Angelo Jovin Yamachui Sitcheu

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.

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 %).