To Örebro University

Traditional approaches to studying cellular morphology rely on geometric metrics from stained images. However, staining processes can disrupt the cell's natural state and diminish accuracy due to photobleaching, while conventional analysis techniques, which categorize cells based on shape to discern pathophysiological conditions, often fail to capture the continuous and asynchronous nature of biological processes such as cell differentiation, immune responses, and cancer progression. In this work, we propose the use of quantitative phase imaging for morphological assessment due to its label-free nature. For analysis, we repurposed the genomic analysis toolbox to perform trajectory inference analysis purely based on morphology information. We applied the developed framework to study the progression of leukemia and breast cancer metastasis. Applying this framework to leukemia and breast cancer metastasis, we identified key shape changes linked to disease progression, highlighting the method's potential to enhance understanding of complex biological dynamics.

LiDAR is used in autonomous driving for navigation, obstacle avoidance, and environment mapping. However, adverse weather conditions introduce noise into sensor data, potentially degrading the performance of perception algorithms and compromising the safety and reliability of autonomous driving systems. Hence, in this paper, we investigate the limitations of LiDAR perception algorithms in adverse weather conditions, explore ways to mitigate the effects of noise, and propose future research directions to achieve all-weather autonomy with LiDAR sensors. Using real-world datasets and synthetically generated dense fog, we characterize the noise in adverse weather such as snow, rain, and fog; their effect on sensor data; and how to effectively mitigate the noise for tasks like object detection, localization, and SLAM. Specifically, we investigate point cloud filtering methods and compare them based on their ability to denoise point clouds, focusing on processing time, accuracy, and limitations. Additionally, we evaluate the impact of adverse weather on state-of-the-art 3D object detection, localization, and SLAM methods, as well as the effect of point cloud filtering on the algorithms' performance. We find that point cloud filtering methods are partially successful at removing noise due to adverse weather, but must be fine-tuned for the specific LiDAR, application scenario, and type of adverse weather. 3D object detection was negatively affected by adverse weather, but performance improved with dynamic filtering algorithms. We found that heavy snowfall does not affect localization when using a map constructed in clear weather, but it fails in dense fog due to a low number of feature points. SLAM also failed in thick fog outdoors, but it performed well in heavy snowfall. Filtering algorithms have varied effects on SLAM performance depending on the type of scan-matching algorithm.

Large Language Models (LLMs) excel at generating contextually relevant text but lack logical reasoning abilities. They rely on statistical patterns rather than logical inference, making them unreliable for structured decision-making. Integrating LLMs with task planning can address this limitation by combining their natural language understanding with the precise, goal-oriented reasoning of planners. This paper introduces ViPlan, a hybrid system that leverages Vision Language Models (VLMs) to extract high-level semantic information from visual and textual inputs while integrating classical planners for logical reasoning. ViPlan utilizes VLMs to generate syntactically correct and semantically meaningful PDDL problem files from images and natural language instructions, which are then processed by a task planner to generate an executable plan. The entire process is embedded within a behavior tree framework, enhancing efficiency, reactivity, replanning, modularity, and flexibility. The generation and planning capabilities of ViPlan are empirically evaluated with simulated and real-world experiments.

We propose a context-aware navigation framework designed to support the navigation of autonomous ground vehicles, including articulated ones. The proposed framework employs a behavior tree with novel nodes to manage the navigation tasks: planner and controller selections, path planning, path following, and recovery. It incorporates a weather detection system and configurable global path planning and controller strategy selectors implemented as behavior tree action nodes. These components are integrated into a sub-tree that supervises and manages available options and parameters for global planners and control strategies by evaluating map and real-time sensor data. The proposed approach offers three key benefits: overcoming the limitations of single planner strategies in challenging scenarios; ensuring efficient path planning by balancing between optimization and computational effort; and achieving smoother navigation by reducing path curvature and improving drivability. The performance of the proposed framework is analyzed empirically, and compared against state of the art navigation systems with single path planning strategies.

Cellular morphology, shaped by various genetic and environmental influences, is pivotal to studying experimental cell biology, necessitating precise measurement and analysis techniques. Traditional approaches, which rely on geometric metrics derived from stained images, encounter obstacles stemming from both the imaging and analytical domains. Staining processes can disrupt the cell's natural state and diminish accuracy due to photobleaching, while conventional analysis techniques, which categorize cells based on shape to discern pathophysiological conditions, often fail to capture the continuous and asynchronous nature of biological processes such as cell differentiation, immune responses, and cancer progression. In this work, we propose the use of quantitative phase imaging for morphological assessment due to its label-free nature. For analysis, we repurposed the genomic analysis toolbox to perform trajectory inference analysis purely based on morphology information. We applied the developed framework to study the progression of leukemia and breast cancer metastasis. Our approach revealed a clear pattern of morphological evolution tied to the diseases' advancement, highlighting the efficacy of our method in identifying functionally significant shape changes where conventional techniques falter. This advancement offers a fresh perspective on analyzing cellular morphology and holds significant potential for the broader research community, enabling a deeper understanding of complex biological dynamics.

Object detection is crucial in diverse autonomous systems like surveillance, autonomous driving, and driver assistance, ensuring safety by recognizing pedestrians, vehicles, traffic lights, and signs. However, adverse weather conditions such as snow, fog, and rain pose a challenge, affecting detection accuracy and risking accidents and damage. This clearly demonstrates the need for robust object detection solutions that work in all weather conditions. We employed three strategies to enhance deep learningbased object detection in adverse weather: training on real world all-weather images, training on images with synthetic augmented weather noise, and integrating object detection with adverse weather image denoising. The synthetic weather noise is generated using analytical methods, GAN networks, and style-transfer networks. We compared the performance of these strategies by training object detection models using real-world all-weather images from the BDD100K dataset and, for assessment, employed unseen real-world adverse weather images. Adverse weather denoising methods were evaluated by denoising real-world adverse weather images, and the results of object detection denoised and original noisy images were compared. We found that the model trained using all-weather real-world images performed best, while the strategy of doing object detection on denoised images performed worst.

