Self-supervised denoising of Nyquist-sampled volumetric images via deep learning.

Purpose: Deep learning has demonstrated excellent performance enhancing noisy or degraded biomedical images. However, many of these models require access to a noise-free version of the images to provide supervision during training, which limits their utility. Here, we develop an algorithm (noise2Nyquist) that leverages the fact that Nyquist sampling provides guarantees about the maximum difference between adjacent slices in a volumetric image, which allows denoising to be performed without access to clean images.

Real-Time Handheld Probe Tracking and Image Formation Using Digital Frequency-Domain Diffuse Optical Spectroscopy.

Objective: Frequency-domain diffuse optical spectroscopic imaging (FD-DOS) is a non-invasive method for measuring absolute concentrations of tissue chromophores such as oxy- and deoxy-hemoglobin in vivo. The utility of FD-DOS for clinical applications such as monitoring chemotherapy response in breast cancer has previously been demonstrated, but challenges for further clinical translation, such as slow acquisition speed and lack of user feedback, remain. Here, we propose a new high speed FD-DOS instrument that allows users to freely acquire measurements over the tissue surface, and is capable of rapidly imaging large volumes of tissue.

Dual-DMD hyperspectral spatial frequency domain imaging (SFDI) using dispersed broadband illumination with a demonstration of blood stain spectral monitoring.

Spatial frequency domain imaging (SFDI) is a widefield diffuse optical measurement technique capable of generating 2D maps of sub-surface absorption and scattering in biological tissue. We developed a new hyperspectral SFDI instrument capable of collecting images at wavelengths from the visible to the near infrared. The system utilizes a custom-built monochromator with a digital micromirror device (DMD) that can dynamically select illumination wavelength bands from a broadband quartz tungsten halogen lamp, and a second DMD to provide spatially modulated sample illumination.

Distinguishing Tumor from Associated Fibrosis to Increase Diagnostic Biopsy Yield with Polarization-Sensitive Optical Coherence Tomography.

Purpose: With recent advancements in personalized medicine, biopsies must contain sufficient tumor for histologic diagnosis and molecular testing. However, inadvertent biopsy of tumor-associated fibrosis compromises tumor yield, resulting in delayed diagnoses and/or repeat procedures when additional tumor is needed. The ability to differentiate tumor from fibrosis intraprocedurally during biopsy could significantly increase tumor yield.

Quantitative assessment of airway remodelling and response to allergen in asthma.

Background And Objective: In vivo evaluation of the microstructural differences between asthmatic and non-asthmatic airways and their functional consequences is relevant to understanding and, potentially, treating asthma. In this study, we use endobronchial optical coherence tomography to investigate how allergic airways with asthma differ from allergic non-asthmatic airways in baseline microstructure and in response to allergen challenge.

Methods: A total of 45 subjects completed the study, including 20 allergic, mildly asthmatic individuals, 22 non-asthmatic allergic controls and 3 healthy controls.

Multi-distance diffuse optical spectroscopy with a single optode via hypotrochoidal scanning.

Frequency-domain diffuse optical spectroscopy (FD-DOS) is an established technique capable of determining optical properties and chromophore concentrations in biological tissue. Most FD-DOS systems use either manually positioned, handheld probes or complex arrays of source and detector fibers to acquire data from many tissue locations, allowing for the generation of 2D or 3D maps of tissue. Here, we present a new method to rapidly acquire a wide range of source-detector (SD) separations by mechanically scanning a single SD pair.

High-speed spatial frequency domain imaging with temporally modulated light.

Spatial frequency domain imaging (SFDI) is a wide-field diffuse optical technique used to obtain optical properties and chromophore concentrations in highly scattering media, such as biological tissue. Here, we present a method for rapidly acquiring multispectral SFDI data by modulating each illumination wavelength at a different temporal frequency. In the remitted signal, each wavelength is temporally demodulated and processed using conventional SFDI techniques.

Photo-induced structural modification of silk gels containing azobenzene side groups.

Azobenzene modification of Bombyx mori silkworm silk creates a photo-responsive 'azosilk' biomaterial, allowing for 3D laser patterning. Written regions fluoresce, and become fluid-filled raised 'micro-blisters' with a 10-fold photo-softening effect of the modulus. Patterning is facile and versatile, with potential applications as soft tunable materials for dynamic cell guidance and microfluidics.

Directed assembly of bio-inspired hierarchical materials with controlled nanofibrillar architectures.

In natural systems, directed self-assembly of structural proteins produces complex, hierarchical materials that exhibit a unique combination of mechanical, chemical and transport properties. This controlled process covers dimensions ranging from the nano- to the macroscale. Such materials are desirable to synthesize integrated and adaptive materials and systems.

Evaluation of Silk Inverse Opals for "Smart" Tissue Culture.

Visually tracking the subtle aspects of biological systems in real time during tissue culture remains challenging. Herein, we demonstrate the use of bioactive, cytocompatible, and biodegradable inverse opals from silk as a multifunctional substrate to transduce both the optical information and cells during tissue culture. We show that these substrates can visually track substrate degradation in various proteases during tissue digestion and protein deposition during the growth of mesenchymal stem cells.

