Going Beyond Classification: Imaging Flow Cytometry Signals in Phytoplankton

durch Gulce Kurtay (GEOMAR)

Mittwoch 21.10.2026, 13:15 → 14:30 Europe/Berlin

5-1.213 - PAZIFIK / PACIFIC- Rechte Seite - Großer, unterteilbarer Konferenzraum (GEOMAR - Standort Ostufer / GEOMAR - East Shore)

Abstract:

Automated imaging is commonly used to sort microorganisms into taxonomic categories, but combining images with fluorescence-based features can reveal more than identity, including a cell’s physiological condition. In our lab, we are exploring methods that use an imaging flow cytometer (CytoSense) on environmental and cultured phytoplankton samples to test whether this kind of data can go beyond species classification towards cell-level status. This includes three ongoing directions: (1) using expert-annotated images as training labels, we train a neural network on flow cytometer signal data (light scattering and fluorescence recorded for every particle), (2) developing a threshold-based method, validated against images, to detect a dormant resting-cell stage in a chain-forming cyanobacteria from a fluorescence pattern, with a parallel attempt to detect a second, nitrogen-fixing specialized cell type proving less reliable so far, and (3) testing for fluorescence differences between visually distinct cell types of one species, identified from images. Together, this work explores how combining imaging with fluorescence features can train and validate algorithms that extend flow cytometry from simple counting towards detecting physiological state in natural samples.

Meeting Link:

https://geomar.webex.com/geomar/j.php?MTID=m5aafe889ba4ee9d8d574eab3fbd47e34