient access to commonly used epi-fluorescence platforms. We demonstrate the effectiveness of LFC in assaying, analyzing, and enumerating intricate subcellular morphology, function, and heterogeneity using various phantoms and biological specimens. The advancement offered by the LFC system presents a promising methodological pathway for broad cell biological and translational discoveries, with the potential for widespread adoption in biomedical research.

Portable light-sheet optofluidic microscopy for 3D fluorescence imaging flow cytometry

Published in Lab on a Chip, 2023

Imaging flow cytometry (IFC) combines conventional flow cytometry with optical microscopy, allowing for high-throughput, multi-parameter screening of single-cell specimens with morphological and spatial information. However, current 3D IFC systems are limited by instrumental complexity and incompatibility with available microfluidic devices or operations. Here, we report portable light-sheet optofluidic microscopy (PLSOM) for 3D fluorescence cytometric imaging. PLSOM exploits a compact, open-top light-sheet configuration compatible with commonly adopted microfluidic chips. The system offers a subcellular resolution (2-4 μm) in all three dimensions, high throughput (∼1000 cells per s), and portability (30 cm (l) × 10 cm (w) × 26 cm (h)). We demonstrated PLSOM for 3D IFC using various phantom and cell systems. The low-cost and custom-built architecture of PLSOM permits easy adaptability and dissemination for broad 3D flow cytometric investigations.

Optimal sparsity allows reliable system-aware restoration of fluorescence microscopy images

Published in Science Advances, 2023

Fluorescence microscopy is one of the most indispensable and informative driving forces for biological research, but the extent of observable biological phenomena is essentially determined by the content and quality of the acquired images. To address the different noise sources that can degrade these images, we introduce an algorithm for multiscale image restoration through optimally sparse representation (MIRO). MIRO is a deterministic framework that models the acquisition process and uses pixelwise noise correction to improve image quality. Our study demonstrates that this approach yields a remarkable restoration of the fluorescence signal for a wide range of microscopy systems, regardless of the detector used (e.g., electron-multiplying charge-coupled device, scientific complementary metal-oxide semiconductor, or photomultiplier tube). MIRO improves current imaging capabilities, enabling fast, low-light optical microscopy, accurate image analysis, and robust machine intelligence when integrated with deep neural networks. This expands the range of biological knowledge that can be obtained from fluorescence microscopy.

Biospeckle Analysis and Biofilm Electrostatic Tests, Two Useful Methods in Microbiology

Published in Applied Microbiology, 2021

The development of more sensitive methodologies, capable of quickly detecting and monitoring a microbial population present in a specific biological matrix, as well as performing to allow for the study of all its metabolic changes (e.g., during the formation of biofilm) to occur, is an essential requirement for both well-being and the food industry. Two techniques, in particular, have gained the attention of scientists: The first is “biospeckle”, an optical technique representing an innovative tool for applications in food quality, food safety, and nutraceuticals. With this technique, we can quickly evaluate and monitor the presence of bacteria (or their proliferation) in a solid or liquid biological matrix. In addition, the technique is helpful in quantifying and optimizing the correct storage time of the pro-biotics, if they are entrapped in matrices such as alginate and follow their survival rate in simulated gastro-intestinal conditions. A second technique with great chances is the “biofilm electrostatic test” (BET). BET undoubtedly represents a fast, simple, and highly reproducible tool suitable for admitting the evaluation of the in vitro bacterial capacity in order to adhere through an electrostatic interaction with a pyro-electrified carrier after only 2 h of incubation. BET could represent the way for a quick and standardized evaluation of bacterial resistance among biofilm-producing microorganisms through a fast evaluation of the potential presence of the biofilm.

Super-resolution optofluidic scanning microscopy

Published in Lab on a Chip, 2021

Optofluidics enables visualizing diverse anatomical and functional traits of single-cell specimens with new degrees of imaging capabilities. However, the current optofluidic microscopy systems suffer from either low resolution to reveal subcellular details or incompatibility with general microfluidic devices or operations. Here, we report optofluidic scanning microscopy (OSM) for super-resolution, live-cell imaging. The system exploits multi-focal excitation using the innate fluidic motion of the specimens, allowing for minimal instrumental complexity and full compatibility with various microfluidic configurations. The results present effective resolution doubling, optical sectioning and contrast enhancement. We anticipate the OSM system to offer a promising super-resolution optofluidic paradigm for miniaturization and different levels of integration at the chip scale.

