Optical Setup Research Articles

Multifunctional computational fluorescence self-interference holographic microscopy

Fluorescence microscopy is crucial in various fields such as biology, medicine, and life sciences. Fluorescence self-interference holographic microscopy has great potential in bio-imaging owing to its unique wavefront coding characteristics; thus, it can be employed as three-dimensional (3D) scanning-free super-resolution microscopy. However, the available approaches are limited to low optical efficiency, complex optical setups, and single imaging functions. The geometric phase lens can efficiently manipulate the optical field’s amplitude, phase, and polarization. Inspired by geometric phase and self-interference holography, a self-interference fluorescent holographic microscope-based geometric phase lens is proposed. This system allows for wide-field, 3D fluorescence holographic imaging, and edge-enhancement from the reconstruction of only one complex-valued hologram. Experiments demonstrate the effectiveness of our method in imaging biological samples, with improved resolution and signal-to-noise ratio. Furthermore, its simplicity and convenience make it easily compatible with existing optical microscope setups, making it a powerful tool for observing biological samples and detecting industrial defects.

Transport-of-intensity differential phase contrast imaging: defying weak object approximation and matched-illumination condition

Quantitative phase imaging (QPI) has emerged as a promising label-free imaging technique with growing importance in biomedical research, optical metrology, materials science, and other fields. Partially coherent illumination provides resolution twice that of the coherent diffraction limit, along with improved robustness and signal-to-noise ratio, making it an increasingly significant area of study in QPI. Partially coherent QPI, represented by differential phase contrast (DPC), linearizes the phase-to-intensity transfer process under the weak object approximation (WOA). However, the nonlinear errors caused by WOA in DPC can lead to phase underestimation. Additionally, DPC requires strict matching of the illumination numerical aperture (NA) to ensure the complete transmission of low-frequency information. This necessitates precise alignment of the optical system and limits the flexible use of objective and illumination. In this study, the applicability of the WOA under different coherence parameters is explored, and a method to defy WOA by reducing the illumination NA is proposed. The proposed method uses the transport-of-intensity equation through an additional defocused intensity image to recover the lost low-frequency information due to illumination mismatch, without requiring any iterative procedure. This method overcomes the limitations of DPC being unable to recover large phase objects and does not require the strict illumination matching conditions. The accurate quantitative morphological characterization of customized artifact and microlens arrays that do not satisfy WOA under non-matched-illumination conditions demonstrated the precise quantitative capability of the proposed method and its excellent performance in the field of measurement. Meanwhile, the phase retrieval of tongue slices and oral epithelial cells demonstrated its application potential in the biomedical field. The ability to accurately recover phase under a concise and implementable optical setup makes it a promising solution for widespread application in various label-free imaging domains.

Benefits of front coating crystalline scintillator screens for phase-contrast synchrotron micro-tomography

Transparent crystalline scintillators such as cerium-doped YAG or LuAG are widely used in X-ray imaging for the indirect detection of X-rays. The application of reflective coatings on the front side to improve the optical gain is common practice for flat panel detectors with CsI or Gd2O2S powder scintillators but still largely unknown for crystalline scintillators such as LuAG. This work shows experimentally and quantitatively how a black and reflective coating on the X-ray side of a 2 mm LuAG:Ce scintillator improves the image quality compared to a 2 mm LuAG:Ce scintillator without a coating. The measurements have been done for two different distances, with 2 m and 29.7 m on the BM18 beamline of the European Synchrotron. The Modulation Transfer Function (MTF) and the Signal-to-Noise-Ratio (SNR2) power spectrum as well as contrast-to-noise ratio are used for comparing image quality. Propagation-based phase contrast strongly enhances the SNR2 amplitudes (gain ≈10 from 2 m to 29.7 m object-detector distance) of the raw images’ spectrum independent of the scintillator coating. For both detector positions, the reflective coating is able to raise SNR2 by up to 80% through the improved optical gain, while black coating does the opposite (decrease SNR2 by 20%) with respect to no coating. With the tested optical setups, changes in MTF /sharpness between the coatings are minor. Comparing CNR2 in CT scans of a multi-material sample, in this case an electric motor, we observe the reflective coating yielding better material contrast for plastic and air. Application and effect of Wiener-deconvolution, along with Paganin-type phase retrieval, are also discussed in the context of CT image quality.