Adverse weather (rain, snow, and fog) can negatively impact computer vision tasks by introducing noise in sensor data; therefore, it is essential to recognize weather conditions for building safe and robust autonomous systems in the agricultural and autonomous driving/drone sectors. The performance degradation in computer vision tasks due to adverse weather depends on the type of weather and the intensity, which influences the amount of noise in sensor data. However, existing weather recognition datasets often lack intensity labels, limiting their effectiveness. To address this limitation, we present VARG, a novel video-based weather recognition dataset with weather intensity labels. The dataset comprises a diverse set of short video sequences collected from various social media platforms and videos recorded by the authors, processed into usable clips, and categorized into three major weather categories, rain, fog, and snow, with three intensity classes: absent/no, moderate, and high. The dataset contains 6742 annotated clips from 1079 videos, with the training set containing 5159 clips and the test set containing 1583 clips. Two sets of annotations are provided for training, the first set to train the models as a multi-label weather intensity classifier and the second set to train the models as a multi-class classifier for three weather scenarios. This paper describes the dataset characteristics and presents an evaluation study using several deep learning-based video recognition approaches for weather intensity prediction.

Registration of point cloud data containing both depth and color information is critical for a variety of applications, including in-field robotic plant manipulation, crop growth modeling, and autonomous navigation. However, current state-of-the-art registration methods often fail in challenging agricultural field conditions due to factors such as occlusions, plant density, and variable illumination. To address these issues, we propose the NDT-6D registration method, which is a color-based variation of the Normal Distribution Transform (NDT) registration approach for point clouds. Our method computes correspondences between pointclouds using both geometric and color information and minimizes the distance between these correspondences using only the three-dimensional (3D) geometric dimensions. We evaluate the method using the GRAPES3D data set collected with a commercial-grade RGB-D sensor mounted on a mobile platform in a vineyard. Results show that registration methods that only rely on depth information fail to provide quality registration for the tested data set. The proposed color-based variation outperforms state-of-the-art methods with a root mean square error (RMSE) of 1.1-1.6 cm for NDT-6D compared with 1.1-2.3 cm for other color-information-based methods and 1.2-13.7 cm for noncolor-information-based methods. The proposed method is shown to be robust against noises using the TUM RGBD data set by artificially adding noise present in an outdoor scenario. The relative pose error (RPE) increased similar to 14% for our method compared to an increase of similar to 75% for the best-performing registration method. The obtained average accuracy suggests that the NDT-6D registration methods can be used for in-field precision agriculture applications, for example, crop detection, size-based maturity estimation, and growth modeling.

Normal Distribution Transformation (NDT) registration is a fast, learning-free point cloud registration algorithm that works well in diverse environments. It uses the compact NDT representation to represent point clouds or maps as a spatial probability function that models the occupancy likelihood in an environment. However, because of the grid discretization in NDT maps, the global minima of the registration cost function do not always correlate to ground truth, particularly for rotational alignment. In this study, we examined the NDT registration cost function in-depth. We evaluated three modifications (Student-t likelihood function, inflated covariance/heavily broadened likelihood curve, and overlapping grid cells) that aim to reduce the negative impact of discretization in classical NDT registration. The first NDT modification improves likelihood estimates for matching the distributions of small population sizes; the second modification reduces discretization artifacts by broadening the likelihood tails through covariance inflation; and the third modification achieves continuity by creating the NDT representations with overlapping grid cells (without increasing the total number of cells). We used the Pomerleau Dataset evaluation protocol for our experiments and found significant improvements compared to the classic NDT D2D registration approach (27.7% success rate) using the registration cost functions "heavily broadened likelihood NDT" (HBL-NDT) (34.7% success rate) and "overlapping grid cells NDT" (OGC-NDT) (33.5% success rate). However, we could not observe a consistent improvement using the Student-t likelihood-based registration cost function (22.2% success rate) over the NDT P2D registration cost function (23.7% success rate). A comparative analysis with other state-of-art registration algorithms is also presented in this work. We found that HBL-NDT worked best for easy initial pose difficulties scenarios making it suitable for consecutive point cloud registration in SLAM application.

Automated forest machines are becoming important due to human operators' complex and dangerous working conditions, leading to a labor shortage. This study proposes a new method for robust SLAM and tree mapping using low-resolution LiDAR sensors in forestry conditions. Our method relies on tree detection to perform scan registration and pose correction using only low-resolution LiDAR sensors (16Ch, 32Ch) or narrow field of view Solid State LiDARs without additional sensory modalities like GPS or IMU. We evaluate our approach on three datasets, including two private and one public dataset, and demonstrate improved navigation accuracy, scan registration, tree localization, and tree diameter estimation compared to current approaches in forestry machine automation. Our results show that the proposed method yields robust scan registration using detected trees, outperforming generalized feature-based registration algorithms like Fast Point Feature Histogram, with an above 3 m reduction in RMSE for the 16Chanel LiDAR sensor. For Solid-State LiDAR the algorithm achieves a similar RMSE of 3.7 m. Additionally, our adaptive pre-processing and heuristic approach to tree detection increased the number of detected trees by 13% compared to the current approach of using fixed radius search parameters for pre-processing. Our automated tree trunk diameter estimation method yields a mean absolute error of 4.3 cm (RSME = 6.5 cm) for the local map and complete trajectory maps.