EAP4EMSIG -- Enhancing Event-Driven Microscopy for Microfluidic Single-Cell Analysis

Nils Friederich; Angelo Jovin Yamachui Sitcheu; Annika Nassal; Erenus Yildiz; Matthias Pesch; Maximilian Beichter; Lukas Scholtes; Bahar Akbaba; Thomas Lautenschlager; Oliver Neumann; Dietrich Kohlheyer; Hanno Scharr; Johannes Seiffarth; Katharina Nöh; Ralf Mikut

arXiv · 2504.00047

EAP4EMSIG -- Enhancing Event-Driven Microscopy for Microfluidic Single-Cell Analysis

Nils Friederich·Angelo Jovin Yamachui Sitcheu·Annika Nassal·Erenus Yildiz·Matthias Pesch·Maximilian Beichter·Lukas Scholtes·Bahar Akbaba·Thomas Lautenschlager·Oliver Neumann·Dietrich Kohlheyer·Hanno Scharr·Johannes Seiffarth·Katharina Nöh·Ralf Mikut

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Abstract

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 $\mu$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 %).

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q-bio.QM cs.AI cs.CV

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Nils Friederich, Angelo Jovin Yamachui Sitcheu, Annika Nassal, Erenus Yildiz, Matthias Pesch, Maximilian Beichter, Lukas Scholtes, Bahar Akbaba, Thomas Lautenschlager, Oliver Neumann, Dietrich Kohlheyer, Hanno Scharr, Johannes Seiffarth, Katharina Nöh, Ralf Mikut. 2025-03-30. EAP4EMSIG -- Enhancing Event-Driven Microscopy for Microfluidic Single-Cell Analysis. https://arxiv.org/abs/2504.00047

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