Double refractive particle tracking and sizing

We present a novel bifocal imaging method enabling three-dimensional particle tracking and size determination employing a single camera only. The method is based on double refraction causing a particle to be imaged twice, each particle image of different blur. From these double images, a linear calibration function can be derived allowing to determine the three-dimensional particle position unambiguously over the entire depth of measurement volume. As this calibration function is independent of the particle size used, the particle size can be determined simultaneously by relating size of the double images and depth position of the particle. To prove the applicability, a co-laminar flow of two particle suspensions with particles of 1.14 μ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\upmu$$\\end{document}m and 2.47 μ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\upmu$$\\end{document}m in diameter was measured in a Y-shaped microchannel. While the laminar flow field was measured with very low uncertainty and independent of the particle size, the particle size distributions determined reproduced reliably the size distributions expected for the co-laminar flow applied, with a precision of about 98.6 %\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\%$$\\end{document} regarding the particle size discrimination. The progress for research is a new method readily to implement in common optical setups, promising, for example, valuable insights in polydisperse suspension flows—the vast majority of flows in fundamental research and applications.Graphical abstract

Postselection Technique for Optical Quantum Key Distribution with Improved de Finetti Reductions

The postselection technique is an important proof technique for proving the security of quantum key distribution protocols against coherent attacks via the uplift of any security proof against independent identically distributed collective attacks. In this work, we go through multiple steps to rigorously apply the postselection technique to optical quantum key distribution protocols. First, we place the postselection technique on a rigorous mathematical foundation by fixing a technical flaw in the original postselection paper. Second, we extend the applicability of the postselection technique to prepare-and-measure protocols by using a de Finetti reduction with a fixed marginal. Third, we show how the postselection technique can be used for decoy-state protocols by tagging the source. Finally, we extend the applicability of the postselection technique to realistic optical setups by developing a new variant of the flag-state squasher. We also improve existing de Finetti reductions, which reduce the effect of using the postselection technique on the key rate. These improvements can be more generally applied to other quantum information processing tasks. As an example to demonstrate the applicability of our work, we apply our results to the time-bin-encoded three-state protocol. We observe that the postselection technique performs better than all other known proof techniques against coherent attacks. Published by the American Physical Society 2024

Adaptive-modulated fast fluctuation super-resolution microscopy

Fluorescence microscopy has significantly advanced biological imaging at the nanoscale, particularly with the advent of super-resolution microscopy (SRM), which transcends the Abbe diffraction limit. Most cutting-edge SR methods require high-precision optical setups, which constrain the widespread adoption of SRM. Fluorescence fluctuation-based SRM (FF-SRM) can break the diffraction limit without complex optical components, making it particularly well-suited for biological imaging. However, conventional FF-SRM methods, such as super-resolution optical fluctuation imaging (SOFI), still require specific fluorescent molecular blinking properties. Instead of enhancing the intrinsic blinking characteristics by finding specific fluorescent markers, employing optical methods such as spatial light modulation to adjust the excitation light field allows for easier and more flexible matching of the on-time ratio with the analysis of temporal stochastic intensity fluctuations. Nevertheless, the specific parameters of the modulation patterns have not been thoroughly explored, despite their crucial influence on the reconstruction quality. Herein, we propose adaptive-modulated fast fluctuation super-resolution microscopy. Our method demonstrates theoretically and experimentally that restricting the size of modulation units in a certain range ensures better image quality with fewer artifacts and signal losses. We find it still significantly effective when applied to other FF-SRM. Overall, the further development of the adaptive modulation technique has made it more stable in behavior and maintained high-quality imaging, presenting broader prospects for super resolution imaging based on statistical analysis.

Micro-integrated crossed-beam optical dipole trap system with long-term alignment stability for mobile atomic quantum technologies

Quantum technologies extensively use laser light for state preparation, manipulation, and readout. For field applications, these systems must be robust and compact, driving the need for miniaturized and highly stable optical setups and system integration. In this work, we present a micro-integrated crossed-beam optical dipole trap setup, the µXODT, designed for trapping and cooling 87Rb. This fiber-coupled setup operates at 1064 nm wavelength with up to 2.5 W optical power and realizes a free-space crossed beam geometry. The µXODT precisely overlaps two focused beams (w0 ≈ 33 µm) at their waists in a 45° crossing angle, achieving a position difference of ≤3.4 µm and a 0.998 power ratio between both beams with long-term stability. We describe the design and assembly process in detail, along with optical and thermal tests with temperatures of up to 65 °C. The system’s volume of 25 ml represents a reduction of more than two orders of magnitude compared to typically used macroscopic setups while demonstrating exceptional mechanical robustness and thermal stability. The µXODT is integrated with an 87Rb 3D MOT setup, trapping 3 × 105 atoms from a laser-cooled atomic cloud, and has shown no signs of degradation after two years of operation.

