Christoph Reich

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 19k 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.

Atrial Fibrillation (AF) is a severe cardiac arrhythmia affecting a significant amount of the human population [1]. Quick diagnosis and treatment are critical in reducing the risk of severe sequelae such as stroke or heart failure. Rohr et al . [2] recently proposed ECG-DualNet, a neural network for accurate AF detection in single-lead electrocardiogram (ECG) data. This short paper reports additional empirical results of ECG-DualNet to gain new insights on AF detection in single-lead ECG data with deep neural networks. We systematically analyze which ingredients of ECG-DualNet are crucial for achieving competitive AF detection results. We also scale the ECG-DualNet architecture to 130M parameters and perform large-scale supervised pre-training, providing additional empirical results. Finally, we provide recommendations for future research toward accurate and robust AF detection.

During the lockdown of universities and the COVID-Pandemic most students were restricted to their homes. Novel and instigating teaching methods were required to improve the learning experience and so recent implementations of the annual PhysioNet/Computing in Cardiology (CinC) Challenges posed as a reference. For over 20 years, the challenges have proven repeatedly to be of immense educational value, besides leading to technological advances for specific problems. In this paper, we report results from the class ‘Artificial Intelligence in Medicine Challenge’, which was implemented as an online project seminar at Technical University Darmstadt, Germany, and which was heavily inspired by the PhysioNet/CinC Challenge 2017 ‘AF Classification from a Short Single Lead ECG Recording’. Atrial fibrillation is a common cardiac disease and often remains undetected. Therefore, we selected the two most promising models of the course and give an insight into the Transformer-based DualNet architecture as well as into the CNN-LSTM-based model and finally a detailed analysis for both. In particular, we show the model performance results of our internal scoring process for all submitted models and the near state-of-the-art model performance for the two named models on the official 2017 challenge test set. Several teams were able to achieve F₁ scores above/close to 90% on a hidden test-set of Holter recordings. We highlight themes commonly observed among participants, and report the results from the self-assessed student evaluation. Finally, the self-assessment of the students reported a notable increase in machine learning knowledge.

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.