NIRis: A low-cost, versatile imaging system for near-infrared fluorescence detection of phototrophic cell colonies used in research and education.

A variety of costly research-grade imaging devices are available for the detection of spectroscopic features. Here we present an affordable, open-source and versatile device, suitable for a range of applications. We provide the files to print the imaging chamber with commonly available 3D printers and instructions to assemble it with easily available hardware. The imager is suitable for rapid sample screening in research, as well as for educational purposes. We provide details and results for an already proven set-up which suits the needs of a research group and students interested in UV-induced near-infrared fluorescence detection of microbial colonies grown on Petri dishes. The fluorescence signal confirms the presence of bacteriochlorophyll a in aerobic anoxygenic phototrophic bacteria (AAPB). The imager allows for the rapid detection and subsequent isolation of AAPB colonies on Petri dishes with diverse environmental samples. To this date, 15 devices have been build and more than 7000 Petri dishes have been analyzed for AAPB, leading to over 1000 new AAPB isolates. Parts can be modified depending on needs and budget. The latest version with automated switches and double band pass filters costs around 350€ in materials and resolves bacterial colonies with diameters of 0.5 mm and larger. The low cost and modular build allow for the integration in high school classes to educate students on light properties, fluorescence and microbiology. Computer-aided design of 3D-printed parts and programming of the employed Raspberry Pi computer could be incorporated in computer sciences classes. Students have been also inspired to do agar art with microbes. The device is currently used in seven different high schools in Finland. Additionally, a science education network of Finnish universities has incorporated it in its program for high school students. Video guides have been produced to facilitate easy operation and accessibility of the device.

Improving the spatial resolution and signal-to-noise ratio of ultrasound switchable fluorescence imaging.

Ultrasound switchable fluorescence (USF) imaging, a hybrid imaging technology that combines the advantages of both fluorescence sensitivity and acoustic resolution in centimeter-deep tissue, has great potential for biomedical different applications. A camera-based USF imaging system reveals its capability of capturing both spatial and temporal dynamics of the USF signal in tissue. In this study, various algorithms were explored to enhance the spatial resolution and signal-to-noise ratio (SNR) of USF images, utilizing temporal and spatial information from a camera-based time-domain USF imaging system. The correlation method proved effective in boosting SNR, while the ascending-slope-weighted method enhanced spatial resolution. Additionally, the spatially back-projection method significantly improved spatial resolution in silicone phantoms. The results underscore the advantages of incorporating temporal and spatial information from USF signals.

A Novel Fit-Flexible Fluorescence Soft Imager: Tri-Sensing of Intensity, Fall-Time, and Life Profile.

Time-resolved fluorescence imaging techniques, like confocal fluorescence lifetime imaging microscopy, are powerful photonic instrumentation tools of modern science with diverse applications, including: biology, medicine, and chemistry. However, complexities of the systems, both at specimen and device levels, cause difficulties in quantifying soft biomarkers. To address the problems, we first aim to understand and model the underlying photophysics of fluorescence decay curves. For this purpose, we provide a set of mathematical functions, called "life models", fittable with the real temporal recordings of histogram of photon counts. For each model, an equivalent electrical circuit, called a "life circuit", is derived for explaining the whole process. In confocal endomicroscopy, the components of excitation laser, specimen, and fluorescence-emission signal as the histogram of photon counts are modelled by a power source, network of resistor-inductor-capacitor circuitry, and multimetre, respectively. We then design a novel pixel-level temporal classification algorithm, called a "fit-flexible approach", where qualities of "intensity", "fall-time", and "life profile" are identified for each point. A model selection mechanism is used at each pixel to flexibly choose the best representative life model based on a proposed Misfit-percent metric. A two-dimensional arrangement of the quantified information detects some kind of structural information. This approach showed a potential of separating microbeads from lung tissue, distinguishing the tri-sensing from conventional methods. We alleviated by 7% the error of the Misfit-percent for recovering the histograms on real samples than the best state-of-the-art competitor. Codes are available online.

A preliminary study of multispectral Cherenkov imaging and a Fricke-xylenol orange gel film (MCIFF) for online, absolute dose measurement.