A liquid crystal device-based apparatus for observing optical vortex and manipulating micro-particles

Abstract In this paper, we disclose a self-developed liquid crystal device-based optical apparatus for the teaching experiment of college students. Three relevant experiments have been presented. Through the teaching experiment class, the students have learnt the knowledge on the light-matter interaction, the photo-patterning of a liquid crystal q-plate and the generation of optical vortex, and the manipulation of micro-particle via angular momentum. Most students held positive remarks on the optical apparatus, and were satisfied with the assigned tasks in the experiment. Indeed, our proposed optical apparatus is not only applicable to the explorative research work, but also suitable for the college students’ teaching laboratories.

Second-order electrogyration effect in BSO crystal

Using a non-holographic optical setup, we employed a Mueller–Stokes polarimeter to measure both the linear electro-optic and second-order electrogyration effects. The second-order electrogyration effect was observed in a Bi12SiO20\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$Bi_{12}SiO_{20}$$\\end{document} (BSO) crystal with a (110) cut. This response was found for the electric field applied both parallel and perpendicular to the [001] direction, where the values for the second-order electrogyration are 4.86×107pm2/V2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$4.86\ imes 10^{7} \\, \ ext {pm}^{2}/\ ext {V}^{2}$$\\end{document} and 1.87×107pm2/V2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$1.87\ imes 10^{7} \\, \ ext {pm}^{2}/\ ext {V}^{2}$$\\end{document}, respectively. Additionally, the linear electro-optic coefficient γ41\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\gamma _{41}$$\\end{document} was measured to be 1.17pm/V\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$1.17 \\, \ ext {pm/V}$$\\end{document} for 660.5nm\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$660.5 \\, \ ext {nm}$$\\end{document}.

Sinusoidal PWM Generation for 3 Phase Inverter and RPM Measurement using Hercules TMS570LC43xx Launchpad

This project focuses on implementing a 3 phase Sinusoidal PWM generation using the Hercules TMS570LC43xx Launchpad Development Kit (Launchpad). The primary objective is to generate synchronized Sinusoidal nature PWM signals using the onboard High-End Timer (HET) and Enhanced Pulse Width Modulation (ePWM) module, which can be given to the Inverter for conversion of Direct current (DC) power into Alternating current (AC) power. This conversion is essential in various applications where AC power is required but the power source provides DC power. It is used in Solar photovoltaic (PV) systems and other renewable energy installations. These systems generate power suitable for powering household appliances or feeding into the electrical grid. Itis alsoused in electric vehicles (EVs) to drive the electric motor with variable speed. For verification of the wave nature, we have used an external lowpass filter (LPF) to transform the dynamic PWM signals into sinusoidal waveforms, ensuring compatibility with various applications like Inverters which can be further used in equipment and machinery such as Brushless DC motors, pumps and compressors. With the addon functionality to control the signal’s frequency which will be given to the Inverter to control the speed of the motor. Additionally, the project incorporates RPM measurement of the motor using an optical encoder setup interfaced with the Enhanced Quadrature Encoder Pulse (eQEP) module on the Launchpad. This feature enables accurate measurement of rotational speeds, position and Revolution per minute (RPM), enhancing the functionality of the system in real world applications like the speed of conveyor belts and other automated transport systems. Through successful implementation, this project demonstrates wide control for the Inverter, achieving reliable synchronized 3 phase signals with its variable speed having 120-degree phase shift signals alongside precise RPM measurement. The project highlights the Launchpad’s capabilities in handling complex signal processing tasks essential for modern power electronics applications. Looking forward, this project establishes a foundation for future enhancements and innovations in power electronics.

Optogenetic stimulation recruits cortical neurons in a morphology-dependent manner.

