Christoph Reich

Christoph Reich, Biplob Debnath, Deep Patel et al.

JPEG remains one of the most widespread lossy image coding methods. However, the non-differentiable nature of JPEG restricts the application in deep learning pipelines. Several differentiable approximations of JPEG have recently been proposed to address this issue. This paper conducts a comprehensive review of existing diff. JPEG approaches and identifies critical details that have been missed by previous methods. To this end, we propose a novel diff. JPEG approach, overcoming previous limitations. Our approach is differentiable w.r.t. the input image, the JPEG quality, the quantization tables, and the color conversion parameters. We evaluate the forward and backward performance of our diff. JPEG approach against existing methods. Additionally, extensive ablations are performed to evaluate crucial design choices. Our proposed diff. JPEG resembles the (non-diff.) reference implementation best, significantly surpassing the recent-best diff. approach by $3.47$dB (PSNR) on average. For strong compression rates, we can even improve PSNR by $9.51$dB. Strong adversarial attack results are yielded by our diff. JPEG, demonstrating the effective gradient approximation. Our code is available at https://github.com/necla-ml/Diff-JPEG.

Christoph Reich, Oliver Hahn, Nikita Araslanov et al.

Video panoptic segmentation (VPS) aims to jointly detect, segment, and track all objects while partitioning the video into semantically consistent regions. We introduce the task setting of unsupervised VPS, omitting any human supervision. Existing unsupervised scene understanding works mainly focused on image segmentation tasks; the video domain remains underexplored. We propose VideoCUPS, the first unsupervised VPS approach. VideoCUPS generates temporally consistent panoptic video pseudo-labels from scene-centric videos by exploiting unsupervised depth, motion, and visual cues. Training on these pseudo-labels using a novel Video DropLoss yields an accurate, unsupervised VPS model. To benchmark progress, we introduce a comprehensive evaluation protocol and four competitive baselines, extending state-of-the-art unsupervised panoptic image and instance video segmentation models to VPS. VideoCUPS outperforms all baselines and demonstrates strong label-efficient learning. With VideoCUPS, our evaluation protocol, and baselines, we provide a strong foundation for future research on unsupervised VPS.

Claudia Cuttano, Gabriele Trivigno, Christoph Reich et al.

In-context segmentation (ICS) aims to segment arbitrary concepts, e.g., objects, parts, or personalized instances, given one annotated visual examples. Existing work relies on (i) fine-tuning vision foundation models (VFMs), which improves in-domain results but harms generalization, or (ii) combines multiple frozen VFMs, which preserves generalization but yields architectural complexity and fixed segmentation granularities. We revisit ICS from a minimalist perspective and ask: Can a single self-supervised backbone support both semantic matching and segmentation, without any supervision or auxiliary models? We show that scaled-up dense self-supervised features from DINOv3 exhibit strong spatial structure and semantic correspondence. We introduce INSID3, a training-free approach that segments concepts at varying granularities only from frozen DINOv3 features, given an in-context example. INSID3 achieves state-of-the-art results across one-shot semantic, part, and personalized segmentation, outperforming previous work by +7.5 % mIoU, while using 3x fewer parameters and without any mask or category-level supervision. Code is available at https://github.com/visinf/INSID3 .

Ahmet Gokberk Gul, Oezdemir Cetin, Christoph Reich et al.

Whole Slide Image (WSI) analysis is a powerful method to facilitate the diagnosis of cancer in tissue samples. Automating this diagnosis poses various issues, most notably caused by the immense image resolution and limited annotations. WSIs commonly exhibit resolutions of 100Kx100K pixels. Annotating cancerous areas in WSIs on the pixel level is prohibitively labor-intensive and requires a high level of expert knowledge. Multiple instance learning (MIL) alleviates the need for expensive pixel-level annotations. In MIL, learning is performed on slide-level labels, in which a pathologist provides information about whether a slide includes cancerous tissue. Here, we propose Self-ViT-MIL, a novel approach for classifying and localizing cancerous areas based on slide-level annotations, eliminating the need for pixel-wise annotated training data. Self-ViT- MIL is pre-trained in a self-supervised setting to learn rich feature representation without relying on any labels. The recent Vision Transformer (ViT) architecture builds the feature extractor of Self-ViT-MIL. For localizing cancerous regions, a MIL aggregator with global attention is utilized. To the best of our knowledge, Self-ViT- MIL is the first approach to introduce self-supervised ViTs in MIL-based WSI analysis tasks. We showcase the effectiveness of our approach on the common Camelyon16 dataset. Self-ViT-MIL surpasses existing state-of-the-art MIL-based approaches in terms of accuracy and area under the curve (AUC).