BACKGROUND: Cherenkov luminescence imaging has shown potential for relative dose distribution and field verification in radiation therapy. However, to date, limited research utilizing Cherenkov luminescence for absolute dose calibration has been conducted owing to uncertainties arising from camera positioning and tissue surface optical properties. PURPOSE: This paper introduces a novel approach to multispectral Cherenkov luminescence imaging combined with Fricke-xylenol orange gel (FXG) film, termed MCIFF, which can enable online full-field absolute dose measurement. By integrating these two approaches, MCIFF allows for calibration of the ratio between two spectral intensities with absorbed dose, thereby enabling absolute dose measurement. METHODS: All experiments are conducted on a Varian Clinac 23EX, utilizing an electron multiplying charge-coupled device (EMCCD) camera and a two-way image splitter for simultaneous capture of two-spectral Cherenkov imaging. In the first part of this study, the absorbance curves of the prepared FXG film, which receives different doses, are measured using a fluorescence spectrophotometer to verify the correlation between absorbance and dose. In the second part, the FXG film is positioned directly under the radiation beam to corroborate the dose measurement capacity of MCIFF across various beams. In the third part, the feasibility of MCIFF is tested in actual radiotherapy settings via a humanoid model, demonstrating its versatility with various radiotherapy materials. RESULTS: The results of this study indicate that the logarithmic ratios of spectral intensities at wavelengths of 550 ± 50 and 700 ± 100 nm accurately reflect variations in radiation dose (R2 > 0.96) across different radiation beams, particle energies, and dose rates. The slopes of the fitting lines remain consistent under varying beam conditions, with discrepancies of less than 8%. The optical profiles obtained using the MCIFF exhibit a satisfactory level of agreement with the measured results derived from the treatment planning system (TPS) and EBT3 films. Specifically, for photon beams, the lateral distances between the 80% and 20% isodose lines, referred to as the penumbra (P80-20) values, obtained through TPS, EBT3 films, and MCIFF, are determined as 0.537, 0.664, and 0.848 cm, respectively. Similarly, for electron beams, the P80-20 values obtained through TPS, EBT3 films, and MCIFF are found to be 0.432, 0.561, and 0.634 cm, respectively. Furthermore, imaging of the anthropomorphic phantom demonstrates the practical application of MCIFF in real radiotherapy environments. CONCLUSION: By combining an FXG film with Cherenkov luminescence imaging, MCIFF can calibrate Cherenkov luminescence to absorbed dose, filling the gap in online 2D absolute dose measurement methods in clinical practice, and providing a new direction for the clinical application of optical imaging to radiation therapy.

Frameworks of wavelength selection in diffuse reflectance spectroscopy for tissue differentiation in orthopedic surgery.

Significance: Wavelength selection from a large diffuse reflectance spectroscopy (DRS) dataset enables removal of spectral multicollinearity and thus leads to improved understanding of the feature domain. Feature selection (FS) frameworks are essential to discover the optimal wavelengths for tissue differentiation in DRS-based measurements, which can facilitate the development of compact multispectral optical systems with suitable illumination wavelengths for clinical translation. Aim: The aim was to develop an FS methodology to determine wavelengths with optimal discriminative power for orthopedic applications, while providing the frameworks for adaptation to other clinical scenarios. Approach: An ensemble framework for FS was developed, validated, and compared with frameworks incorporating conventional algorithms, including principal component analysis (PCA), linear discriminant analysis (LDA), and backward interval partial least squares (biPLS). Results: Via the one-versus-rest binary classification approach, a feature subset of 10 wavelengths was selected from each framework yielding comparable balanced accuracy scores (PCA: 94.8±3.47%, LDA: 98.2±2.02%, biPLS: 95.8±3.04%, and ensemble: 95.8±3.16%) to those of using all features (100%) for cortical bone versus the rest class labels. One hundred percent balanced accuracy scores were generated for bone cement versus the rest. Different feature subsets achieving similar outcomes could be identified due to spectral multicollinearity. Conclusions: Wavelength selection frameworks provide a means to explore domain knowledge and discover important contributors to classification in spectroscopy. The ensemble framework generated a model with improved interpretability and preserved physical interpretation, which serves as the basis to determine illumination wavelengths in optical instrumentation design.

Ultra high-speed single-molecule fluorescence imaging.

