Fons J. Verbeek

Solomiia Kurchaba, Jasper van Vliet, Fons J. Verbeek et al.

The shipping industry is one of the strongest anthropogenic emitters of $\text{NO}_\text{x}$ -- substance harmful both to human health and the environment. The rapid growth of the industry causes societal pressure on controlling the emission levels produced by ships. All the methods currently used for ship emission monitoring are costly and require proximity to a ship, which makes global and continuous emission monitoring impossible. A promising approach is the application of remote sensing. Studies showed that some of the $\text{NO}_\text{2}$ plumes from individual ships can visually be distinguished using the TROPOspheric Monitoring Instrument on board the Copernicus Sentinel 5 Precursor (TROPOMI/S5P). To deploy a remote sensing-based global emission monitoring system, an automated procedure for the estimation of $\text{NO}_\text{2}$ emissions from individual ships is needed. The extremely low signal-to-noise ratio of the available data as well as the absence of ground truth makes the task very challenging. Here, we present a methodology for the automated segmentation of $\text{NO}_\text{2}$ plumes produced by seagoing ships using supervised machine learning on TROPOMI/S5P data. We show that the proposed approach leads to a more than a 20\% increase in the average precision score in comparison to the methods used in previous studies and results in a high correlation of 0.834 with the theoretically derived ship emission proxy. This work is a crucial step toward the development of an automated procedure for global ship emission monitoring using remote sensing data.

Solomiia Kurchaba, Jasper van Vliet, Fons J. Verbeek et al.

Starting from 2021, more demanding $\text{NO}_\text{x}$ emission restrictions were introduced for ships operating in the North and Baltic Sea waters. Since all methods currently used for ship compliance monitoring are financially and time demanding, it is important to prioritize the inspection of ships that have high chances of being non-compliant. The current state-of-the-art approach for a large-scale ship $\text{NO}_\text{2}$ estimation is a supervised machine learning-based segmentation of ship plumes on TROPOMI/S5P images. However, challenging data annotation and insufficiently complex ship emission proxy used for the validation limit the applicability of the model for ship compliance monitoring. In this study, we present a method for the automated selection of potentially non-compliant ships using a combination of machine learning models on TROPOMI satellite data. It is based on a proposed regression model predicting the amount of $\text{NO}_\text{2}$ that is expected to be produced by a ship with certain properties operating in the given atmospheric conditions. The model does not require manual labeling and is validated with TROPOMI data directly. The differences between the predicted and actual amount of produced $\text{NO}_\text{2}$ are integrated over observations of the ship in time and are used as a measure of the inspection worthiness of a ship. To assure the robustness of the results, we compare the obtained results with the results of the previously developed segmentation-based method. Ships that are also highly deviating in accordance with the segmentation method require further attention. If no other explanations can be found by checking the TROPOMI data, the respective ships are advised to be the candidates for inspection.

Zhan Xiong, Junling He, Pieter Valkema et al.

Renal biopsies are the gold standard for the diagnosis of kidney diseases. Lesion scores made by renal pathologists are semi-quantitative and exhibit high inter-observer variability. Automating lesion classification within segmented anatomical structures can provide decision support in quantification analysis, thereby reducing inter-observer variability. Nevertheless, classifying lesions in regions-of-interest (ROIs) is clinically challenging due to (a) a large amount of densely packed anatomical objects, (b) class imbalance across different compartments (at least 3), (c) significant variation in size and shape of anatomical objects and (d) the presence of multi-label lesions per anatomical structure. Existing models cannot address these complexities in an efficient and generic manner. This paper presents an analysis for a \textbf{generalized solution} to datasets from various sources (pathology departments) with different types of lesions. Our approach utilizes two sub-networks: dense instance segmentation and lesion classification. We introduce \textbf{DiffRegFormer}, an end-to-end dense instance segmentation sub-network designed for multi-class, multi-scale objects within ROIs. Combining diffusion models, transformers, and RCNNs, DiffRegFormer {is a computational-friendly framework that can efficiently recognize over 500 objects across three anatomical classes, i.e., glomeruli, tubuli, and arteries, within ROIs.} In a dataset of 303 ROIs from 148 Jones' silver-stained renal Whole Slide Images (WSIs), our approach outperforms previous methods, achieving an Average Precision of 52.1\% (detection) and 46.8\% (segmentation). Moreover, our lesion classification sub-network achieves 89.2\% precision and 64.6\% recall on 21889 object patches out of the 303 ROIs. Lastly, our model demonstrates direct domain transfer to PAS-stained renal WSIs without fine-tuning.

