Advances in Kidney Biopsy Structural Assessment through Dense Instance Segmentation

The kidney biopsy is the gold standard for the diagnosis of kidney diseases. Lesion scores made by expert renal pathologists are semi-quantitative and suffer from high inter-observer variability. Automatically obtaining statistics per segmented anatomical object, therefore, can bring significant benefits in reducing labor and this inter-observer variability. Instance segmentation for a biopsy, however, has been a challenging problem due to (a) the on average large number (around 300 to 1000) of densely touching anatomical structures, (b) with multiple classes (at least 3) and (c) in different sizes and shapes. The currently used instance segmentation models cannot simultaneously deal with these challenges in an efficient yet generic manner. In this paper, we propose the first anchor-free instance segmentation model that combines diffusion models, transformer modules, and RCNNs (regional convolution neural networks). Our model is trained on just one NVIDIA GeForce RTX 3090 GPU, but can efficiently recognize more than 500 objects with 3 common anatomical object classes in renal biopsies, i.e., glomeruli, tubuli, and arteries. Our data set consisted of 303 patches extracted from 148 Jones' silver-stained renal whole slide images (WSIs), where 249 patches were used for training and 54 patches for evaluation. In addition, without adjustment or retraining, the model can directly transfer its domain to generate decent instance segmentation results from PAS-stained WSIs. Importantly, it outperforms other baseline models and reaches an AP 51.7% in detection as the new state-of-the-art.

Detection of anomalously emitting ships through deviations from predicted TROPOMI NO2 retrievals

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 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/S5P 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 different observations of the same 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.

Supervised segmentation of NO2 plumes from individual ships using TROPOMI satellite data

Starting from 2021, the International Maritime Organization significantly tightened the $\text{NO}_\text{x}$ emission requirements for ships entering the Baltic and North Sea waters. Since all methods currently used for the ships' compliance monitoring are costly and require proximity to the ship, the performance of a global and continuous monitoring of the emission standards' fulfillment has been impossible up to now. A promising approach is the use of remote sensing with the recently launched TROPOMI/S5P satellite. Due to its unprecedentedly high spatial resolution, it allows for the visual distinction of $\text{NO}_\text{2}$ plumes of individual ships. To successfully deploy a compliance monitoring system that is based on TROPOMI data, an automated procedure for the attribution of $\text{NO}_\text{2}$ to individual ships has to be developed. However, due to the extremely low signal-to-noise ratio, interference with the signal from other - often stronger - sources, and the absence of ground truth, the task is very challenging. In this study, we present an automated method for segmentation of plumes produced by individual ships using TROPOMI satellite data - a first step towards the automated procedure for global ship compliance monitoring. We develop a multivariate plume segmentation method based on various ships', wind's and spatial properties. For this, we propose to automatically define a region of interest - a ship sector that we normalize with respect to scale and orientation. We create a dataset, where each pixel has a label for belonging to the respective ship plume or not. We train five linear and nonlinear classifiers. The results show a significant improvement over the threshold-based baselines. Moreover, the aggregated $\text{NO}_\text{2}$ levels of the segmented plumes show high correlation with the theoretically derived measure of ship's emission potential.

Probabilistic Inference for Camera Calibration in Light Microscopy under Circular Motion

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.

Creating a new Ontology: a Modular Approach

Creating a new Ontology: a Modular Approach