Nils Friederich

Nils Friederich, Andreas Specker, Jürgen Beyerer

To ensure the security of airports, it is essential to protect the airside from unauthorized access. For this purpose, security fences are commonly used, but they require regular inspection to detect damages. However, due to the growing shortage of human specialists and the large manual effort, there is the need for automated methods. The aim is to automatically inspect the fence for damage with the help of an autonomous robot. In this work, we explore object detection methods to address the fence inspection task and localize various types of damages. In addition to evaluating four State-of-the-Art (SOTA) object detection models, we analyze the impact of several design criteria, aiming at adapting to the task-specific challenges. This includes contrast adjustment, optimization of hyperparameters, and utilization of modern backbones. The experimental results indicate that our optimized You Only Look Once v5 (YOLOv5) model achieves the highest accuracy of the four methods with an increase of 6.9% points in Average Precision (AP) compared to the baseline. Moreover, we show the real-time capability of the model. The trained models are published on GitHub: https://github.com/N-Friederich/airport_fence_inspection.

Angelo Yamachui Sitcheu, Nils Friederich, Simon Baeuerle et al.

Nowadays, Machine Learning (ML) is experiencing tremendous popularity that has never been seen before. The operationalization of ML models is governed by a set of concepts and methods referred to as Machine Learning Operations (MLOps). Nevertheless, researchers, as well as professionals, often focus more on the automation aspect and neglect the continuous deployment and monitoring aspects of MLOps. As a result, there is a lack of continuous learning through the flow of feedback from production to development, causing unexpected model deterioration over time due to concept drifts, particularly when dealing with scarce data. This work explores the complete application of MLOps in the context of scarce data analysis. The paper proposes a new holistic approach to enhance biomedical image analysis. Our method includes: a fingerprinting process that enables selecting the best models, datasets, and model development strategy relative to the image analysis task at hand; an automated model development stage; and a continuous deployment and monitoring process to ensure continuous learning. For preliminary results, we perform a proof of concept for fingerprinting in microscopic image datasets.

David Exler, Nils Friederich, Martin Krüger et al.

Myotubes are multinucleated muscle fibers serving as key model systems for studying muscle physiology, disease mechanisms, and drug responses. Mechanistic studies and drug screening thereby rely on quantitative morphological readouts such as diameter, length, and branching degree, which in turn require precise three-dimensional instance segmentation. Yet established pretrained biomedical segmentation models fail to generalize to this domain due to the absence of large annotated myotube datasets. We introduce a geometry-driven synthesis pipeline that models individual myotubes via polynomial centerlines, locally varying radii, branching structures, and ellipsoidal end caps derived from real microscopy observations. Synthetic volumes are rendered with realistic noise, optical artifacts, and CycleGAN-based Domain Adaptation (DA). A compact 3D U-Net with self-supervised encoder pretraining, trained exclusively on synthetic data, achieves a mean IPQ of 0.22 on real data, significantly outperforming three established zero-shot segmentation models, demonstrating that biophysics-driven synthesis enables effective instance segmentation in annotation-scarce biomedical domains.

Nils Friederich, Angelo Yamachui Sitcheu, Oliver Neumann et al.

In the biomedical environment, experiments assessing dynamic processes are primarily performed by a human acquisition supervisor. Contemporary implementations of such experiments frequently aim to acquire a maximum number of relevant events from sometimes several hundred parallel, non-synchronous processes. Since in some high-throughput experiments, only one or a few instances of a given process can be observed simultaneously, a strategy for planning and executing an efficient acquisition paradigm is essential. To address this problem, we present two new methods in this paper. The first method, Encoded Dynamic Process (EDP), is Artificial Intelligence (AI)-based and represents dynamic processes so as to allow prediction of pseudo-time values from single still images. Second, with Experiment Automation Pipeline for Dynamic Processes (EAPDP), we present a Machine Learning Operations (MLOps)-based pipeline that uses the extracted knowledge from EDP to efficiently schedule acquisition in biomedical experiments for dynamic processes in practice. In a first experiment, we show that the pre-trained State-Of-The- Art (SOTA) object segmentation method Contour Proposal Networks (CPN) works reliably as a module of EAPDP to extract the relevant object for EDP from the acquired three-dimensional image stack.

Nils Friederich, Angelo Jovin Yamachui Sitcheu, Annika Nassal et al.

Microfluidic Live-Cell Imaging (MLCI) generates high-quality data that allows biotechnologists to study cellular growth dynamics in detail. However, obtaining these continuous data over extended periods is challenging, particularly in achieving accurate and consistent real-time event classification at the intersection of imaging and stochastic biology. To address this issue, we introduce the Experiment Automation Pipeline for Event-Driven Microscopy to Smart Microfluidic Single-Cells Analysis (EAP4EMSIG). In particular, we present initial zero-shot results from the real-time segmentation module of our approach. Our findings indicate that among four State-Of-The- Art (SOTA) segmentation methods evaluated, Omnipose delivers the highest Panoptic Quality (PQ) score of 0.9336, while Contour Proposal Network (CPN) achieves the fastest inference time of 185 ms with the second-highest PQ score of 0.8575. Furthermore, we observed that the vision foundation model Segment Anything is unsuitable for this particular use case.