Megan Mirnalini Sundaram Rajaraman, Fons J. Verbeek, Vincent J. Kalkman et al.

The correlation between insect morphological traits and climate has been documented in physiological studies, but such studies remain limited by the time-consuming nature of the data analysis. In particular, the open source datasets often lack annotations of species' morphological traits, making dedicated annotations campaigns necessary; these efforts are typically local in scale and costly. In this paper, we propose a pipeline to identify and segment body parts of Odonates (dragonflies and damselflies) using deep neural networks, with the ultimate goal of extracting body parts' colouration. The pipeline is trained on a limited annotated dataset and refined with pseudo supervised data. We show that, by using open source images from citizen science platforms, our approach can segment each visible subject (Odonates) into head, thorax, abdomen, and wings and then extract a colour palette for each body part. This will enable large-scale statistical analysis of ecological correlations (e.g., between colouration and climate change, habitat loss, or geolocation) which are crucial for quantifying and assessing ecosystem biodiversity status.

Fatemeh Fazel Hesar, Mojtaba Raouf, Amirmohammad Chegeni et al.

We present an innovative, cost-effective framework integrating laboratory Hyperspectral Imaging (HSI) of the Bechar010 Lunar meteorite with ground-based lunar HSI and supervised Machine Learning(ML) to generate high-fidelity mineralogical maps. A 3mm thin section of Bechar010 was imaged under a microscope with a 30mm focal length lens at 150mm working distance, using 6x binning to increase the signal-to-noise ratio, producing a data cube (X $\times$ Y $\times$ $λ$ = $791 \times 1024 \times 224$, 0.24mm $\times$ 0.2mm resolution) across 400-1000}nm (224 bands, 2.7nm spectral sampling, 5.5nm full width at half maximum spectral resolution) using a Specim FX10 camera. Ground-based lunar HSI was captured with a Celestron 8SE telescope (3km/pixel), yielded a data cube ($371 \times 1024 \times 224$). Solar calibration was performed using a Spectralon reference ({99}\% reflectance {<2}\% error) ensured accurate reflectance spectra. A Support Vector Machine (SVM) with a radial basis function kernel, trained on expert-labeled spectra, achieved {93.7}\% classification accuracy(5-fold cross-validation) for olivine ({92}\% precision, {90}\% recall) and pyroxene ({88}\% precision, {86}{\%} recall) in Bechar 010. LIME analysis identified key wavelengths (e.g., 485nm, {22.4}\% for M3; 715nm, {20.6}\% for M6) across 10 pre-selected regions (M1 to M10), indicating olivine-rich (Highland-like) and pyroxene-rich (Mare-like) compositions. SAM analysis revealed angles from 0.26 radian to 0.66 radian, linking M3 and M9 to Highlands and M6 and M10 to Mares. K-means clustering of Lunar data identified 10 mineralogical clusters ({88}\% accuracy), validated against Chandrayaan-1 Moon mineralogy Mapper ($\rm M^3$) data (140m/pixel, 10nm spectral resolution).A novel push-broom HSI approach with a telescope achieves 0.8 arcsec resolution for lunar spectroscopy, inspiring full-sky multi-object spectral mapping.

Fatemeh Fazel Hesar, Bernard Foing, Ana M. Heras et al.