Christoph Reich, Biplob Debnath, Deep Patel et al.

Standardized lossy video coding is at the core of almost all real-world video processing pipelines. Rate control is used to enable standard codecs to adapt to different network bandwidth conditions or storage constraints. However, standard video codecs (e.g., H.264) and their rate control modules aim to minimize video distortion w.r.t. human quality assessment. We demonstrate empirically that standard-coded videos vastly deteriorate the performance of deep vision models. To overcome the deterioration of vision performance, this paper presents the first end-to-end learnable deep video codec control that considers both bandwidth constraints and downstream deep vision performance, while adhering to existing standardization. We demonstrate that our approach better preserves downstream deep vision performance than traditional standard video coding.

Christoph Reich, Tim Prangemeier, André O. Françani et al.

Extracting single-cell information from microscopy data requires accurate instance-wise segmentations. Obtaining pixel-wise segmentations from microscopy imagery remains a challenging task, especially with the added complexity of microstructured environments. This paper presents a novel dataset for segmenting yeast cells in microstructures. We offer pixel-wise instance segmentation labels for both cells and trap microstructures. In total, we release 493 densely annotated microscopy images. To facilitate a unified comparison between novel segmentation algorithms, we propose a standardized evaluation strategy for our dataset. The aim of the dataset and evaluation strategy is to facilitate the development of new cell segmentation approaches. The dataset is publicly available at https://christophreich1996.github.io/yeast_in_microstructures_dataset/ .

Christoph Reich, Tim Prangemeier, Heinz Koeppl

Segmenting cells and tracking their motion over time is a common task in biomedical applications. However, predicting accurate instance-wise segmentation and cell motions from microscopy imagery remains a challenging task. Using microstructured environments for analyzing single cells in a constant flow of media adds additional complexity. While large-scale labeled microscopy datasets are available, we are not aware of any large-scale dataset, including both cells and microstructures. In this paper, we introduce the trapped yeast cell (TYC) dataset, a novel dataset for understanding instance-level semantics and motions of cells in microstructures. We release $105$ dense annotated high-resolution brightfield microscopy images, including about $19$k instance masks. We also release $261$ curated video clips composed of $1293$ high-resolution microscopy images to facilitate unsupervised understanding of cell motions and morphology. TYC offers ten times more instance annotations than the previously largest dataset, including cells and microstructures. Our effort also exceeds previous attempts in terms of microstructure variability, resolution, complexity, and capturing device (microscopy) variability. We facilitate a unified comparison on our novel dataset by introducing a standardized evaluation strategy. TYC and evaluation code are publicly available under CC BY 4.0 license.

Oliver Hahn, Christoph Reich, Nikita Araslanov et al.

Unsupervised panoptic segmentation aims to partition an image into semantically meaningful regions and distinct object instances without training on manually annotated data. In contrast to prior work on unsupervised panoptic scene understanding, we eliminate the need for object-centric training data, enabling the unsupervised understanding of complex scenes. To that end, we present the first unsupervised panoptic method that directly trains on scene-centric imagery. In particular, we propose an approach to obtain high-resolution panoptic pseudo labels on complex scene-centric data, combining visual representations, depth, and motion cues. Utilizing both pseudo-label training and a panoptic self-training strategy yields a novel approach that accurately predicts panoptic segmentation of complex scenes without requiring any human annotations. Our approach significantly improves panoptic quality, e.g., surpassing the recent state of the art in unsupervised panoptic segmentation on Cityscapes by 9.4% points in PQ.

Christoph Reich, Oliver Hahn, Daniel Cremers et al.

Resource-constrained hardware, such as edge devices or cell phones, often rely on cloud servers to provide the required computational resources for inference in deep vision models. However, transferring image and video data from an edge or mobile device to a cloud server requires coding to deal with network constraints. The use of standardized codecs, such as JPEG or H.264, is prevalent and required to ensure interoperability. This paper aims to examine the implications of employing standardized codecs within deep vision pipelines. We find that using JPEG and H.264 coding significantly deteriorates the accuracy across a broad range of vision tasks and models. For instance, strong compression rates reduce semantic segmentation accuracy by more than 80% in mIoU. In contrast to previous findings, our analysis extends beyond image and action classification to localization and dense prediction tasks, thus providing a more comprehensive perspective.