In two articles in this issue, Fujiwara et al. developed an ultrasensitive high-speed camera capable of single-molecule fluorescence imaging at a microsecond timescale (2023. J. Cell Biol.https://doi.org/10.1083/jcb.202110160). This major leap in detection speed enables the organization of plasma membrane and integrin-based adhesions to be probed in unprecedented detail (2023. J. Cell Biol.https://doi.org/10.1083/jcb.202110162).

Non-invasive estimation of hemoglobin, bilirubin and oxygen saturation of neonates simultaneously using whole optical spectrum analysis at point of care.

The study was aimed to evaluate the performance of a newly developed spectroscopy-based non-invasive and noncontact device (SAMIRA) for the simultaneous measurement of hemoglobin, bilirubin and oxygen saturation as an alternative to the invasive biochemical method of blood sampling. The accuracy of the device was assessed in 4318 neonates having incidences of either anemia, jaundice, or hypoxia. Transcutaneous bilirubin, hemoglobin and blood saturation values were obtained by the newly developed instrument which was corroborated with the biochemical blood tests by expert clinicians. The instrument is trained using Artificial Neural Network Analysis to increase the acceptability of the data. The artificial intelligence incorporated within the instrument determines the disease condition of the neonate. The Pearson's correlation coefficient, r was found to be 0.987 for hemoglobin estimation and 0.988 for bilirubin and blood gas saturation respectively. The bias and the limits of agreement for the measurement of all the three parameters were within the clinically acceptance limit.

Enhanced incorporation of subnanometer tags into cellular proteins for fluorescence nanoscopy via optimized genetic code expansion.

With few-nanometer resolution recently achieved by a new generation of fluorescence nanoscopes (MINFLUX and MINSTED), the size of the tags used to label proteins will increasingly limit the ability to dissect nanoscopic biological structures. Bioorthogonal (click) chemical groups are powerful tools for the specific detection of biomolecules. Through the introduction of an engineered aminoacyl-tRNA synthetase/tRNA pair (tRNA: transfer ribonucleic acid), genetic code expansion allows for the site-specific introduction of amino acids with "clickable" side chains into proteins of interest. Well-defined label positions and the subnanometer scale of the protein modification provide unique advantages over other labeling approaches for imaging at molecular-scale resolution. We report that, by pairing a new N-terminally optimized pyrrolysyl-tRNA synthetase (chPylRS2020) with a previously engineered orthogonal tRNA, clickable amino acids are incorporated with improved efficiency into bacteria and into mammalian cells. The resulting enhanced genetic code expansion machinery was used to label ß-actin in U2OS cell filopodia for MINFLUX imaging with minimal separation of fluorophores from the protein backbone. Selected data were found to be consistent with previously reported high-resolution information from cryoelectron tomography about the cross-sectional filament bundling architecture. Our study underscores the need for further improvements to the degree of labeling with minimal-offset methods in order to fully exploit molecular-scale optical three-dimensional resolution.

Achromatic doublet electrowetting prism array for beam steering device in foveated display.

A foveated display is a technology that can solve the problem of insufficient angular resolution (relative to the human eye) for near-eye display. In a high-resolution foveated display, a beam steering element is required to track the human gaze. An electrowetting prism array is a transmissive non-mechanical beam steering device, that allows a light and compact optical system to be configured and a large aperture possible. However, the view is obstructed by the sidewall of the prism array. When the size of the cell prism is 7mm, the prism array has an 87% fill-factor. To push the fill-factor to 100%, the cell prisms were magnified using a lens array. Image processing was performed such that the image produced by the lens array was identical to the original. Beam steering by refraction is accompanied by chromatic dispersion, which causes chromatic aberration, making colors appear blurry. The refractive index condition to reduce chromatic dispersion was obtained using the doublet structure of the electrowetting prism. The chromatic dispersion was reduced by 70% on average.

Live-dead assay on unlabeled cells using phase imaging with computational specificity.