Single-photon optogenetics enables precise, cell-type-specific modulation of neuronal circuits, making it a crucial tool in neuroscience. Its miniaturization in the form of fully implantable wide-field stimulator arrays enables long-term interrogation of cortical circuits and bares promise for Brain-Machine Interfaces for sensory and motor function restoration. However, achieving selective activation of functional cortical representations poses a challenge, as studies show that targeted optogenetic stimulation results in activity spread beyond one functional domain. While recurrent network mechanisms contribute to activity spread, here we demonstrate with detailed simulations of isolated pyramidal neurons from cat of unknown sex that already neuron morphology causes a complex spread of optogenetic activity at the scale of one cortical column. Since the shape of a neuron impacts its optogenetic response, we find that a single stimulator at the cortical surface recruits a complex spatial distribution of neurons that can be inhomogeneous and vary with stimulation intensity and neuronal morphology across layers. We explore strategies to enhance stimulation precision, finding that optimizing stimulator optics may offer more significant improvements than preferentially somatic expression of the opsin through genetic targeting. Our results indicate that, with the right optical setup, single-photon optogenetics can precisely activate isolated neurons at the scale of functional cortical domains spanning several hundred micrometers.Significance Statement Sensory features, such as the position or orientation of a visual stimulus, are mapped onto the surface of cortex as functional domains. Their selective activation, that may enable eliciting complex percepts, is intensively pursued for basic science and clinical applications. However, delivery of light into one functional domain in optogenetically transfected cortex results in complex, widespread neuronal activity, spreading beyond the targeted domain. Our computational study reveals that neuron morphology contributes to this diffuse response in a cortical-layer and intensity-dependent manner. We show that enhancing the stimulator optics is more effective than soma-targeting of the opsin in increasing spatial precision of stimulation. Our simulations provide insights for designing optogenetic stimulation protocols and hardware to achieve selective activation of functional domains.

Illuminating cellular architecture and dynamics with fluorescence polarization microscopy.

Ever since Robert Hooke's 17th century discovery of the cell using a humble compound microscope, light-matter interactions have continuously redefined our understanding of cell biology. Fluorescence microscopy has been particularly transformative and remains an indispensable tool for many cell biologists. The subcellular localization of biomolecules is now routinely visualized simply by manipulating the wavelength of light. Fluorescence polarization microscopy (FPM) extends these capabilities by exploiting another optical property - polarization - allowing researchers to measure not only the location of molecules, but also their organization or alignment within larger cellular structures. With only minor modifications to an existing fluorescence microscope, FPM can reveal the nanoscale architecture, orientational dynamics, conformational changes and interactions of fluorescently labeled molecules in their native cellular environments. Importantly, FPM excels at imaging systems that are challenging to study through traditional structural approaches, such as membranes, membrane proteins, cytoskeletal networks and large macromolecular complexes. In this Review, we discuss key discoveries enabled by FPM, compare and contrast the most common optical setups for FPM, and provide a theoretical and practical framework for researchers to apply this technique to their own research questions.

Ultrafast diffraction algorithms for light-in-flight holography

Digital light-in-flight (LIF) holography is an ultrafast imaging technique capable of single-shot simultaneous 3D and femtosecond time resolution acquisitions of light pulse propagation. However, the numerical diffraction algorithms used to model light on femtosecond timescales are currently limited in scope, accuracy, and efficiency. We derive an analytical model capable of modeling LIF hologram formation for various optical setup configurations, able to model 3D objects and precisely account for the limited temporal coherence of the signal. We design an efficient algorithmic implementation and validate the system in numerical simulations and with an experimental LIF holographic recording setup. We report ultrafast numerical diffraction over 10,000 times faster than the reference technique, with higher accuracy and capable of modeling 3D samples, thereby broadening its application domain.

Feasibility of loop-gain tuning for general measurement systems inspired by quantum locking for DECIGO

Abstract A series of quantum locking theories have been proposed to enhance the quantum-noise-limited target sensitivity of the DECi-hertz Interferometer Gravitational wave Observatory. The quantum locking that uses a square completion optimizes the sensitivity across all frequencies. However, a substantial amount of data-series must be post-processed since the square completion is a form of signal processing technique. This paper approaches the optimal sensitivity across all frequencies from an alternative perspective: by optimizing the frequency dependence of a servo gain in a feedback loop. The optimal servo gain is formulated by comparing the alternative method with the square completion method for the same optical setup. This will be shown in general noise issues extending the framework of the quantum locking. We find that the optimal servo gain forms a non-feasible filter but has certain characteristics. We also find that the noise of the measurement signal deteriorates proportionally to the noise measured in the feedback loop when the servo gain is slightly imperfect.

