Project description:
How cells are arranged within a tumor can be as informative as which cells are present. In Nature Methods, Meyer-Bender and colleagues introduce spatialproteomics, an open-source Python toolbox that turns complex tissue images into maps of cell types and their neighborhoods. The software connects image processing, cell identification and spatial analysis in a flexible workflow compatible with established single-cell analysis tools. Applied to lymph node and lymphoma samples from 132 patients, it analyzed more than 3.5 million cells and revealed a loss of normal tissue organization in aggressive lymphomas. The team also demonstrated its scalability on gigapixel whole-slide images. By making spatial protein data easier to analyze and integrate, spatialproteomics provides a versatile resource for investigating the tumor microenvironment and how cellular architecture changes across diseases.
Publication:
Meyer-Bender M, Vöhringer H, Schniederjohann C, Koziel S, Chung E, Popova E, Brobeil A, Griese N, Kolks N, Held LM, Munir A; Scverse Community; Dietrich S, Bruch PM, Huber W. Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data. Nat Methods. 2026.
Submitting the Paper of the Month:
Else Kröner-Fresenius-Stiftung is using the series “Paper of the Month” to report in an exemplary and hot-off-the-press style on the outstanding work being done by the scientists it supports. We regularly present publications which have recently appeared in especially renowned journals, have emerged from foundation funding and been given appropriate acknowledgment. This is done in the respective categories “Original Paper” and “Review”. In the case of each of these publications, the first author and/or senior author are being funded by the foundation.
We invite all project managers, fellowship recipients and members of graduate study programs to send their work in accordance with the stated criteria as proposal for Paper of the Month to Ms. Anne Asschenfeldt (a.asschenfeldt@ekfs.de).
More Paper of the Month can be found here.