Existing approaches to evaluate cell viability involve cell staining with chemical reagents. However, the step of exogenous staining makes these methods undesirable for rapid, nondestructive, and long-term investigation. Here, we present an instantaneous viability assessment of unlabeled cells using phase imaging with computation specificity. This concept utilizes deep learning techniques to compute viability markers associated with the specimen measured by label-free quantitative phase imaging. Demonstrated on different live cell cultures, the proposed method reports approximately 95% accuracy in identifying live and dead cells. The evolution of the cell dry mass and nucleus area for the labeled and unlabeled populations reveal that the chemical reagents decrease viability. The nondestructive approach presented here may find a broad range of applications, from monitoring the production of biopharmaceuticals to assessing the effectiveness of cancer treatments.

Quantitative Indocyanine Green Fluorescence Imaging Assessment for Nonmucinous Peritoneal Metastases: Preliminary Results of the ICCP Study.

BACKGROUND: In selected patients with peritoneal metastases of colorectal origin, complete cytoreduction has been the main single prognostic factor influencing long-term outcomes. In these patients, indocyanine green fluorescence imaging seems to be useful in detecting small subclinical peritoneal implants. However, quantitative fluorescence analysis has not yet been established as standard. OBJECTIVE: This study aimed to evaluate the sensitivity and specificity of quantitative indocyanine green fluorescence assessment in the detection of peritoneal metastases of nonmucinous colorectal origin. DESIGN: This is a single-center, single-arm, low-intervention prospective trial. SETTINGS: A fluorescence assessment device was used for intraoperative fluorescence quantitative assessment. PATIENTS: Consecutive patients diagnosed with peritoneal metastases of colorectal origin who met the inclusion criteria were selected for curative surgery. INTERVENTIONS: Intravenous indocyanine green was administered 12 hours before surgery. Cytoreduction was performed through nodule identification under white light and then under indocyanine green. Finally, ex vivo fluorescence was assessed. MAIN OUTCOME MEASURES: The primary outcomes measured were the sensitivity and specificity of quantitative fluorescence. RESULTS: The first 11 enrolled patients were included in this preliminary analysis. In total, 52 nodules were resected, with 37 (71.1%) being diagnosed as malignant in the histopathological analysis. Of those, 5 (13.5%) were undetectable under white light and were identified only with fluorescence. A total of 15 nonmalignant nodules were detected under white light, 8 (53.3%) of which were fluorescence negative. Fluorescence greater than 181 units might be the threshold of malignancy, with a sensitivity and specificity of 89.0% and 85.0%, whereas uptake less than 100 units appears to correlate with a benign pathology. LIMITATIONS: The limited sample size, the physiological uptake, and excretion of indocyanine green might interfere with the assessment of unnoticed implants in the bowel serosa and liver. CONCLUSIONS: Quantitative indocyanine green seems to be useful for the assessment of nonmucinous colorectal peritoneal metastases. Fluorescence uptake greater than 181 units appears to correlate with malignancy, whereas uptake less than 100 units appears to correlate with a benign pathology. See Video Abstract at http://links.lww.com/DCR/B743. EVALUACIN CUANTITATIVA DE IMGENES DE FLUORESCENCIA CON VERDE DE INDOCIANINA PARA METSTASIS PERITONEALES NO MUCINOSAS RESULTADOS PRELIMINARES DEL ESTUDIO ICCP: ANTECEDENTES:En pacientes seleccionados con metástasis peritoneales de origen colorrectal, la citorreducción com-pleta ha sido el único factor pronóstico principal que influye en el resultado a largo plazo. En estos pacientes, las imágenes de fluorescencia con verde de indocianina parecen ser útiles para detectar pequeños implantes peritoneales subclínicos. Sin embargo, el análisis cuantitativo de fluorescencia aún no se ha establecido como estándar.OBJETIVO:Evaluar la sensibilidad y especificidad de la evaluación cuantitativa de fluorescencia verde de indo-cianina, en la detección de metástasis peritoneales de origen colorrectal no mucinoso.DISEÑO:Ensayo prospectivo de intervención baja de un solo brazo y un solo centro.ENTORNO CLINICO:El dispositivo se utilizó para la evaluación cuantitativa de fluorescencia intraoperatoria.PACIENTES:Pacientes consecutivos diagnosticados con metástasis peritoneales de origen colorrectal, selecciona-dos para cirugía curativa y que cumplieron con los criterios de inclusión.INTERVENCIONES:Se administró verde de indocianina por vía intravenosa 12 h antes de la cirugía. La citorreducción se realizó mediante identificación de nódulos con luz blanca y luego con verde de indocianina. Final-mente, se evaluó la fluorescencia ex vivo.PRINCIPALES MEDIDAS DE VALORACION:Sensibilidad y especificidad cuantitativa de la fluorescencia.RESULTADOS:Los primeros 11 pacientes fueron incluidos en este análisis preliminar. En total se resecaron 52 nódu-los, siendo 37 (71,1%) diagnosticados como malignos en el análisis histopatológico. De ellos, 5 (13,5%) eran indetectables bajo luz blanca y solamente se identificaron con fluorescencia. Se detec-taron un total de 15 nódulos no malignos bajo luz blanca, de los cuales 8 (53,3%) fueron fluorescen-tes negativos. La fluorescencia superior a 181 unidades podría ser el umbral de malignidad, con una sensibilidad y especificidad del 89,0% y el 85,0% respectivamente; mientras que la captación por debajo de 100 unidades parece correlacionarse con una patología benigna.LIMITACIONES:El tamaño limitado de la muestra; la captación fisiológica y la excreción de verde de indocianina pueden interferir con la evaluación de implantes inadvertidos en la serosa intestinal y el hígado.CONCLUSIONES:La cuantificación del verde de indocianina, parece ser útil en la evaluación de metástasis peritonea-les colorrectales no mucinosas. La captación de fluorescencia por encima de 181 unidades parece correlacionarse con la malignidad, mientras que la captación por debajo de 100 unidades parece co-rrelacionarse con una patología benigna. Consulte Video Resumen en http://links.lww.com/DCR/B743. (Traducción - Dr. Fidel Ruiz Healy).