Ciphertext only attack on QR code optical encryption system with spatially incoherent illumination using a neural network

Abstract Optical encryption methods attract a lot of attention owing to their high encryption speed and bandwidth. Recently, neural networks (NNs) have been used for cryptanalysis of optical encryption techniques. In this paper, we for the first time to our knowledge applied a NN for ciphertext only attack on an optical encryption system with spatially incoherent illumination. A NN was used to extract encryption keys from ciphertexts, which can be used to decrypt the plaintext QR codes. Additionally, an optically encrypted QR code was successfully decoded after using the key extracted by the trained NN, that has been processed to account for discrepancies between the numerical model and the optical setup. The results show the vulnerability of the existing optical encryption system with incoherent light to attacks of this type, which indicates the need for improved optical encryption security.

One-grating common-path phase-shifting interferometer for quantitative phase imaging

A one-grating common-path phase-shifting interferometer for quantitative phase imaging is proposed as an improvement over the original interferometer design. In the original version, the setup is long, involving a grating pair, and requires precise mechanical translation of the grating, which poses difficulties for practical applications. The proposed interferometer utilizes grating multiplexing to reduce the length of the optical setup and uses a phase-only spatial light modulator to implement pinhole filtering and phase shifting simultaneously without any moving parts, making it more conducive for the realization of a practical version.

A Low-Cost, Portable, Multi-Cancer Screening Device Based on a Ratio Fluorometry and Signal Correlation Technique.

The autofluorescence of erythrocyte porphyrins has emerged as a potential method for multi-cancer early detection (MCED). With this method's dependence on research-grade spectrofluorometers, significant improvements in instrumentation are necessary to translate its potential into clinical practice, as with any promising medical technology. To fill this gap, in this paper, we present an automated ratio porphyrin analyzer for cancer screening (ARPA-CS), a low-cost, portable, and automated instrument for MCED via the ratio fluorometry of porphyrins. The ARPA-CS aims to facilitate cancer screening in an inexpensive, rapid, non-invasive, and reasonably accurate manner for use in primary clinics or at point of care. To accomplish this, the ARPA-CS uses an ultraviolet-excited optical apparatus for ratio fluorometry that features two photodetectors for detection at 590 and 630 nm. Additionally, it incorporates a synchronous detector for the precision measurement of signals based on the Walsh-ordered Walsh-Hadamard transform (WHT)w and circular shift. To estimate its single-photodetector capability, we established a linear calibration curve for the ARBA-CS exceeding four orders of magnitude with a linearity of up to 0.992 and a low detection limit of 0.296 µg/mL for riboflavin. The ARPA-CS also exhibited excellent repeatability (0.21%) and stability (0.60%). Moreover, the ratio fluorometry of three serially diluted standard solutions of riboflavin yielded a ratio of 0.4, which agrees with that expected based on the known emission spectra of riboflavin. Additionally, the ratio fluorometry of the porphyrin solution yielded a ratio of 49.82, which was ascribed to the predominant concentration of protoporphyrin IX in the brown eggshells, as confirmed in several studies. This study validates this instrument for the ratio fluorometry of porphyrins as a biomarker for MCED. Nevertheless, large and well-designed clinical trials are necessary to further elaborate more on this matter.

B-211 Quantum dot-DNA nanocomposite enhanced single-molecule flow (SiM-Flow) for ultrasensitive microRNA detection in metastatic castrate-resistant prostate cancer

