Session 4 - Technologies and Challenges with Session Chair Chair: Gerald Pfister (Co-chair: Charlotte Petersen)
"Beyond IDEAS: A Non-Proprietary Imaging Flow Cytometry Workflow Demonstrated in Bacterial Cords"
Richard Haindl: Investigator in Host-Pathogen Imaging at the Center for Medical Physics and Biomedical Engineering at the Medical University of Vienna
We present an open-source, reproducible workflow for imaging flow cytometry of bacterial cords. A built-in Python exporter reads instrument .rif files and converts images into portable OME-Zarr datasets with associated metadata, so analysis can continue outside the vendor software. Researchers can interactively review quality control and segmentation, quantify cord morphology, skeleton structure, internal texture and masked fluorescence, then replay workflows across samples and compare replicate-aware experiment packages.