Lukas Scholtes

Johannes Seiffarth, Matthias Pesch, Lukas Scholtes et al.

High-throughput microfluidic live-cell imaging generates rich single-cell data. Yet semi-automated procedures for locating regions of interest (RoIs), each containing one cell population, and removing surrounding microfluidic structures from recorded images, scale with the number of RoIs. This prevents real-time image analysis and delays time-to-insight by hours to days. We introduce the Design-Aware and Real-Time capable (DART) paradigm for microfluidic cultivation chips, which aligns the CAD blueprint with the physical chip and thereby enables throughput-independent localization of all RoIs and fully automated image processing across diverse RoI geometries and chip layouts. DART establishes this alignment through embedded fiducial markers and deep-learning-based marker detection. We validate DART using the Swiss Army Knife chip, which combines eight structurally distinct RoI designs across 1164 RoI locations. DART localizes all RoIs in five minutes, removes microfluidic structures from raw microscopy images in 40 ms, and performs fully automated image analysis, including cell segmentation, in under 1.1 s per image. Together, these capabilities establish DART as an end-to-end hardware-software paradigm with real-time-capable analysis that paves the way toward closed-loop and outcome-driven smart microscopy.

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.

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 %).