In routine colorectal cancer management, histologic samples stained with hematoxylin and eosin are commonly used. Nonetheless, their potential for defining objective biomarkers for patient stratification and treatment selection is still being explored. The current gold standard relies on expensive and time-consuming genetic tests. However, recent research highlights the potential of convolutional neural networks (CNNs) to facilitate the extraction of clinically relevant biomarkers from these readily available images. These CNN-based biomarkers can predict patient outcomes comparably to golden standards, with the added advantages of speed, automation, and minimal cost. The predictive potential of CNN-based biomarkers fundamentally relies on the ability of CNNs to accurately classify diverse tissue types from whole slide microscope images. Consequently, enhancing the accuracy of tissue class decomposition is critical to amplifying the prognostic potential of imaging-based biomarkers. This study introduces a hybrid deep transfer learning and ensemble machine learning model that improves upon previous approaches, including a transformer and neural architecture search baseline for this task. We employed a pairing of the EfficientNetV2 architecture with a random forest classification head. Our model achieved 96.74% accuracy (95% CI: 96.3%-97.1%) on the external test set and 99.89% on the internal test set. Recognizing the potential of these models in the task, we have made them publicly available.

Several optical imaging techniques have been developed to ease the burden of skin cancer disease on our health care system. Hyperspectral images can be used to identify biological tissues by their diffuse reflected spectra. In this second part of a three-phase pilot study, we used a novel hand-held SICSURFIS Spectral Imager with an adaptable field of view and target-wise selectable wavelength channels to provide detailed spectral and spatial data for lesions on complex surfaces. The hyperspectral images (33 wavelengths, 477–891 nm) provided photometric data through individually controlled illumination modules, enabling convolutional networks to utilise spectral, spatial, and skin-surface models for the analyses. In total, 42 lesions were studied: 7 melanomas, 13 pigmented and 7 intradermal nevi, 10 basal cell carcinomas, and 5 squamous cell carcinomas. All lesions were excised for histological analyses. A pixel-wise analysis provided map-like images and classified pigmented lesions with a sensitivity of 87% and a specificity of 93%, and 79% and 91%, respectively, for non-pigmented lesions. A majority voting analysis, which provided the most probable lesion diagnosis, diagnosed 41 of 42 lesions correctly. This pilot study indicates that our non-invasive hyperspectral imaging system, which involves shape and depth data analysed by convolutional neural networks, is feasible for differentiating between malignant and benign pigmented and non-pigmented skin tumours, even on complex skin surfaces.

Miniaturized hyperspectral imaging techniques have developed rapidly in recent years and have become widely available for different applications. Combining calibrated hyperspectral imagery with inverse physically based reflectance models is an interesting approach for estimating chlorophyll concentrations that are good indicators of vegetation health. The objective of this study was to develop a novel approach for retrieving chlorophyll a and b values from remotely sensed data by inverting the stochastic model of leaf optical properties using a one-dimensional convolutional neural network. The inversion results and retrieved values are validated in two ways: A classical machine learning validation dataset and calculating chlorophyll maps from empirical remotely sensed hyperspectral data and comparing them to $\frac{\mathrm{TCARI}}{\mathrm{OSAVI}}$ , an index that has strong negative correlation with chlorophyll concentration. With the validation dataset, coefficients of determination ( $R^2$ ) of 0.97 were obtained for chlorophyll a and 0.95 for chlorophyll b. The chlorophyll maps correlate with the $\frac{\mathrm{TCARI}}{\mathrm{OSAVI}}$ map. The correlation coefficient (R) is −0.87 for chlorophyll a and −0.68 for chlorophyll b in selected plots. These results indicate that the approach is highly promising approach for estimating vegetation chlorophyll content.

Diagnosing knee joint osteoarthritis (KOA), a major cause of disability worldwide, is challenging due to subtle radiographic indicators and the varied progression of the disease. Using deep learning for KOA diagnosis requires broad, comprehensive datasets. However, obtaining these datasets poses significant challenges due to patient privacy and data collection restrictions. Additive data augmentation, which enhances data variability, emerges as a promising solution. Yet, it’s unclear which augmentation techniques are most effective for KOA. Our study explored data augmentation methods, including adversarial techniques. We used strategies like horizontal cropping and region of interest (ROI) extraction, alongside adversarial methods such as noise injection and ROI removal. Interestingly, rotations improved performance, while methods like horizontal split were less effective. We discovered potential confounding regions using adversarial augmentation, shown in our models’ accurate classification of extreme KOA grades, even without the knee joint. This indicated a potential model bias towards irrelevant radiographic features. Removing the knee joint paradoxically increased accuracy in classifying early-stage KOA. Grad-CAM visualizations helped elucidate these effects. Our study contributed to the field by pinpointing augmentation techniques that either improve or impede model performance, in addition to recognizing potential confounding regions within radiographic images of knee osteoarthritis.

Modified Atmosphere Packaging (MAP) is a conventional method used to prolong the shelf-life of fresh-cut vegetables, including lettuce. However, MAP-stored lettuce remains perishable, and its deterioration mechanism is not fully understood. Here, we utilized non-targeted LC-MS metabolomics to evaluate the effects of cutting and extended storage time on metabolite profiles of lettuce stored in MAP. Additionally, hyperspectral imaging was used to measure perceptual changes. Our findings reveal a bipartite response to wounding. In early storage, enzymatic browning was the main response to wounding, evidenced by accumulation of caffeic acid derivatives and flavonoids, substrates for polyphenol oxidases. As storage progressed, enzymatic browning was inhibited, and a shift towards lignification became apparent, evidenced by accumulation of monolignol derivatives. These findings offer new insights into the deterioration mechanism of fresh-cut lettuce occurring in MAP.

Skin cancers are a world wide deathly health problem, where significant life and cost savings could be achieved if detection of cancer can be done in early phase. Hypespectral imaging is prominent tool for non-invasive screening. In this study we compare how use of both spectral and spatial domain increase classification performance of convolutional neural networks. We compare five different neural network architectures for real patient data. Our models gain same or slightly better positive predictive value as clinicians. Towards more general and reliable model more data is needed and collection of training data should be systematic.