004 Datenverarbeitung; Informatik
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Packets sent over a network can either get lost or reach their destination. Protocols like TCP try to solve this problem by resending the lost packets. However, retransmissions consume a lot of time and are cumbersome for the transmission of critical data. Multipath solutions are quite common to address this reliability issue and are available on almost every layer of the ISO/OSI model. We propose a solution based on a P4 network to duplicate packets in order to send them to their destination via multiple routes. The last network hop ensures that only a single copy of the traffic is further forwarded to its destination by adopting a concept similar to Bloom filters. Besides, if fast delivery is requested we provide a P4 prototype, which randomly forwards the packets over different transmission paths. For reproducibility, we implement our approach in a container-based network emulation system called Kathará.
Crowdsourced network measurements (CNMs) are becoming increasingly popular as they assess the performance of a mobile network from the end user's perspective on a large scale. Here, network measurements are performed directly on the end-users' devices, thus taking advantage of the real-world conditions end-users encounter. However, this type of uncontrolled measurement raises questions about its validity and reliability. The problem lies in the nature of this type of data collection. In CNMs, mobile network subscribers are involved to a large extent in the measurement process, and collect data themselves for the operator. The collection of data on user devices in arbitrary locations and at uncontrolled times requires means to ensure validity and reliability. To address this issue, our paper defines concepts and guidelines for analyzing the precision of CNMs; specifically, the number of measurements required to make valid statements. In addition to the formal definition of the aspect, we illustrate the problem and use an extensive sample data set to show possible assessment approaches. This data set consists of more than 20.4 million crowdsourced mobile measurements from across France, measured by a commercial data provider.
Given the growing interest of corporate stakeholders in Metaverse applications, there is a need to understand accessibility of these technologies for marginalized populations such as people living with dementia to ensure inclusive design of Metaverse applications. We assessed the accessibility of extended reality technology for people living with mild cognitive impairment and dementia to develop accessibility guidelines for these technologies. We used four strategies to synthesize evidence for barriers and facilitators of accessibility: (1) Findings from a non-systematic literature review, (2) guidelines from well-researched technology, (3) exploration of selected mixed reality technologies, and (4) observations from four sessions and video data of people living with dementia using mixed reality technologies. We utilized template analysis to develop codes and themes towards accessibility guidelines. Future work can validate our preliminary findings by applying them on video recordings or testing them in experiments.
Deep learning enables enormous progress in many computer vision-related tasks. Artificial Intel- ligence (AI) steadily yields new state-of-the-art results in the field of detection and classification. Thereby AI performance equals or exceeds human performance. Those achievements impacted many domains, including medical applications.
One particular field of medical applications is gastroenterology. In gastroenterology, machine learning algorithms are used to assist examiners during interventions. One of the most critical concerns for gastroenterologists is the development of Colorectal Cancer (CRC), which is one of the leading causes of cancer-related deaths worldwide. Detecting polyps in screening colonoscopies is the essential procedure to prevent CRC. Thereby, the gastroenterologist uses an endoscope to screen the whole colon to find polyps during a colonoscopy. Polyps are mucosal growths that can vary in severity.
This thesis supports gastroenterologists in their examinations with automated detection and clas- sification systems for polyps. The main contribution is a real-time polyp detection system. This system is ready to be installed in any gastroenterology practice worldwide using open-source soft- ware. The system achieves state-of-the-art detection results and is currently evaluated in a clinical trial in four different centers in Germany.
The thesis presents two additional key contributions: One is a polyp detection system with ex- tended vision tested in an animal trial. Polyps often hide behind folds or in uninvestigated areas. Therefore, the polyp detection system with extended vision uses an endoscope assisted by two additional cameras to see behind those folds. If a polyp is detected, the endoscopist receives a vi- sual signal. While the detection system handles the additional two camera inputs, the endoscopist focuses on the main camera as usual.
The second one are two polyp classification models, one for the classification based on shape (Paris) and the other on surface and texture (NBI International Colorectal Endoscopic (NICE) classification). Both classifications help the endoscopist with the treatment of and the decisions about the detected polyp.
The key algorithms of the thesis achieve state-of-the-art performance. Outstandingly, the polyp detection system tested on a highly demanding video data set shows an F1 score of 90.25 % while working in real-time. The results exceed all real-time systems in the literature. Furthermore, the first preliminary results of the clinical trial of the polyp detection system suggest a high Adenoma Detection Rate (ADR). In the preliminary study, all polyps were detected by the polyp detection system, and the system achieved a high usability score of 96.3 (max 100). The Paris classification model achieved an F1 score of 89.35 % which is state-of-the-art. The NICE classification model achieved an F1 score of 81.13 %.
Furthermore, a large data set for polyp detection and classification was created during this thesis. Therefore a fast and robust annotation system called Fast Colonoscopy Annotation Tool (FastCAT) was developed. The system simplifies the annotation process for gastroenterologists. Thereby the
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gastroenterologists only annotate key parts of the endoscopic video. Afterward, those video parts are pre-labeled by a polyp detection AI to speed up the process. After the AI has pre-labeled the frames, non-experts correct and finish the annotation. This annotation process is fast and ensures high quality. FastCAT reduces the overall workload of the gastroenterologist on average by a factor of 20 compared to an open-source state-of-art annotation tool.
