EP69 (US Session): Analyzing CosMx Data on SpatialX

Learn the end-to-end workflow for CosMx data on SpatialX. We’ll be using public datasets directly from the Bruker website to show you exactly how to move from raw output to meaningful discovery. What we’re covering: 📤 Submission: A step-by-step guide to uploading files to SpatialX. 🛠️ Formatting: The special considerations you need to know to avoid errors. 👁️ Visualization: See your multiplex images overlaid with transcripts and cell centers. 📊 Analysis: Move beyond gene visualization to extract biological insights. 📅 Date: Friday, March 20th, 2026 ⏰ Time: 9AM PT | 12PM ET | 5PM CET 🔗 Register here: bioturing.com/SCSE_signup 0:00 Introduction 1:58 Submit CosMx Decoded Files 5:53 Submit CosMx Seurat objects 7:58 Add images 9:41 Image alignment 12:33 Submit CosMx (now available!) 13:46 Combine data 17:11 Batch correction 18:49 Norrmalization 22:47 Cell type prediction 27:14 Cell-cell communication 29:23 Q&A