Exploring local spatial features in hyperspectral image

We propose a methodological framework to extract spatial features in hyperspectral imaging data and establish a link between these features and the spectral regions, capturing the observed structural patterns. The proposed approach consists of five main steps: i) two dimensional Stationary Wavelet Transform (2D-SWT) is applied to a hyperspectral data cube, decomposing each single-channel image with a selected wavelet filter up to the maximum decomposition level; ii) a grey-level co-occurrence matrix is calculated for every 2D-SWT image resulting from stage i); iii) distinctive spatial features are determined by computing morphological descriptors from each grey-level co-occurrence matrix; iv) the morphological descriptors are rearranged in a two dimensional data array; v) this data matrix is subjected to Principal Component Analysis (PCA) for exploring the variability of the aforementioned descriptors across spectral channels. As a result, groups of spectral wavelengths associated to specific spatial features can be pointed out yielding a better understanding and interpretation of the data. In principle, this information can also be further exploited, e.g. to improve the separation of pure spectral profiles in a multivariate curve resolution context

Impact of Bentonite Clay on In Situ Pyrolysis vs. Hydrothermal Carbonization of Avocado Pit Biomass

Biofuels produced via thermochemical conversions of waste biomass could be sustainable alternatives to fossil fuels but currently require costly downstream upgrading to be used in existing infrastructure. In this work, we explore how a low-cost, abundant clay mineral, bentonite, could serve as an in situ heterogeneous catalyst for two different thermochemical conversion processes: pyrolysis and hydrothermal carbonization (HTC). Avocado pits were combined with 20 wt% bentonite clay and were pyrolyzed at 600 °C and hydrothermally carbonized at 250 °C, commonly used conditions across the literature. During pyrolysis, bentonite clay promoted Diels–Alder reactions that transformed furans to aromatic compounds, which decreased the bio-oil oxygen content and produced a fuel closer to being suitable for existing infrastructure. The HTC bio-oil without the clay catalyst contained 100% furans, mainly 5-methylfurfural, but in the presence of the clay, approximately 25% of the bio-oil was transformed to 2-methyl-2-cyclopentenone, thereby adding two hydrogen atoms and removing one oxygen. The use of clay in both processes decreased the relative oxygen content of the bio-oils. Proximate analysis of the resulting chars showed an increase in fixed carbon (FC) and a decrease in volatile matter (VM) with clay inclusion. By containing more FC, the HTC-derived char may be more stable than pyrolysis-derived char for environmental applications. The addition of bentonite clay to both processes did not produce significantly different bio-oil yields, such that by adding a clay catalyst, a more valuable bio-oil was produced without reducing the amount of bio-oil recovered

Biomass-Based Fuels and Activated Carbon Electrode Materials: An Integrated Approach to Green Energy Systems

Although pyrolysis holds promise for extracting biofuels from biomass, the low value of the biochar produced, combined with process energy requirements, make thermochemical conversion marginally viable. Likewise, while supercapacitors and fuel cells may satisfy growing demands for portable electronics and electric vehicles, current fossil-fuel based activated carbon electrodes are not sustainable. Both of these issues are addressed using a new approach to the integrated biorefinery. Pyrolysis of pistachio nutshell biomass yields a bio-oil high in benzenediols and pyrolysis gas enriched in methane and hydrogen. By impregnating the biochars produced via pyrolysis with potassium hydroxide, followed by heat treatment in an inert atmosphere, the total biofuel yield increased up to 25% while producing high surface area (>1900 m²/g) activated carbon biochar for use in electrochemical cells. Coin cell electrodes fabricated with these sustainable activated carbons provide almost 100% coulombic efficiency over 4000 charge–discharge cycles with a specific capacitance of 45 F/g at a scan rate of 1 mV/s using a Li-salt electrolyte. Such integrated processes will hasten the transition to a renewable energy future

Intraoperative Tumor Assessment Using Real-Time Molecular Imaging in Head and Neck Cancer Patients

Background: In head and neck cancer, surgical resection using primarily visual and tactile feedback is considered the gold standard for solid tumors. Due to high numbers of tumor-involved surgical margins, which are directly correlated to poor clinical outcomes, intraoperative optical imaging trials have rapidly proliferated over the past 5 years. However, few studies report on intraoperative in situ imaging data that could support surgical resection. To demonstrate the clinical application of in situ surgical imaging, we report on the imaging data that are directly (ie in real-time) available to the surgeon. Study Design: Fluorescence intensities and tumor-to-background ratios (TBRs) were determined from the intraoperative imaging data–the view as seen by the surgeon during tumor resection–of 20 patients, and correlated to patient and tumor characteristics including age, sex, tumor site, tumor size, histologic differentiation, and epidermal growth factor receptor (EGFR) expression. Furthermore, different lighting conditions in regard to surgical workflow were evaluated. Results: Under these circumstances, intraoperative TBRs of the primary tumors averaged 2.2 ± 0.4 (range 1.5 to 2.9). Age, sex, tumor site, and tumor size did not have a significant effect on open-field intraoperative molecular imaging of the primary tumors (p > 0.05). In addition, variation in EGFR expression levels or the presence of ambient light did not seem to alter TBRs. Conclusions: We present the results of successful in situ intraoperative imaging of primary tumors alongside the optimal conditions with respect to both molecular image acquisition and surgical workflow. This study illuminates the potentials of open-field molecular imaging to assist the surgeon in achieving successful cancer removal