Within the healthcare environment, mobile health (mHealth) applications (apps) are becoming more and more important. The number of new mHealth apps has risen steadily in the last years. Especially the COVID-19 pandemic has led to an enormous amount of app releases. In most countries, mHealth applications have to be compliant with several regulatory aspects to be declared a “medical app”. However, the latest applicable medical device regulation (MDR) does not provide more details on the requirements for mHealth applications. When developing a medical app, it is essential that all contributors in an interdisciplinary team — especially software engineers — are aware of the specific regulatory requirements beforehand. The development process, however, should not be stalled due to integration of the MDR. Therefore, a developing framework that includes these aspects is required to facilitate a reliable and quick development process. The paper at hand introduces the creation of such a framework on the basis of the Corona Health and Corona Check apps. The relevant regulatory guidelines are listed and summarized as a guidance for medical app developments during the pandemic and beyond. In particular, the important stages and challenges faced that emerged during the entire development process are highlighted.
Visual stimuli are frequently used to improve memory, language learning or perception, and understanding of metacognitive processes. However, in virtual reality (VR), there are few systematically and empirically derived databases. This paper proposes the first collection of virtual objects based on empirical evaluation for inter-and transcultural encounters between English- and German-speaking learners. We used explicit and implicit measurement methods to identify cultural associations and the degree of stereotypical perception for each virtual stimuli (n = 293) through two online studies, including native German and English-speaking participants. The analysis resulted in a final well-describable database of 128 objects (called InteractionSuitcase). In future applications, the objects can be used as a great interaction or conversation asset and behavioral measurement tool in social VR applications, especially in the field of foreign language education. For example, encounters can use the objects to describe their culture, or teachers can intuitively assess stereotyped attitudes of the encounters.
Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial.
Interactive system for similarity-based inspection and assessment of the well-being of mHealth users
(2021)
Recent digitization technologies empower mHealth users to conveniently record their Ecological Momentary Assessments (EMA) through web applications, smartphones, and wearable devices. These recordings can help clinicians understand how the users' condition changes, but appropriate learning and visualization mechanisms are required for this purpose. We propose a web-based visual analytics tool, which processes clinical data as well as EMAs that were recorded through a mHealth application. The goals we pursue are (1) to predict the condition of the user in the near and the far future, while also identifying the clinical data that mostly contribute to EMA predictions, (2) to identify users with outlier EMA, and (3) to show to what extent the EMAs of a user are in line with or diverge from those users similar to him/her. We report our findings based on a pilot study on patient empowerment, involving tinnitus patients who recorded EMAs with the mHealth app TinnitusTips. To validate our method, we also derived synthetic data from the same pilot study. Based on this setting, results for different use cases are reported.
The holy grail of structural biology is to study a protein in situ, and this goal has been fast approaching since the resolution revolution and the achievement of atomic resolution. A cell's interior is not a dilute environment, and proteins have evolved to fold and function as needed in that environment; as such, an investigation of a cellular component should ideally include the full complexity of the cellular environment. Imaging whole cells in three dimensions using electron cryotomography is the best method to accomplish this goal, but it comes with a limitation on sample thickness and produces noisy data unamenable to direct analysis. This thesis establishes a novel workflow to systematically analyse whole-cell electron cryotomography data in three dimensions and to find and identify instances of protein complexes in the data to set up a determination of their structure and identity for success. Mycoplasma pneumoniae is a very small parasitic bacterium with fewer than 700 protein-coding genes, is thin enough and small enough to be imaged in large quantities by electron cryotomography, and can grow directly on the grids used for imaging, making it ideal for exploratory studies in structural proteomics. As part of the workflow, a methodology for training deep-learning-based particle-picking models is established.
As a proof of principle, a dataset of whole-cell Mycoplasma pneumoniae tomograms is used with this workflow to characterize a novel membrane-associated complex observed in the data. Ultimately, 25431 such particles are picked from 353 tomograms and refined to a density map with a resolution of 11 Å. Making good use of orthogonal datasets to filter search space and verify results, structures were predicted for candidate proteins and checked for suitable fit in the density map. In the end, with this approach, nine proteins were found to be part of the complex, which appears to be associated with chaperone activity and interact with translocon machinery.
Visual proteomics refers to the ultimate potential of in situ electron cryotomography: the comprehensive interpretation of tomograms. The workflow presented here is demonstrated to help in reaching that potential.
Heat and excessive solar radiation can produce abiotic stresses during apple maturation, resulting fruit quality. Therefore, the monitoring of temperature on fruit surface (FST) over the growing period can allow to identify thresholds, above of which several physiological disorders such as sunburn may occur in apple.
The current approaches neglect spatial variation of FST and have reduced repeatability, resulting in unreliable predictions. In this study, LiDAR laser scanning and thermal imaging were employed to detect the temperature on fruit surface by means of 3D point cloud. A process for calibrating the two sensors based on an active board target and producing a 3D thermal point cloud was suggested. After calibration, the sensor system was utilised to scan the fruit trees, while temperature values assigned in the corresponding 3D point cloud were based on the extrinsic calibration. Whereas a fruit detection algorithm was performed to segment the FST from each apple.
• The approach allows the calibration of LiDAR laser scanner with thermal camera in order to produce a 3D thermal point cloud.
• The method can be applied in apple trees for segmenting FST in 3D. Whereas the approach can be utilised to predict several physiological disorders including sunburn on fruit surface.