Nondestructive nitrogen content estimation in tomato plant leaves by Vis-NIR hyperspectral imaging and regression data models.

The present study aims to estimate nitrogen (N) content in tomato (Solanum lycopersicum L.) plant leaves using optimal hyperspectral imaging data by means of computational intelligence [artificial neural networks and the differential evolution algorithm (ANN-DE), partial least squares regression (PLSR), and convolutional neural network (CNN) regression] to detect potential plant stress to nutrients at early stages. First, pots containing control and treated tomato plants were prepared; three treatments (categories or classes) consisted in the application of an overdose of 30%, 60%, and 90% nitrogen fertilizer, called N-30%, N-60%, N-90%, respectively. Tomato plant leaves were then randomly picked up before and after the application of nitrogen excess and imaged. Leaf images were captured by a hyperspectral camera, and nitrogen content was measured by laboratory ordinary destructive methods. Two approaches were studied: either using all the spectral data in the visible (Vis) and near infrared (NIR) spectral bands, or selecting only the three most effective wavelengths by an optimization algorithm. Regression coefficients (R) were 0.864±0.027 for ANN-DE, 0.837±0.027 for PLSR, and 0.875±0.026 for CNN in the first approach, over the test set. The second approach used different models for each treatment, achieving R values for all the regression methods above 0.96; however, it needs a previous classification stage of the samples in one of the three nitrogen excess classes under consideration.

Comparison of 2D and 3D convolutional neural networks in hyperspectral image analysis of fruits applied to orange bruise detection.

Recent advances in hyperspectral imaging (HSI) have demonstrated its ability to detect defects in fruit that may not be visible in RGB images. HSIs can be considered 3D images containing two spatial dimensions and one spectral dimension. Therefore, the first question that arises is how to process this type of information, either using 2D or 3D models. In this study, HSI in the 550-900 nm spectral range was used to detect bruising in oranges. Sixty samples of Thompson oranges were subjected to a mechanical bruising process, and HSIs were taken at different time intervals: before bruising, and 8 and 16 h after bruising. The samples were then classified using two convolutional neural network (CNN) models, a shallow 7-layer network (CNN-7) and a deep 18-layer network (CNN-18). In addition, two different input processing approaches are used: using 2D information from each band, and using the full 3D data from each HSI. The 3D models were the most accurate, with 94% correct classification for 3D-CNN-18, compared to 90% for 3D-CNN-7, and less than 83% for the 2D models. Our study suggests that 3D HSI may be a more effective technique for detecting fruit bruising, allowing the development of a fast, accurate, and nondestructive method for fruit sorting. PRACTICAL APPLICATION: Orange bruises can reduce the market value of food, which is why the food processing industry needs to carry out quality inspections. An effective way to perform this inspection is by using hyperspectral images that can be processed with 2D or 3D models, either with deep or shallow neural networks. The results of the comparison performed in this work can be useful for the development of more accurate and efficient bruise detection methods for fruit inspection.

A multiparametric activity profiling platform for neuron disease phenotyping and drug screening.

Patient stem cell-derived models enable imaging of complex disease phenotypes and the development of scalable drug discovery platforms. Current preclinical methods for assessing cellular activity do not, however, capture the full intricacies of disease-induced disturbances and instead typically focus on a single parameter, which impairs both the understanding of disease and the discovery of effective therapeutics. Here, we describe a cloud-based image processing and analysis platform that captures the intricate activity profile revealed by GCaMP fluorescence recordings of intracellular calcium changes and enables the discovery of molecules that correct 153 parameters that define the amyotrophic lateral sclerosis motor neuron disease phenotype. In a high-throughput screen, we identified compounds that revert the multiparametric disease profile to that found in healthy cells, a novel and robust measure of therapeutic potential quite distinct from unidimensional screening. This platform can guide the development of therapeutics that counteract the multifaceted pathological features of diseased cellular activity.

Morphology and gene expression profiling provide complementary information for mapping cell state.

Morphological and gene expression profiling can cost-effectively capture thousands of features in thousands of samples across perturbations by disease, mutation, or drug treatments, but it is unclear to what extent the two modalities capture overlapping versus complementary information. Here, using both the L1000 and Cell Painting assays to profile gene expression and cell morphology, respectively, we perturb human A549 lung cancer cells with 1,327 small molecules from the Drug Repurposing Hub across six doses, providing a data resource including dose-response data from both assays. The two assays capture both shared and complementary information for mapping cell state. Cell Painting profiles from compound perturbations are more reproducible and show more diversity but measure fewer distinct groups of features. Applying unsupervised and supervised methods to predict compound mechanisms of action (MOAs) and gene targets, we find that the two assays not only provide a partially shared but also a complementary view of drug mechanisms. Given the numerous applications of profiling in biology, our analyses provide guidance for planning experiments that profile cells for detecting distinct cell types, disease phenotypes, and response to chemical or genetic perturbations.

Virtual screening for small-molecule pathway regulators by image-profile matching.

Identifying the chemical regulators of biological pathways is a time-consuming bottleneck in developing therapeutics and research compounds. Typically, thousands to millions of candidate small molecules are tested in target-based biochemical screens or phenotypic cell-based screens, both expensive experiments customized to each disease. Here, our uncustomized, virtual, profile-based screening approach instead identifies compounds that match to pathways based on the phenotypic information in public cell image data, created using the Cell Painting assay. Our straightforward correlation-based computational strategy retrospectively uncovered the expected, known small-molecule regulators for 32% of positive-control gene queries. In prospective, discovery mode, we efficiently identified new compounds related to three query genes and validated them in subsequent gene-relevant assays, including compounds that phenocopy or pheno-oppose YAP1 overexpression and kill a Yap1-dependent sarcoma cell line. This image-profile-based approach could replace many customized labor- and resource-intensive screens and accelerate the discovery of biologically and therapeutically useful compounds.

Capturing single-cell heterogeneity via data fusion improves image-based profiling.

Single-cell resolution technologies warrant computational methods that capture cell heterogeneity while allowing efficient comparisons of populations. Here, we summarize cell populations by adding features' dispersion and covariances to population averages, in the context of image-based profiling. We find that data fusion is critical for these metrics to improve results over the prior alternatives, providing at least ~20% better performance in predicting a compound's mechanism of action (MoA) and a gene's pathway.

A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay.

Background: Large-scale image sets acquired by automated microscopy of perturbed samples enable a detailed comparison of cell states induced by each perturbation, such as a small molecule from a diverse library. Highly multiplexed measurements of cellular morphology can be extracted from each image and subsequently mined for a number of applications. Findings: This microscopy dataset includes 919 265 five-channel fields of view, representing 30 616 tested compounds, available at "The Cell Image Library" (CIL) repository. It also includes data files containing morphological features derived from each cell in each image, both at the single-cell level and population-averaged (i.e., per-well) level; the image analysis workflows that generated the morphological features are also provided. Quality-control metrics are provided as metadata, indicating fields of view that are out-of-focus or containing highly fluorescent material or debris. Lastly, chemical annotations are supplied for the compound treatments applied. Conclusions: Because computational algorithms and methods for handling single-cell morphological measurements are not yet routine, the dataset serves as a useful resource for the wider scientific community applying morphological (image-based) profiling. The dataset can be mined for many purposes, including small-molecule library enrichment and chemical mechanism-of-action studies, such as target identification. Integration with genetically perturbed datasets could enable identification of small-molecule mimetics of particular disease- or gene-related phenotypes that could be useful as probes or potential starting points for development of future therapeutics.