Rapid, non-invasive fluorescence margin assessment: Optical specimen mapping in oral squamous cell carcinoma

Objective: Surgical resection remains the primary treatment for the majority of solid tumors. Despite efforts to obtain wide margins, close or positive surgical margins (<5 mm) are found in 15–30% of head and neck cancer patients. Obtaining negative margins requires immediate, intraoperative feedback of margin status. To this end, we propose optical specimen mapping of resected tumor specimens immediately after removal. Materials and methods: A first-in-human pilot study was performed in patients (n = 8) after infusion of fluorescently labeled antibody, panitumumab-IRDye800 to allow surgical mapping of the tumor specimen. Patients underwent standard of care surgical resection for head and neck squamous cell carcinoma (HNSCC). Optical specimen mapping was performed on the primary tumor specimen and correlated with pathological findings after tissue processing. Results: Optical mapping of the specimen had a 95% sensitivity and 89% specificity to detect cancer within 5 mm (n = 160) of the cut surface. To detect tumor within 2 mm of the specimen surface, the sensitivity of optical specimen mapping was 100%. The maximal observed penetration depth of panitumumab-IRDye800 through human tissue in our study was 6.3 mm. Conclusion: Optical specimen mapping is a highly sensitive and specific method for evaluation of margins within <5 mm of the tumor mass in HNSCC specimens. This technology has potentially broad applications for ensuring adequate tumor resection and negative margins in head and neck cancers

The clinical application of fluorescence-guided surgery in head and neck cancer

Although surgical resection has been the primary treatment modality of solid tumors for decades, surgeons still rely on visual cues and palpation to delineate healthy from cancerous tissue. This may contribute to the high rate (up to 30%) of positive margins in head and neck cancer resections. Margin status in these patients is the most important prognostic factor for overall survival. In addition, second primary lesions may be present at the time of surgery. Although often unnoticed by the medical team, these lesions can have significant survival ramifications. We hypothesize that real-time fluorescence imaging can enhance intraoperative decision making by aiding the surgeon in detecting close or positive margins and visualizing unanticipated regions of primary disease. The purpose of this study was to assess the clinical utility of real-time fluorescence imaging for intraoperative decision making. Methods: Head and neck cancer patients (n 5 14) scheduled for curative resection were enrolled in a clinical trial evaluating panitumumab-IRDye800CW for surgical guidance (NCT02415881). Open-field fluorescence imaging was performed throughout the surgical procedure. The fluorescence signal was quantified as signal-to-background ratios to characterize the fluorescence contrast of regions of interest relative to background. Results: Fluorescence imaging was able to improve surgical decision making in 3 cases (21.4%): identification of a close margin (n 5 1) and unanticipated regions of primary disease (n 5 2). Conclusion: This study demonstrates the clinical applications of fluorescence imaging on intraoperative decision making. This information is required for designing phase III clinical trials using this technique. Furthermore, this study is the first to demonstrate this application for intraoperative decision making during resection of primary tumors

Table_1_A real-time GPU-accelerated parallelized image processor for large-scale multiplexed fluorescence microscopy data.xlsx

Highly multiplexed, single-cell imaging has revolutionized our understanding of spatial cellular interactions associated with health and disease. With ever-increasing numbers of antigens, region sizes, and sample sizes, multiplexed fluorescence imaging experiments routinely produce terabytes of data. Fast and accurate processing of these large-scale, high-dimensional imaging data is essential to ensure reliable segmentation and identification of cell types and for characterization of cellular neighborhoods and inference of mechanistic insights. Here, we describe RAPID, a Real-time, GPU-Accelerated Parallelized Image processing software for large-scale multiplexed fluorescence microscopy Data. RAPID deconvolves large-scale, high-dimensional fluorescence imaging data, stitches and registers images with axial and lateral drift correction, and minimizes tissue autofluorescence such as that introduced by erythrocytes. Incorporation of an open source CUDA-driven, GPU-assisted deconvolution produced results similar to fee-based commercial software. RAPID reduces data processing time and artifacts and improves image contrast and signal-to-noise compared to our previous image processing pipeline, thus providing a useful tool for accurate and robust analysis of large-scale, multiplexed, fluorescence imaging data.</p