Abstract Background MicroRNAs (miRs) like miR-375 and miR-1290 are associated with cancer progression and chemoresistance in metastatic castrate-resistant prostate cancer (mCRPC). However, these prognostic biomarkers are typically present in low abundance (0.1∼1 fM) in patient plasma, which is close to the detection limit of the current gold standard techniques, quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR). Therefore, we tested a nanomaterial that incorporates quantum dots (QDs) and DNA amplicons for enhanced in-solution counting applications in plasma from a cohort of mCRPC patients. The QD-DNA nanocomposite increases the fluorescent intensity of an individual amplicon for ultrasensitive flow-counting and provides higher multiplex capacity due to the narrow emission band of QD for simple instrumentation. Methods QDs were synthesized with spectrally distinct emission bands by tuning the size or composition of CdSe core. QDs were then coated with multidentate polymer allowing further bioconjugations and better solubility in aqueous solution. The oligonucleotides complementary to amplicons generated from selected miR targets (prognostic biomarkers: miR-1290 and miR-375; normalization biomarkers: miR-16, miR-30a-5p, and cel-39) were then conjugated to QDs with optimized ratio. Total RNA was extracted from a screening cohort of 14 mCRPC patients from Huntsman Cancer Institute where platelet-poor plasma was uniformly processed with exogenous spike-in, cel-39, added in. qRT-PCR was performed using TaqMan miRNA assays, and SiM-Flow was conducted using a commercial flow cytometry to count QD barcoded enzymatic-extended miRs nanoparticles. The DNA template used for extending miRs was designed by our lab and purchased from IDT-DNA. Pearson correlation and interclass agreement analysis were applied to evaluate the concordance between the two assays. The mCRPC cohort was followed for clinical outcomes, and survival analysis for the time of progression from mCRPC to death/last follow-up was performed to determine the prognostic value of the QD-DNA nanoparticle counts. The Cox proportional hazards model was applied to linearly incorporate multiple hazard factors of patients for multivariate survival analysis. Results We demonstrated the multiplex ability of QDs with less than 5% false positive rate. The machine learning-guided optimized assay shows a 1000-time improved limit of detection of assay compared to the published literature. Interclass agreement > 0.9 and Pearson correlation of 0.94 between SiM-Flow and RT-qPCR on human plasma extracts suggest high specificity of SiM-Flow on miR detection. Also, miR-375 was identified among all the samples through SiM-Flow, although it was unidentified by qRT-PCR in 14 samples. Higher levels of miR-1290, miR-375, and prostate-specific antigen were significantly associated with poor overall survival (p=0.019) in the initial survival analysis. Survival analysis replication is ongoing in an independent mCRPC cohort. Conclusions SiM-Flow was able to detect target miRs in mCRPC patients’ plasma with a high agreement with qRT-PCR and lower detection limit and demonstrated multiplex ability with a simple optical set-up. This shows technological advancement in the detection of cancer-associated biomarkers and will aid in precision medicine therapeutic and point-of-care applications with both prognostic and predictive potential.

Visible diffuse reflectance smartphone spectrometer with high spectral accuracy

A smartphone-based spectrometer employing principle of diffuse reflection is reported for the surface analysis of solid samples. The instrument utilizes a thin-film grating to diffract incoming light, while a diffuse reflecting surface projects the image of this diffracted light onto the detector plane. The CMOS camera of smartphone camera directly captures the diffusely reflected photons within its limited field-of-view thus eliminating the need for collection, conditioning and converging optics. The optical setup of the instrument provides facility to calibrate the spectral response considering the nonlinear distribution of the wavelength across the diffraction direction. Additional correction in the detector response at different light intensity results a reduced spectral error with a maximum wavelength resolution of δλ=0.08 nm/pixel in the camera within the spectral range Δλ = (400 – 700) nm. As a proof of the concept, the instrument demonstrates successful detection of color pigments in food samples by absorption measurement of the samples at an average spectral error < 6 %. The distinct absorption peak associated with standard food colors are compared against the absorption profile of unknown food colors used in pastry cake. This field-functional smart analysis with internet connectivity opens opportunity of identifying food adulteration by using toxic chemical colors at the point-of-test and immediate reporting to others. The overall instrument is fabricated by utilizing low-cost and light weight plastic wood to make compact (110 mm × 105 mm × 125 mm), robust, inexpensive (∼$ 50) and suitable for field-portable (∼145 gm) hand-held operation.

POLCAM: instant molecular orientation microscopy for the life sciences

Current methods for single-molecule orientation localization microscopy (SMOLM) require optical setups and algorithms that can be prohibitively slow and complex, limiting widespread adoption for biological applications. We present POLCAM, a simplified SMOLM method based on polarized detection using a polarization camera, which can be easily implemented on any wide-field fluorescence microscope. To make polarization cameras compatible with single-molecule detection, we developed theory to minimize field-of-view errors, used simulations to optimize experimental design and developed a fast algorithm based on Stokes parameter estimation that can operate over 1,000-fold faster than the state of the art, enabling near-instant determination of molecular anisotropy. To aid in the adoption of POLCAM, we developed open-source image analysis software and a website detailing hardware installation and software use. To illustrate the potential of POLCAM in the life sciences, we applied our method to study α-synuclein fibrils, the actin cytoskeleton of mammalian cells, fibroblast-like cells and the plasma membrane of live human T cells.