This study applied machine learning models to estimate stellar rotation periods from corrected light curve data obtained by the NASA Kepler mission. Traditional methods often struggle to estimate rotation periods accurately due to noise and variability in the light curve data. The workflow involved using initial period estimates from the LS-Periodogram and Transit Least Squares techniques, followed by splitting the data into training, validation, and testing sets. We employed several machine learning algorithms, including Decision Tree, Random Forest, K-Nearest Neighbors, and Gradient Boosting, and also utilized a Voting Ensemble approach to improve prediction accuracy and robustness. The analysis included data from multiple Kepler IDs, providing detailed metrics on orbital periods and planet radii. Performance evaluation showed that the Voting Ensemble model yielded the most accurate results, with an RMSE approximately 50\% lower than the Decision Tree model and 17\% better than the K-Nearest Neighbors model. The Random Forest model performed comparably to the Voting Ensemble, indicating high accuracy. In contrast, the Gradient Boosting model exhibited a worse RMSE compared to the other approaches. Comparisons of the predicted rotation periods to the photometric reference periods showed close alignment, suggesting the machine learning models achieved high prediction accuracy. The results indicate that machine learning, particularly ensemble methods, can effectively solve the problem of accurately estimating stellar rotation periods, with significant implications for advancing the study of exoplanets and stellar astrophysics.

Jens van Bijsterveld, Daniele Avitabile, Fons J. Verbeek et al.

In this paper, we explore deep learning techniques for individual identification of animals based on their skin patterns. Individual identification is crucial in biodiversity monitoring, since it enables analysis of decline or growth of populations, or intra-species interactions within populations. Models trained for the task of individual identification often do not focus on the skin pattern of animals, but on background details or body shape details. These characteristics are not individually specific, or can change drastically through time. We focus on techniques that will make machine learning models more responsive to skin pattern structure when extracting individual visual embeddings from images. For this, we explore image inpainting of task-specific masks as an auxiliary task to enhance ML-based individual identification from animal skin patterns. We propose a comparative analysis among four models as an encoder backbone for the individual identification task. We focus on the case study of zebrafish, which is a widely recognized biological model organism, and which exhibits individually identifying skin patterns. To evaluate encoder backbone performance, we present standard metrics for classification accuracy, embedding clustering metrics, and GradCAM visualizations.

Fatemeh Fazel Hesar, Mojtaba Raouf, Peyman Soltani et al.

This study examines the mineral composition of volcanic samples similar to lunar materials, focusing on olivine and pyroxene. Using hyperspectral imaging from 400 to 1000 nm, we created data cubes to analyze the reflectance characteristics of samples from samples from Vulcano, a volcanically active island in the Aeolian Archipelago, north of Sicily, Italy, categorizing them into nine regions of interest and analyzing spectral data for each. We applied various unsupervised clustering algorithms, including K-Means, Hierarchical Clustering, GMM, and Spectral Clustering, to classify the spectral profiles. Principal Component Analysis revealed distinct spectral signatures associated with specific minerals, facilitating precise identification. Clustering performance varied by region, with K-Means achieving the highest silhouette-score of 0.47, whereas GMM performed poorly with a score of only 0.25. Non-negative Matrix Factorization aided in identifying similarities among clusters across different methods and reference spectra for olivine and pyroxene. Hierarchical clustering emerged as the most reliable technique, achieving a 94\% similarity with the olivine spectrum in one sample, whereas GMM exhibited notable variability. Overall, the analysis indicated that both Hierarchical and K-Means methods yielded lower errors in total measurements, with K-Means demonstrating superior performance in estimated dispersion and clustering. Additionally, GMM showed a higher root mean square error compared to the other models. The RMSE analysis confirmed K-Means as the most consistent algorithm across all samples, suggesting a predominance of olivine in the Vulcano region relative to pyroxene. This predominance is likely linked to historical formation conditions similar to volcanic processes on the Moon, where olivine-rich compositions are common in ancient lava flows and impact melt rocks.

Yuanhao Guo, Fons J. Verbeek, Ge Yang

Robust and accurate camera calibration is essential for 3D reconstruction in light microscopy under circular motion. Conventional methods require either accurate key point matching or precise segmentation of the axial-view images. Both remain challenging because specimens often exhibit transparency/translucency in a light microscope. To address those issues, we propose a probabilistic inference based method for the camera calibration that does not require sophisticated image pre-processing. Based on 3D projective geometry, our method assigns a probability on each of a range of voxels that cover the whole object. The probability indicates the likelihood of a voxel belonging to the object to be reconstructed. Our method maximizes a joint probability that distinguishes the object from the background. Experimental results show that the proposed method can accurately recover camera configurations in both light microscopy and natural scene imaging. Furthermore, the method can be used to produce high-fidelity 3D reconstructions and accurate 3D measurements.