Aleksandar Jevtić, Christoph Reich, Felix Wimbauer et al.

Semantic scene completion (SSC) aims to infer both the 3D geometry and semantics of a scene from single images. In contrast to prior work on SSC that heavily relies on expensive ground-truth annotations, we approach SSC in an unsupervised setting. Our novel method, SceneDINO, adapts techniques from self-supervised representation learning and 2D unsupervised scene understanding to SSC. Our training exclusively utilizes multi-view consistency self-supervision without any form of semantic or geometric ground truth. Given a single input image, SceneDINO infers the 3D geometry and expressive 3D DINO features in a feed-forward manner. Through a novel 3D feature distillation approach, we obtain unsupervised 3D semantics. In both 3D and 2D unsupervised scene understanding, SceneDINO reaches state-of-the-art segmentation accuracy. Linear probing our 3D features matches the segmentation accuracy of a current supervised SSC approach. Additionally, we showcase the domain generalization and multi-view consistency of SceneDINO, taking the first steps towards a strong foundation for single image 3D scene understanding.

Malte Tölle, Mohamad Scharaf, Samantha Fischer et al.

A patient undergoes multiple examinations in each hospital stay, where each provides different facets of the health status. These assessments include temporal data with varying sampling rates, discrete single-point measurements, therapeutic interventions such as medication administration, and images. While physicians are able to process and integrate diverse modalities intuitively, neural networks need specific modeling for each modality complicating the training procedure. We demonstrate that this complexity can be significantly reduced by visualizing all information as images along with unstructured text and subsequently training a conventional vision-text transformer. Our approach, Vision Transformer for irregular sampled Multi-modal Measurements (ViTiMM), not only simplifies data preprocessing and modeling but also outperforms current state-of-the-art methods in predicting in-hospital mortality and phenotyping, as evaluated on 6,175 patients from the MIMIC-IV dataset. The modalities include patient's clinical measurements, medications, X-ray images, and electrocardiography scans. We hope our work inspires advancements in multi-modal medical AI by reducing the training complexity to (visual) prompt engineering, thus lowering entry barriers and enabling no-code solutions for training. The source code will be made publicly available.

Johannes Meier, Jonathan Michel, Oussema Dhaouadi et al.

Real-time monocular 3D object detection remains challenging due to severe depth ambiguity, viewpoint shifts, and the high computational cost of 3D reasoning. Existing approaches either rely on LiDAR or geometric priors to compensate for missing depth, or sacrifice efficiency to achieve competitive accuracy. We introduce LeAD-M3D, a monocular 3D detector that achieves state-of-the-art accuracy and real-time inference without extra modalities. Our method is powered by three key components. Asymmetric Augmentation Denoising Distillation (A2D2) transfers geometric knowledge from a clean-image teacher to a mixup-noised student via a quality- and importance-weighted depth-feature loss, enabling stronger depth reasoning without LiDAR supervision. 3D-aware Consistent Matching (CM3D) improves prediction-to-ground truth assignment by integrating 3D MGIoU into the matching score, yielding more stable and precise supervision. Finally, Confidence-Gated 3D Inference (CGI3D) accelerates detection by restricting expensive 3D regression to top-confidence regions. Together, these components set a new Pareto frontier for monocular 3D detection: LeAD-M3D achieves state-of-the-art accuracy on KITTI and Waymo, and the best reported car AP on Rope3D, while running up to 3.6x faster than prior high-accuracy methods. Our results demonstrate that high fidelity and real-time efficiency in monocular 3D detection are simultaneously attainable - without LiDAR, stereo, or geometric assumptions.

Xinrui Gong, Oliver Hahn, Christoph Reich et al.

Unsupervised multi-object discovery (MOD) aims to detect and localize distinct object instances in visual scenes without any form of human supervision. Recent approaches leverage object-centric learning (OCL) and motion cues from video to identify individual objects. However, these approaches use supervision to generate pseudo labels to train the OCL model. We address this limitation with MR-DINOSAUR -- Motion-Refined DINOSAUR -- a minimalistic unsupervised approach that extends the self-supervised pre-trained OCL model, DINOSAUR, to the task of unsupervised multi-object discovery. We generate high-quality unsupervised pseudo labels by retrieving video frames without camera motion for which we perform motion segmentation of unsupervised optical flow. We refine DINOSAUR's slot representations using these pseudo labels and train a slot deactivation module to assign slots to foreground and background. Despite its conceptual simplicity, MR-DINOSAUR achieves strong multi-object discovery results on the TRI-PD and KITTI datasets, outperforming the previous state of the art despite being fully unsupervised.

