Dataset Information

DeepNIR: Datasets for Generating Synthetic NIR Images and Improved Fruit Detection System Using Deep Learning Techniques.

ABSTRACT: This paper presents datasets utilised for synthetic near-infrared (NIR) image generation and bounding-box level fruit detection systems. A high-quality dataset is one of the essential building blocks that can lead to success in model generalisation and the deployment of data-driven deep neural networks. In particular, synthetic data generation tasks often require more training samples than other supervised approaches. Therefore, in this paper, we share the NIR+RGB datasets that are re-processed from two public datasets (i.e., nirscene and SEN12MS), expanded our previous study, deepFruits, and our novel NIR+RGB sweet pepper (capsicum) dataset. We oversampled from the original nirscene dataset at 10, 100, 200, and 400 ratios that yielded a total of 127 k pairs of images. From the SEN12MS satellite multispectral dataset, we selected Summer (45 k) and All seasons (180k) subsets and applied a simple yet important conversion: digital number (DN) to pixel value conversion followed by image standardisation. Our sweet pepper dataset consists of 1615 pairs of NIR+RGB images that were collected from commercial farms. We quantitatively and qualitatively demonstrate that these NIR+RGB datasets are sufficient to be used for synthetic NIR image generation. We achieved Frechet inception distances (FIDs) of 11.36, 26.53, and 40.15 for nirscene1, SEN12MS, and sweet pepper datasets, respectively. In addition, we release manual annotations of 11 fruit bounding boxes that can be exported in various formats using cloud service. Four newly added fruits (blueberry, cherry, kiwi and wheat) compound 11 novel bounding box datasets on top of our previous work presented in the deepFruits project (apple, avocado, capsicum, mango, orange, rockmelon and strawberry). The total number of bounding box instances of the dataset is 162 k and it is ready to use from a cloud service. For the evaluation of the dataset, Yolov5 single stage detector is exploited and reported impressive mean-average-precision, mAP[0.5:0.95] results of min:0.49, max:0.812. We hope these datasets are useful and serve as a baseline for future studies.

SUBMITTER: Sa I

PROVIDER: S-EPMC9269522 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundThree-way data started to gain popularity due to their increasing capacity to describe inherently multivariate and temporal events, such as biological responses, social interactions along time, urban dynamics, or complex geophysical phenomena. Triclustering, subspace clustering of three-way data, enables the discovery of patterns corresponding to data subspaces (triclusters) with values correlated across the three dimensions (observations [Formula: see text] features [Formula: see text] contexts). With increasing number of algorithms being proposed, effectively comparing them with state-of-the-art algorithms is paramount. These comparisons are usually performed using real data, without a known ground-truth, thus limiting the assessments. In this context, we propose a synthetic data generator, G-Tric, allowing the creation of synthetic datasets with configurable properties and the possibility to plant triclusters. The generator is prepared to create datasets resembling real 3-way data from biomedical and social data domains, with the additional advantage of further providing the ground truth (triclustering solution) as output.ResultsG-Tric can replicate real-world datasets and create new ones that match researchers needs across several properties, including data type (numeric or symbolic), dimensions, and background distribution. Users can tune the patterns and structure that characterize the planted triclusters (subspaces) and how they interact (overlapping). Data quality can also be controlled, by defining the amount of missing, noise or errors. Furthermore, a benchmark of datasets resembling real data is made available, together with the corresponding triclustering solutions (planted triclusters) and generating parameters.ConclusionsTriclustering evaluation using G-Tric provides the possibility to combine both intrinsic and extrinsic metrics to compare solutions that produce more reliable analyses. A set of predefined datasets, mimicking widely used three-way data and exploring crucial properties was generated and made available, highlighting G-Tric's potential to advance triclustering state-of-the-art by easing the process of evaluating the quality of new triclustering approaches.

Project description:BackgroundHigh quality 3D information of the microscopic plant tissue morphology-the spatial organization of cells and intercellular spaces in tissues-helps in understanding physiological processes in a wide variety of plants and tissues. X-ray micro-CT is a valuable tool that is becoming increasingly available in plant research to obtain 3D microstructural information of the intercellular pore space and individual pore sizes and shapes of tissues. However, individual cell morphology is difficult to retrieve from micro-CT as cells cannot be segmented properly due to negligible density differences at cell-to-cell interfaces. To address this, deep learning-based models were trained and tested to segment individual cells using X-ray micro-CT images of parenchyma tissue samples from apple and pear fruit with different cell and porosity characteristics.ResultsThe best segmentation model achieved an Aggregated Jaccard Index (AJI) of 0.86 and 0.73 for apple and pear tissue, respectively, which is an improvement over the current benchmark method that achieved AJIs of 0.73 and 0.67. Furthermore, the neural network was able to detect other plant tissue structures such as vascular bundles and stone cell clusters (brachysclereids), of which the latter were shown to strongly influence the spatial organization of pear cells. Based on the AJIs, apple tissue was found to be easier to segment, as the porosity and specific surface area of the pore space are higher and lower, respectively, compared to pear tissue. Moreover, samples with lower pore network connectivity, proved very difficult to segment.ConclusionsThe proposed method can be used to automatically quantify 3D cell morphology of plant tissue from micro-CT instead of opting for laborious manual annotations or less accurate segmentation approaches. In case fruit tissue porosity or pore network connectivity is too low or the specific surface area of the pore space too high, native X-ray micro-CT is unable to provide proper marker points of cell outlines, and one should rely on more elaborate contrast-enhancing scan protocols.

Dataset Information

DeepNIR: Datasets for Generating Synthetic NIR Images and Improved Fruit Detection System Using Deep Learning Techniques.

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