Miscalibration-tolerant Fourier ptychography

Published in IEEE Journal of Selected Topics in Quantum Electronics, 2021

Fourier Ptychography probes the sample from different directions to achieve label-free quantitative phase imaging with a large space-bandwidth product. However, special attention has to be paid in the calibration of the optical setup to assure the accurate knowledge of the geometrical parameters involved in the image reconstruction. Any slight misalignment can provoke incorrect synthesis of the observables and, in turn, severe phase errors in the resulting high-resolution image. Here, we present a new processing pipeline that automatically removes such a priori unknown artifacts, thus making Fourier Ptychography miscalibration-tolerant. This result is achieved through a numerical Multi-Look approach that generates and combines multiple reconstructions of the same set of observables where phase artifacts are largely uncorrelated and, thus, automatically suppress each other. The proposed method is non-iterative, fully parallelizable, and completely blind, unlocking the use of Fourier Ptychography as an easy to handle tool or add-on to existing microscopes to be employed by unskilled users, thus paving the way to biomedical and clinical practices.

Miniaturized modular-array fluorescence microscopy

Published in Biomedical Optics Express, 2020

Fast and accurate sCMOS noise correction for fluorescence microscopy

Published in Nature Communications, 2020

The rapid development of scientific CMOS (sCMOS) technology has greatly advanced optical microscopy for biomedical research with superior sensitivity, resolution, field-of-view, and frame rates. However, for sCMOS sensors, the parallel charge-voltage conversion and different responsivity at each pixel induces extra readout and pattern noise compared to charge-coupled devices (CCD) and electron-multiplying CCD (EM-CCD) sensors. This can produce artifacts, deteriorate imaging capability, and hinder quantification of fluorescent signals, thereby compromising strategies to reduce photo-damage to live samples. Here, we propose a content-adaptive algorithm for the automatic correction of sCMOS-related noise (ACsN) for fluorescence microscopy. ACsN combines camera physics and layered sparse filtering to significantly reduce the most relevant noise sources in a sCMOS sensor while preserving the fine details of the signal. The method improves the camera performance, enabling fast, low-light and quantitative optical microscopy with video-rate denoising for a broad range of imaging conditions and modalities.

Compact off-axis holographic slide microscope: design guidelines

Published in Biomedical Optics Express, 2020

Holographic microscopes are emerging as suitable tools for in situ diagnostics and environmental monitoring, providing high-throughput, label-free, quantitative imaging capabilities through small and compact devices. In-line holographic microscopes can be realized at contained costs, trading off complexity in the phase retrieval process and being limited to sparse samples. Here we present a 3D printed, cost effective and field portable off-axis holographic microscope based on the concept of holographic microfluidic slide. Our scheme removes complexity from the reconstruction process, as phase retrieval is non iterative and obtainable by hologram demodulation. The configuration we introduce ensures flexibility in the definition of the optical scheme, exploitable to realize modular devices with different features. We discuss trade-offs and design rules of thumb to follow for developing DH microscopes based on the proposed solution. Using our prototype, we image flowing marine microalgae, polystyrene beads, E.coli bacteria and microplastics. We detail the effect on the performance and costs of each parameter, design, and hardware choice, guiding readers toward the realization of optimized devices that can be employed out of the lab by non-expert users for point of care testing.

BSSE: An open-source image processing tool for miniaturized microscopy

Published in Optics Express, 2019

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement Single-photon-excitation-based miniaturized microscope, or miniscope, has recently emerged as a powerful tool for imaging neural ensemble activities in freely moving animals. In the meanwhile, this highly flexible and implantable technology promises great potential for studying a broad range of cells, tissues and organs. To date, however, applications have been largely limited by the properties of the imaging modality. It is therefore highly desirable for a method generally applicable for processing miniscopy images, enabling and extending the applications to diverse anatomical and functional traits, spanning various cell types in the brain and other organs. We report an image processing approach, termed BSSE, for background suppression and signal enhancement for miniscope image processing. The BSSE method provides a simple, automatic solution to the intrinsic challenges of overlapping signals, high background and artifacts in miniscopy images. We validated the method by imaging synthetic structures and various biological samples of brain, tumor, and kidney tissues. The work represents a generally applicable tool for miniscopy technology, suggesting broader applications of the miniaturized, implantable and flexible technology for biomedical research.

Biological Lenses as a Photomask for Writing Laser Spots into Ferroelectric Crystals

Published in ACS Applied Bio Materials, 2019

Red blood cells on the surface of a lithium niobate crystal can be used as optical lenses for direct writing of laser-induced refractive index changes. The writing process by such a photomask made of biological lenses is due to the photorefractive effect. Wavefront analysis by a digital holographic microscope is performed for deep and accurate evaluation of local refractive index changes. Different focusing properties can be imprinted on the crystal depending on which type of RBC is employed, discocytes or spherical-like RBCs. The possibility to fix into a solid material the optical fingerprint of the RBCs will have an impact on both diagnostics and cell\material interfacing.