The challenge of determining lysyl oxidase activity: Old methods and novel approaches.

The lysyl oxidase (LOX) family of enzymes catalyze the oxidative deamination of lysine and hydroxylysine residues in collagen and elastin in the initiation step of the formation of covalent cross-linkages, an essential process for extracellular matrix (ECM) maturation. Elevated LOX expression levels leading to increased LOX activity is associated with diverse pathologies including fibrosis, cancer, and cardiovascular diseases. Different protocols have been so far established to detect and quantify LOX activity from tissue samples and cultured cells, all of them showing advantages and drawbacks. This review article presents a critical overview of the main features of currently available methods as well as introduces some recent technologies called to revolutionize our approach to LOX catalysis.

Flexible foveated imaging using a single Risley-prism imaging system.

Foveated imaging, which has the ability to provide overall situational awareness over a large field of view and high-resolution perception of local details, has significant advantages in many specific applications. However, existing artificially foveated imaging systems are complex, bulky, and expensive, and the flexibility of the fovea specifically has many limitations. To overcome these deficiencies, this paper proposes a method for foveated imaging by collecting multiple partially overlapping sub-fields of view. To capture the above special sub-fields of view, we propose a high-efficiency algorithm based on the characteristics of the field of view deflected by the Risley-prism and aimed at solving the prism rotation angles. In addition, we prove the reliability of the proposed algorithm by cross-validation with the particle swarm optimization algorithm. The experimental results show that the proposed method can achieve flexible foveated imaging using a single Risley-prism imaging system.

Waveguide-type see-through dual focus near-eye display with a polarization grating.

Waveguide-type near-eye displays have useful properties such as compact form factor, lightweight and see-through capability. Conventional systems, however, support only a single image plane fixed at a certain distance, which may induce eye fatigue due to the vergence-accommodation conflict. In this paper, we propose a waveguide-type near-eye display with two image planes using a polarization grating. Two images with orthogonal polarizations propagate within the waveguide with different total internal reflection angles and form virtual images at different distances. The use of the polarization grating and two pairs of holographic optical elements enables dual image plane formation by a single waveguide with high transparency for the real scene. Optical experiments confirm the principle of the proposed optical system.

Diesel2p mesoscope with dual independent scan engines for flexible capture of dynamics in distributed neural circuitry.

