TY  - EJOUR
AU  - Friederich, Nils
AU  - Yamachui Sitcheu, A. J.
AU  - Nassal, Annika
AU  - Pesch, Matthias
AU  - Yildiz, Erenus
AU  - Beichter, Maximilian
AU  - Scholtes, Lukas
AU  - Akbaba, Bahar
AU  - Lautenschlager, Thomas
AU  - Neumann, Oliver
AU  - Kohlheyer, Dietrich
AU  - Scharr, Hanno
AU  - Seiffarth, Johannes
AU  - Nöh, Katharina
AU  - Mikut, Ralf
TI  - EAP4EMSIG -- Experiment Automation Pipeline for Event-Driven Microscopy to Smart Microfluidic Single-Cells Analysis
PB  - arXiv
M1  - FZJ-2025-00523
PY  - 2024
N1  - arXiv, arXiv:2411.05030 [q-bio.QM]
AB  - 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.
KW  - Quantitative Methods (q-bio.QM) (Other)
KW  - Computer Vision and Pattern Recognition (cs.CV) (Other)
KW  - Image and Video Processing (eess.IV) (Other)
KW  - FOS: Biological sciences (Other)
KW  - FOS: Computer and information sciences (Other)
KW  - FOS: Electrical engineering, electronic engineering, information engineering (Other)
LB  - PUB:(DE-HGF)25
DO  - DOI:10.48550/ARXIV.2411.05030
UR  - https://juser.fz-juelich.de/record/1037178
ER  -