Marius Memmel, Christoph Reich, Nicolas Wagner et al.

With the increased availability of 3D data, the need for solutions processing those also increased rapidly. However, adding dimension to already reliably accurate 2D approaches leads to immense memory consumption and higher computational complexity. These issues cause current hardware to reach its limitations, with most methods forced to reduce the input resolution drastically. Our main contribution is a novel deep 3D semantic segmentation method for gun detection in baggage CT scans that enables fast training and low video memory consumption for high-resolution voxelized volumes. We introduce a moving pyramid approach that utilizes multiple forward passes at inference time for segmenting an instance.

Kevin Wallis, Christoph Reich, Blesson Varghese et al.

Distributed machine learning algorithms that employ Deep Neural Networks (DNNs) are widely used in Industry 4.0 applications, such as smart manufacturing. The layers of a DNN can be mapped onto different nodes located in the cloud, edge and shop floor for preserving privacy. The quality of the data that is fed into and processed through the DNN is of utmost importance for critical tasks, such as inspection and quality control. Distributed Data Validation Networks (DDVNs) are used to validate the quality of the data. However, they are prone to single points of failure when an attack occurs. This paper proposes QUDOS, an approach that enhances the security of a distributed DNN that is supported by DDVNs using quorums. The proposed approach allows individual nodes that are corrupted due to an attack to be detected or excluded when the DNN produces an output. Metrics such as corruption factor and success probability of an attack are considered for evaluating the security aspects of DNNs. A simulation study demonstrates that if the number of corrupted nodes is less than a given threshold for decision-making in a quorum, the QUDOS approach always prevents attacks. Furthermore, the study shows that increasing the size of the quorum has a better impact on security than increasing the number of layers. One merit of QUDOS is that it enhances the security of DNNs without requiring any modifications to the algorithm and can therefore be applied to other classes of problems.

Christoph Reich, Tim Prangemeier, Özdemir Cetin et al.

Convolutional neural networks (CNNs) are the current state-of-the-art meta-algorithm for volumetric segmentation of medical data, for example, to localize COVID-19 infected tissue on computer tomography scans or the detection of tumour volumes in magnetic resonance imaging. A key limitation of 3D CNNs on voxelised data is that the memory consumption grows cubically with the training data resolution. Occupancy networks (O-Nets) are an alternative for which the data is represented continuously in a function space and 3D shapes are learned as a continuous decision boundary. While O-Nets are significantly more memory efficient than 3D CNNs, they are limited to simple shapes, are relatively slow at inference, and have not yet been adapted for 3D semantic segmentation of medical data. Here, we propose Occupancy Networks for Semantic Segmentation (OSS-Nets) to accurately and memory-efficiently segment 3D medical data. We build upon the original O-Net with modifications for increased expressiveness leading to improved segmentation performance comparable to 3D CNNs, as well as modifications for faster inference. We leverage local observations to represent complex shapes and prior encoder predictions to expedite inference. We showcase OSS-Net's performance on 3D brain tumour and liver segmentation against a function space baseline (O-Net), a performance baseline (3D residual U-Net), and an efficiency baseline (2D residual U-Net). OSS-Net yields segmentation results similar to the performance baseline and superior to the function space and efficiency baselines. In terms of memory efficiency, OSS-Net consumes comparable amounts of memory as the function space baseline, somewhat more memory than the efficiency baseline and significantly less than the performance baseline. As such, OSS-Net enables memory-efficient and accurate 3D semantic segmentation that can scale to high resolutions.

Christoph Reich, Tim Prangemeier, Christian Wildner et al.

Time-lapse fluorescent microscopy (TLFM) combined with predictive mathematical modelling is a powerful tool to study the inherently dynamic processes of life on the single-cell level. Such experiments are costly, complex and labour intensive. A complimentary approach and a step towards in silico experimentation, is to synthesise the imagery itself. Here, we propose Multi-StyleGAN as a descriptive approach to simulate time-lapse fluorescence microscopy imagery of living cells, based on a past experiment. This novel generative adversarial network synthesises a multi-domain sequence of consecutive timesteps. We showcase Multi-StyleGAN on imagery of multiple live yeast cells in microstructured environments and train on a dataset recorded in our laboratory. The simulation captures underlying biophysical factors and time dependencies, such as cell morphology, growth, physical interactions, as well as the intensity of a fluorescent reporter protein. An immediate application is to generate additional training and validation data for feature extraction algorithms or to aid and expedite development of advanced experimental techniques such as online monitoring or control of cells. Code and dataset is available at https://git.rwth-aachen.de/bcs/projects/tp/multi-stylegan.