Dityrosine Cross-Linking in Designing Biomaterials.

The development of functional biomaterials for tissue engineering and medical applications has received increasing attention. While it has been known for decades that dityrosine bonds are a key component to many biopolymer materials in native tissues, only recently have these motifs been exploited in the development of new biomaterials. Here, we first review the importance of tyrosine-tyrosine chemical bonds in the assembly and mechanical properties of natural materials.

Bio-functionalized silk hydrogel microfluidic systems.

Bio-functionalized microfluidic systems were developed based on a silk protein hydrogel elastomeric materials. A facile multilayer fabrication method using gelatin sacrificial molding and layer-by-layer assembly was implemented to construct interconnected, three dimensional (3D) microchannel networks in silk hydrogels at 100 μm minimum feature resolution. Mechanically activated valves were implemented to demonstrate pneumatic control of microflow.

Photocrosslinking of Silk Fibroin Using Riboflavin for Ocular Prostheses.

A novel method to photocrosslink silk fibroin protein is reported, using riboflavin (vitamin B2) as a photoinitiator and the mechanism of crosslinking is determined. Exposure of riboflavin-doped liquid silk solution to light results in the formation of a transparent, elastic hydrogel. Several applications for this new material are investigated including corneal reshaping to restore visual acuity and photolithography.

Biocompatible silk step-index optical waveguides.

Biocompatible optical waveguides were constructed entirely of silk fibroin. A silk film (n=1.54) was encapsulated within a silk hydrogel (n=1.

Transparent, Nanostructured Silk Fibroin Hydrogels with Tunable Mechanical Properties.

Silk fibroin from the caterpillar has been processed into many material forms, with potential applications in areas ranging from optoelectronics to tissue engineering. As a hydrogel, silk fibroin has been engineered as a substrate for the regeneration of soft tissues where hydration and mechanical compatibility are necessary. Current fabrication of silk fibroin hydrogels produces microstructured materials that lack transparency and limits the ability to fully exploit the hydrogel form.

Laser-based three-dimensional multiscale micropatterning of biocompatible hydrogels for customized tissue engineering scaffolds.

Light-induced material phase transitions enable the formation of shapes and patterns from the nano- to the macroscale. From lithographic techniques that enable high-density silicon circuit integration, to laser cutting and welding, light-matter interactions are pervasive in everyday materials fabrication and transformation. These noncontact patterning techniques are ideally suited to reshape soft materials of biological relevance.

Highly tunable elastomeric silk biomaterials.

Elastomeric, fully degradable and biocompatible biomaterials are rare, with current options presenting significant limitations in terms of ease of functionalization and tunable mechanical and degradation properties. We report a new method for covalently crosslinking tyrosine residues in silk proteins, via horseradish peroxidase and hydrogen peroxide, to generate highly elastic hydrogels with tunable properties. The tunable mechanical properties, gelation kinetics and swelling properties of these new protein polymers, in addition to their ability to withstand shear strains on the order of 100%, compressive strains greater than 70% and display stiffness between 200 - 10,000 Pa, covering a significant portion of the properties of native soft tissues.

Determination of multiphoton absorption of silk fibroin using the Z-scan technique.

The multiphoton absorption of silk fibroin at 810 nm was determined by open-aperture Z-scan. Three-photon absorption was confirmed at this wavelength and the three-photon cross section of silk fibroin was measured. Silk fibroin of varying molecular weight was tested and the cross section was found to increase exponentially with increasing molecular weight.

Toward the guidance of transbronchial biopsy: identifying pulmonary nodules with optical coherence tomography.

Background: Solitary pulmonary nodules (SPNs) frequently require transbronchial needle aspiration (TBNA) or biopsy to determine malignant potential, but have variable diagnostic yields. Confirming needle placement within SPNs during TBNA could significantly increase diagnostic yield. Optical coherence tomography (OCT) provides nondestructive, high-resolution, microstructural imaging with potential to distinguish SPN from parenchyma.

Optical frequency domain imaging of ex vivo pulmonary resection specimens: obtaining one to one image to histopathology correlation.

Lung cancer is the leading cause of cancer-related deaths. Squamous cell and small cell cancers typically arise in association with the conducting airways, whereas adenocarcinomas are typically more peripheral in location. Lung malignancy detection early in the disease process may be difficult due to several limitations: radiological resolution, bronchoscopic limitations in evaluating tissue underlying the airway mucosa and identifying early pathologic changes, and small sample size and/or incomplete sampling in histology biopsies.

Volumetric optical frequency domain imaging of pulmonary pathology with precise correlation to histopathology.

Background: Lung cancer is the leading cause of cancer-related mortality. Radiology and bronchoscopy techniques do not have the necessary resolution to evaluate lung lesions on the microscopic scale, which is critical for diagnosis. Bronchial biopsy specimens can be limited by sampling error and small size.