Oliver Hayden

Stefan Röhrl, Alice Hein, Lucie Huang et al.

The quality of datasets plays a crucial role in the successful training and deployment of deep learning models. Especially in the medical field, where system performance may impact the health of patients, clean datasets are a safety requirement for reliable predictions. Therefore, outlier detection is an essential process when building autonomous clinical decision systems. In this work, we assess the suitability of Self-Organizing Maps for outlier detection specifically on a medical dataset containing quantitative phase images of white blood cells. We detect and evaluate outliers based on quantization errors and distance maps. Our findings confirm the suitability of Self-Organizing Maps for unsupervised Out-Of-Distribution detection on the dataset at hand. Self-Organizing Maps perform on par with a manually specified filter based on expert domain knowledge. Additionally, they show promise as a tool in the exploration and cleaning of medical datasets. As a direction for future research, we suggest a combination of Self-Organizing Maps and feature extraction based on deep learning.

Stefan Röhrl, Johannes Groll, Manuel Lengl et al.

Label-free approaches are attractive in cytological imaging due to their flexibility and cost efficiency. They are supported by machine learning methods, which, despite the lack of labeling and the associated lower contrast, can classify cells with high accuracy where the human observer has little chance to discriminate cells. In order to better integrate these workflows into the clinical decision making process, this work investigates the calibration of confidence estimation for the automated classification of leukocytes. In addition, different visual explanation approaches are compared, which should bring machine decision making closer to professional healthcare applications. Furthermore, we were able to identify general detection patterns in neural networks and demonstrate the utility of the presented approaches in different scenarios of blood cell analysis.

Julia Sistermanns, Ellen Emken, Gregor Weirich et al.

In the effort to aid cytologic diagnostics by establishing automatic single cell screening using high throughput digital holographic microscopy for clinical studies thousands of images and millions of cells are captured. The bottleneck lies in an automatic, fast, and unsupervised segmentation technique that does not limit the types of cells which might occur. We propose an unsupervised multistage method that segments correctly without confusing noise or reflections with cells and without missing cells that also includes the detection of relevant inner structures, especially the cell nucleus in the unstained cell. In an effort to make the information reasonable and interpretable for cytopathologists, we also introduce new cytoplasmic and nuclear features of potential help for cytologic diagnoses which exploit the quantitative phase information inherent to the measurement scheme. We show that the segmentation provides consistently good results over many experiments on patient samples in a reasonable per cell analysis time.

Kerem Delikoyun, Qianyu Chen, Win Sen Kuan et al.

Emergency departments worldwide face rising patient volumes, workforce shortages, and variability in triage decisions that threaten the delivery of timely and accurate care. Current triage methods rely primarily on vital signs, routine laboratory values, and clinicians' judgment, which, while effective, often miss emerging biological signals that could improve risk prediction for infection typing or antibiotic administration in acute conditions. To address this challenge, we introduce TriAgent, a large language model (LLM)-based multi-agent framework that couples automated biomarker discovery with deep research for literature-grounded validation and novelty assessment. TriAgent employs a supervisor research agent to generate research topics and delegate targeted queries to specialized sub-agents for evidence retrieval from various data sources. Findings are synthesized to classify biomarkers as either grounded in existing knowledge or flagged as novel candidates, offering transparent justification and highlighting unexplored pathways in acute care risk stratification. Unlike prior frameworks limited to existing routine clinical biomarkers, TriAgent aims to deliver an end-to-end framework from data analysis to literature grounding to improve transparency, explainability and expand the frontier of potentially actionable clinical biomarkers. Given a user's clinical query and quantitative triage data, TriAgent achieved a topic adherence F1 score of 55.7 +/- 5.0%, surpassing the CoT-ReAct agent by over 10%, and a faithfulness score of 0.42 +/- 0.39, exceeding all baselines by more than 50%. Across experiments, TriAgent consistently outperformed state-of-the-art LLM-based agentic frameworks in biomarker justification and literature-grounded novelty assessment. We share our repo: https://github.com/CellFace/TriAgent.

Wei Liu, Kerem Delikoyun, Qianyu Chen et al.

Off-axis digital holographic microscopy is a high-throughput, label-free imaging technology that provides three-dimensional, high-resolution information about samples, particularly useful in large-scale cellular imaging. However, the hologram reconstruction process poses a significant bottleneck for timely data analysis. To address this challenge, we propose a novel reconstruction approach that integrates deep learning with the physical principles of off-axis holography. We initialized part of the network weights based on the physical principle and then fine-tuned them via weakly supersized learning. Our off-axis hologram network (OAH-Net) retrieves phase and amplitude images with errors that fall within the measurement error range attributable to hardware, and its reconstruction speed significantly surpasses the microscope's acquisition rate. Crucially, OAH-Net demonstrates remarkable external generalization capabilities on unseen samples with distinct patterns and can be seamlessly integrated with other models for downstream tasks to achieve end-to-end real-time hologram analysis. This capability further expands off-axis holography's applications in both biological and medical studies.

Kerem Delikoyun, Qianyu Chen, Liu Wei et al.

While analysing rare blood cell aggregates remains challenging in automated haematology, they could markedly advance label-free functional diagnostics. Conventional flow cytometers efficiently perform cell counting with leukocyte differentials but fail to identify aggregates with flagged results, requiring manual reviews. Quantitative phase imaging flow cytometry captures detailed aggregate morphologies, but clinical use is hampered by massive data storage and offline processing. Incorporating hidden biomarkers into routine haematology panels would significantly improve diagnostics without flagged results. We present RT-HAD, an end-to-end deep learning-based image and data processing framework for off-axis digital holographic microscopy (DHM), which combines physics-consistent holographic reconstruction and detection, representing each blood cell in a graph to recognize aggregates. RT-HAD processes >30 GB of image data on-the-fly with turnaround time of <1.5 min and error rate of 8.9% in platelet aggregate detection, which matches acceptable laboratory error rates of haematology biomarkers and solves the big data challenge for point-of-care diagnostics.