Quantitative imaging of the complexity in liquid bubbles’ evolution reveals the dynamics of film retraction

Published in Light: Science and Applications, 2019

The dynamics and stability of thin liquid films have fascinated scientists over many decades. Thin film flows are central to numerous areas of engineering, geophysics, and biophysics and occur over a wide range of lengths, velocities, and liquid property scales. In spite of many significant developments in this area, we still lack appropriate quantitative experimental tools with the spatial and temporal resolution necessary for a comprehensive study of film evolution. We propose tackling this problem with a holographic technique that combines quantitative phase imaging with a custom setup designed to form and manipulate bubbles. The results, gathered on a model aqueous polymeric solution, provide unparalleled insight into bubble dynamics through the combination of a full-field thickness estimation, three-dimensional imaging, and a fast acquisition time. The unprecedented level of detail offered by the proposed methodology will promote a deeper understanding of the underlying physics of thin film dynamics.

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Biospeckle Decorrelation Quantifies the Performance of Alginate-Encapsulated Probiotic Bacteria

Published in IEEE Journal of Selected Topics in Quantum Electronics, 2019

In recent years, the use of probiotics in food and health has increased so much that usually market offers several functional fermented food or nutraceuticals containing probiotics, often also associated to prebiotics. Both in food industry and in pharmaceutics, it is very important the development and use of methodologies that quickly allow a precise overview about the microbial population present in a specific biological matrix, and to monitor over time any changes that it may undergo. In this paper, we propose biospeckle decorrelation as a tool for the fast evaluation of the effectiveness of microencapsulation as a preservation system. Although speckle grains are often treated as an impairment for imaging, they represent a precious source of information. Such information is rich enough to characterize bacterial dynamics in a fast and simple way suitable for applications in food science and industry. In fact, here we show that through biospeckle decorrelation it is possible to quantify the shelf-time of alginate-encapsulated probiotic bacteria and their survival rate under simulated gastrointestinal conditions.

Label-free quantification of the effects of lithium niobate polarization on cell adhesion via holographic microscopy

Published in Journal of Biophotonics, 2018

The surface of a c− cut ferroelectric crystal at room temperature is characterized by the so-called screening surface charges, able to compensate the charge due to the spontaneous polarization. Recently, these charges inspired the investigation of the interaction affinity of live cells with lithium niobate and lithium tantalate crystals. However, different knowledge gaps still remain that prevent a reasonable application of these materials for biological applications. Here, a label-free holographic total internal reflection microscopy is shown; the technique is able to evaluate quantitatively the contact area of live fibroblast cells adhering onto the surface of a ferroelectric lithium niobate crystal. The results show values of contact area significantly different between cells adhering onto the positive or negative face of the crystal. This reinforces the reasons for using the polarization charge of these materials to study and/or control cellular processes and, thus, to develop an innovative platform based on polar dielectric functional substrates.

Holographic microscope slide in a spatiooral imaging modality for reliable 3D cell counting

Published in Lab on a Chip, 2017

In the current trend of miniaturization and simplification of imaging flow cytometry, Lab-on-a-Chip (LoC) microfluidic devices represent an innovative and cost-effective solution. In this framework, we propose for the first time a novel platform based on the compactness of a holographic microscope slide (HMS) in combination with the new computational features of space-time digital holography (STDH) that uses a 1D linear sensor array (LSA) instead of 2D CCD or CMOS cameras to respond to real diagnostic needs. In this LoC platform, computational methods, holography, and microfluidics are intertwined in order to provide an imaging system with a reduced amount of optical components and capability to achieve reliable cell counting even in the absence of very accurate flow control. STDH exploits the sample motion into the microfluidic channel to obtain an unlimited field-of-view along the flow direction, independent of the magnification factor. Furthermore, numerical refocusing typical of a holographic modality allows imaging and visualization of the entire volume of the channel, thus avoiding loss of information due to the limited depth of focus of standard microscopes. Consequently, we believe that this platform could open new perspectives for enhancing the throughput by 3D volumetric imaging.

