SPACEc: a streamlined, interactive Python workflow for multiplexed image processing and analysis
Yuqi Tan, Tim Kempchen, Martin Becker, Maximilian Haist, Dorien Feyaerts, Jiaqi Liu, Marieta Toma, Yang Xiao, Graham Su, Andrew J. Rech, Michael Hölzel, Rong Fan, John W. Hickey, Garry P. Nolan
Abstract
Multiplexed imaging has transformed our ability to study tissue organization by capturing thousands of cells and molecules in their native context. However, these datasets are enormous, often comprising tens of gigabytes per image, and require complex workflows that limit their broader use. Current tools are often fragmented, inefficient, and difficult to adopt across disciplines. Here we show that SPACEc, a scalable Python platform, streamlines spatial imaging analysis from start to finish. The platform integrates image processing, cell segmentation, and data preprocessing into a single workflow, while improving computational performance through parallelization and GPU acceleration. We introduce innovative methods, including patch proximity analysis, to more accurately map local cellular neighborhoods and interactions. SPACEc also simplifies advanced approaches such as deep-learning annotation, making them accessible through an intuitive interface. By combining efficiency, accuracy, and usability, this platform enables researchers from diverse backgrounds to gain deeper insights into tissue architecture and cellular microenvironments.