Christoph Reich

Time-lapse fluorescence microscopy (TLFM) is an important and powerful tool in synthetic biological research. Modeling TLFM experiments based on real data may enable researchers to repeat certain experiments with minor effort. This thesis is a study towards deep learning-based modeling of TLFM experiments on the image level. The modeling of TLFM experiments, by way of the example of trapped yeast cells, is split into two tasks. The first task is to generate synthetic image data based on real image data. To approach this problem, a novel generative adversarial network, for conditionalized and unconditionalized image generation, is proposed. The second task is the simulation of brightfield microscopy images over multiple discrete time-steps. To tackle this simulation task an advanced future frame prediction model is introduced. The proposed models are trained and tested on a novel dataset that is presented in this thesis. The obtained results showed that the modeling of TLFM experiments, with deep learning, is a proper approach, but requires future research to effectively model real-world experiments.

Tim Prangemeier, Christoph Reich, Heinz Koeppl

Detecting and segmenting object instances is a common task in biomedical applications. Examples range from detecting lesions on functional magnetic resonance images, to the detection of tumours in histopathological images and extracting quantitative single-cell information from microscopy imagery, where cell segmentation is a major bottleneck. Attention-based transformers are state-of-the-art in a range of deep learning fields. They have recently been proposed for segmentation tasks where they are beginning to outperforming other methods. We present a novel attention-based cell detection transformer (Cell-DETR) for direct end-to-end instance segmentation. While the segmentation performance is on par with a state-of-the-art instance segmentation method, Cell-DETR is simpler and faster. We showcase the method's contribution in a the typical use case of segmenting yeast in microstructured environments, commonly employed in systems or synthetic biology. For the specific use case, the proposed method surpasses the state-of-the-art tools for semantic segmentation and additionally predicts the individual object instances. The fast and accurate instance segmentation performance increases the experimental information yield for a posteriori data processing and makes online monitoring of experiments and closed-loop optimal experimental design feasible.

Tim Prangemeier, Christian Wildner, André O. Françani et al.

Cell segmentation is a major bottleneck in extracting quantitative single-cell information from microscopy data. The challenge is exasperated in the setting of microstructured environments. While deep learning approaches have proven useful for general cell segmentation tasks, existing segmentation tools for the yeast-microstructure setting rely on traditional machine learning approaches. Here we present convolutional neural networks trained for multiclass segmenting of individual yeast cells and discerning these from cell-similar microstructures. We give an overview of the datasets recorded for training, validating and testing the networks, as well as a typical use-case. We showcase the method's contribution to segmenting yeast in microstructured environments with a typical synthetic biology application in mind. The models achieve robust segmentation results, outperforming the previous state-of-the-art in both accuracy and speed. The combination of fast and accurate segmentation is not only beneficial for a posteriori data processing, it also makes online monitoring of thousands of trapped cells or closed-loop optimal experimental design feasible from an image processing perspective.

Jan Stodt, Christoph Reich

Increased collaborative production and dynamic selection of production partners within industry 4.0 manufacturing leads to ever-increasing automatic data exchange between companies. Automatic and unsupervised data exchange creates new attack vectors, which could be used by a malicious insider to leak secrets via an otherwise considered secure channel without anyone noticing. In this paper we reflect upon approaches to prevent the exposure of secret data via blockchain technology, while also providing auditable proof of data exchange. We show that previous blockchain based privacy protection approaches offer protection, but give the control of the data to (potentially not trustworthy) third parties, which also can be considered a privacy violation. The approach taken in this paper is not utilize centralized data storage for data. It realizes data confidentiality of P2P communication and data processing in smart contracts of blockchains.

Kevin Wallis, Jan Stodt, Eugen Jastremskoj et al.

The digital transformation of companies is expected to increase the digital interconnection between different companies to develop optimized, customized, hybrid business models. These cross-company business models require secure, reliable, and traceable logging and monitoring of contractually agreed information sharing between machine tools, operators, and service providers. This paper discusses how the major requirements for building hybrid business models can be tackled by the blockchain for building a chain of trust and smart contracts for digitized contracts. A machine maintenance use case is used to discuss the readiness of smart contracts for the automation of workflows defined in contracts. Furthermore, it is shown that the number of failures is significantly improved by using these contracts and a blockchain.