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Label free imaging of cell-substrate contacts by holographic total internal reflection microscopy

Published in Journal of Biophotonics, 2017

The study of cell adhesion contacts is pivotal to understand cell mechanics and interaction at substrates or chemical and physical stimuli. We designed and built a HoloTIR microscope for label-free quantitative phase imaging of total internal reflection. Here we show for the first time that HoloTIR is a good choice for label-free study of focal contacts and of cell/substrate interaction as its sensitivity is enhanced in comparison with standard TIR microscopy. Finally, the simplicity of implementation and relative low cost, due to the requirement of less optical components, make HoloTIR a reasonable alternative, or even an addition, to TIRF microscopy for mapping cell/substratum topography. As a proof of concept, we studied the formation of focal contacts of fibroblasts on three substrates with different levels of affinity for cell adhesion. (Figure presented.).

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Direct self-assembling and patterning of semiconductor quantum dots on transferable elastomer layer

Published in Applied Surface Science, 2017

Functionalization of thin and stretchable polymer layers by nano- and micro-patterning of nanoparticles is a very promising field of research that can lead to many different applications in biology and nanotechnology. In this work, we present a new procedure to self-assemble semiconductor quantum dots (QDs) nanoparticles by a simple fabrication process on a freestanding flexible PolyDiMethylSiloxane (PDMS) membrane. We used a Periodically Poled Lithium Niobate (PPLN) crystal to imprint a micrometrical pattern on the PDMS membrane that drives the QDs self-structuring on its surface. This process allows patterning QDs with different wavelength emissions in a single step in order to tune the overall emission spectrum of the composite, tuning the QDs mixing ratio.

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Endowing a plain fluidic chip with micro-optics: A holographic microscope slide

Published in Light: Science and Applications, 2017

Lab-on-a-Chip (LoC) devices are extremely promising in that they enable diagnostic functions at the point-of-care. Within this scope, an important goal is to design imaging schemes that can be used out of the laboratory. In this paper, we introduce and test a pocket holographic slide that allows digital holography microscopy to be performed without an interferometer setup. Instead, a commercial off-the-shelf plastic chip is engineered and functionalized with this aim. The microfluidic chip is endowed with micro-optics, that is, a diffraction grating and polymeric lenses, to build an interferometer directly on the chip, avoiding the need for a reference arm and external bulky optical components. Thanks to the single-beam scheme, the system is completely integrated and robust against vibrations, sharing the useful features of any common path interferometer. Hence, it becomes possible to bring holographic functionalities out of the lab, moving complexity from the external optical apparatus to the chip itself. Label-free imaging and quantitative phase contrast mapping of live samples are demonstrated, along with flexible refocusing capabilities. Thus, a liquid volume can be analyzed in one single shot with no need for mechanical scanning systems.

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Twofold Self-Assembling of Nanocrystals into Nanocomposite Polymer

Published in IEEE Journal on Selected Topics in Quantum Electronics, 2016

In this paper, we introduce a single-step self-assembling process aimed at forming two-dimensional (2-D) array microstructures made from a nanocomposite polymer layer in which are dispersed CdSe-CdS nanocrystals. The novelty of the process reported here is that it operates simultaneously as a two-fold process where the liquid polymer matrix is self-shaped by electrohydrodynamic pressure as a 2-D array of microstructures, while at the same time, the nanocrystals are self-assembled by dielectrophoretic forces. The proposed approach could inspire future smart fabrication techniques for producing self-assembled lensed nanocomposite layers. In principle, the method is scalable down to diameter lens up to few micrometers.

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Surface plasmon resonance imaging by holographic enhanced mapping

Published in Analytical Chemistry, 2015

We designed, constructed and tested a holographic surface plasmon resonance (HoloSPR) objective-based microscope for simultaneous amplitude-contrast and phase-contrast surface plasmon resonance imaging (SPRi). SPRi is a widely spread tool for label-free detection of changes in refractive index and concentration, as well as mapping of thin films. Currently, most of the SPR sensors rely on the detection of amplitude or phase changes of light. Despite the high sensitivities achieved so far, each technique alone has a limited detection range with optimal sensitivity. Here we use a high numerical aperture objective that avoids all the limitations due to the use of a prism-based configuration, yielding highly magnified and distortion-free images. Holographic reconstructions of SPR images and real-time kinetic measurements are presented to show the capability of HoloSPR to provide a versatile imaging method for high-throughput SPR detection complementary to conventional SPR techniques.

Mapping electric fields generated by microelectrodes using optically trapped charged microspheres

Published in Lab on a Chip, 2011

In this work, we show a new technique to measure the direction and amplitude of the electric field generated by microelectrodes in a liquid environment, as often used in microfluidic devices. The method is based on the use of optical tweezers as a force transducer. A trapped, charged particle behaves as a probe. With this technique, it is possible to obtain a detailed map of the electric field, even for very complex electrode structures with a resolution below a micrometre and with a sensitivity as low as a few hundreds of V m-1. © 2011 The Royal Society of Chemistry.