Thomas Lautenschlager, Nils Friederich, Angelo Jovin Yamachui Sitcheu et al.

High-throughput toxicity testing offers a fast and cost-effective way to test large amounts of compounds. A key component for such systems is the automated evaluation via machine learning models. In this paper, we address critical challenges in this domain and demonstrate how representations learned via self-supervised learning can effectively identify toxicant-induced changes. We provide a proof-of-concept that utilizes the publicly available EmbryoNet dataset, which contains ten zebrafish embryo phenotypes elicited by various chemical compounds targeting different processes in early embryonic development. Our analysis shows that the learned representations using self-supervised learning are suitable for effectively distinguishing between the modes-of-action of different compounds. Finally, we discuss the integration of machine learning models in a physical toxicity testing device in the context of the TOXBOX project.

Simon Baeuerle, Pratik Khanna, Nils Friederich et al.

Foundation Models (FMs) have shown impressive performance on various text and image processing tasks. They can generalize across domains and datasets in a zero-shot setting. This could make them suitable for automated quality inspection during series manufacturing, where various types of images are being evaluated for many different products. Replacing tedious labeling tasks with a simple text prompt to describe anomalies and utilizing the same models across many products would save significant efforts during model setup and implementation. This is a strong advantage over supervised Artificial Intelligence (AI) models, which are trained for individual applications and require labeled training data. We test multiple recent FMs on both custom real-world industrial image data and public image data. We show that all of those models fail on our real-world data, while the very same models perform well on public benchmark datasets.

Pascal Zwick, Nils Friederich, Maximilian Beichter et al.

Enhancing the efficiency of high-quality image generation using Diffusion Models (DMs) is a significant challenge due to the iterative nature of the process. Flow Matching (FM) is emerging as a powerful generative modeling paradigm based on a simulation-free training objective instead of a score-based one used in DMs. Typical FM approaches rely on a Gaussian distribution prior, which induces curved, conditional probability paths between the prior and target data distribution. These curved paths pose a challenge for the Ordinary Differential Equation (ODE) solver, requiring a large number of inference calls to the flow prediction network. To address this issue, we present Learned Distribution-guided Flow Matching (LeDiFlow), a novel scalable method for training FM-based image generation models using a better-suited prior distribution learned via a regression-based auxiliary model. By initializing the ODE solver with a prior closer to the target data distribution, LeDiFlow enables the learning of more computationally tractable probability paths. These paths directly translate to fewer solver steps needed for high-quality image generation at inference time. Our method utilizes a State-Of-The-Art (SOTA) transformer architecture combined with latent space sampling and can be trained on a consumer workstation. We empirically demonstrate that LeDiFlow remarkably outperforms the respective FM baselines. For instance, when operating directly on pixels, our model accelerates inference by up to 3.75x compared to the corresponding pixel-space baseline. Simultaneously, our latent FM model enhances image quality on average by 1.32x in CLIP Maximum Mean Discrepancy (CMMD) metric against its respective baseline.

Nils Friederich, Angelo Jovin Yamachui Sitcheu, Annika Nassal et al.

Microfluidic Live-Cell Imaging (MLCI) yields data on microbial cell factories. However, continuous acquisition is challenging as high-throughput experiments often lack real-time insights, delaying responses to stochastic events. We introduce three components in the Experiment Automation Pipeline for Event-Driven Microscopy to Smart Microfluidic Single-Cell Analysis (EAP4EMSIG): a fast, accurate Multi-Layer Perceptron (MLP)-based autofocusing method predicting the focus offset, an evaluation of real-time segmentation methods and a real-time data analysis dashboard. Our MLP-based autofocusing achieves a Mean Absolute Error (MAE) of 0.105 $μ$m with inference times from 87 ms. Among eleven evaluated Deep Learning (DL) segmentation methods, Cellpose reached a Panoptic Quality (PQ) of 93.36 %, while a distance-based method was fastest (121 ms, Panoptic Quality 93.02 %).

Maximilian Beichter, Nils Friederich, Janik Pinter et al.

Time series foundation models provide a universal solution for generating forecasts to support optimization problems in energy systems. Those foundation models are typically trained in a prediction-focused manner to maximize forecast quality. In contrast, decision-focused learning directly improves the resulting value of the forecast in downstream optimization rather than merely maximizing forecasting quality. The practical integration of forecast values into forecasting models is challenging, particularly when addressing complex applications with diverse instances, such as buildings. This becomes even more complicated when instances possess specific characteristics that require instance-specific, tailored predictions to increase the forecast value. To tackle this challenge, we use decision-focused fine-tuning within time series foundation models to offer a scalable and efficient solution for decision-focused learning applied to the dispatchable feeder optimization problem. To obtain more robust predictions for scarce building data, we use Moirai as a state-of-the-art foundation model, which offers robust and generalized results with few-shot parameter-efficient fine-tuning. Comparing the decision-focused fine-tuned Moirai with a state-of-the-art classical prediction-focused fine-tuning Morai, we observe an improvement of 9.45% in average total daily costs.