Imaging the activity of neurons that are widely distributed across brain regions deep in scattering tissue at high speed remains challenging. Here, we introduce an open-source system with Dual Independent Enhanced Scan Engines for Large field-of-view Two-Photon imaging (Diesel2p). Combining optical design, adaptive optics, and temporal multiplexing, the system offers subcellular resolution over a large field-of-view of ~25 mm2, encompassing distances up to 7 mm, with independent scan engines. We demonstrate the flexibility and various use cases of this system for calcium imaging of neurons in the living brain.

Flexible simultaneous mesoscale two-photon imaging of neural activity at high speeds.

Understanding brain function requires monitoring local and global brain dynamics. Two-photon imaging of the brain across mesoscopic scales has presented trade-offs between imaging area and acquisition speed. We describe a flexible cellular resolution two-photon microscope capable of simultaneous video rate acquisition of four independently targetable brain regions spanning an approximate five-millimeter field of view. With this system, we demonstrate the ability to measure calcium activity across mouse sensorimotor cortex at behaviorally relevant timescales.

Full spectrum fluorescence lifetime imaging with 0.5 nm spectral and 50 ps temporal resolution.

The use of optical techniques to interrogate wide ranging samples from semiconductors to biological tissue for rapid analysis and diagnostics has gained wide adoption over the past decades. The desire to collect ever more spatially, spectrally and temporally detailed optical signatures for sample characterization has specifically driven a sharp rise in new optical microscopy technologies. Here we present a high-speed optical scanning microscope capable of capturing time resolved images across 512 spectral and 32 time channels in a single acquisition with the potential for ~0.2 frames per second (256 × 256 image pixels). Each pixel in the resulting images contains a detailed data cube for the study of diverse time resolved light driven phenomena. This is enabled by integration of system control electronics and on-chip processing which overcomes the challenges presented by high data volume and low imaging speed, often bottlenecks in previous systems.

A Two-Photon Microimaging-Microdevice System for Four-Dimensional Imaging of Local Drug Delivery in Tissues.

Advances in the intratumor measurement of drug responses have included a pioneering biomedical microdevice for high throughput drug screening in vivo, which was further advanced by integrating a graded-index lens based two-dimensional fluorescence micro-endoscope to monitor tissue responses in situ across time. While the previous system provided a bulk measurement of both drug delivery and tissue response from a given region of the tumor, it was incapable of visualizing drug distribution and tissue responses in a three-dimensional (3D) way, thus missing the critical relationship between drug concentration and effect. Here we demonstrate a next-generation system that couples multiplexed intratumor drug release with continuous 3D spatial imaging of the tumor microenvironment via the integration of a miniaturized two-photon micro-endoscope. This enables optical sectioning within the live tissue microenvironment to effectively profile the entire tumor region adjacent to the microdevice across time. Using this novel microimaging-microdevice (MI-MD) system, we successfully demonstrated the four-dimensional imaging (3 spatial dimensions plus time) of local drug delivery in tissue phantom and tumors. Future studies include the use of the MI-MD system for monitoring of localized intra-tissue drug release and concurrent measurement of tissue responses in live organisms, with applications to study drug resistance due to nonuniform drug distribution in tumors, or immune cell responses to anti-cancer agents.

Developing diagnostic assessment of breast lumpectomy tissues using radiomic and optical signatures.

High positive margin rates in oncologic breast-conserving surgery are a pressing clinical problem. Volumetric X-ray scanning is emerging as a powerful ex vivo specimen imaging technique for analyzing resection margins, but X-rays lack contrast between non-malignant and malignant fibrous tissues. In this study, combined micro-CT and wide-field optical image radiomics were developed to classify malignancy of breast cancer tissues, demonstrating that X-ray/optical radiomics improve malignancy classification. Ninety-two standardized features were extracted from co-registered micro-CT and optical spatial frequency domain imaging samples extracted from 54 breast tumors exhibiting seven tissue subtypes confirmed by microscopic histological analysis. Multimodal feature sets improved classification performance versus micro-CT alone when adipose samples were included (AUC = 0.88 vs. 0.90; p-value = 3.65e-11) and excluded, focusing the classification task on exclusively non-malignant fibrous versus malignant tissues (AUC = 0.78 vs. 0.85; p-value = 9.33e-14). Extending the radiomics approach to high-dimensional optical data-termed "optomics" in this study-offers a promising optical image analysis technique for cancer detection. Radiomic feature data and classification source code are publicly available.