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. 2024 Jun 18;7:737. doi: 10.1038/s42003-024-06426-9

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Overview of the GeoMx DSP method. The Whole Transcriptome Atlas (WTA) panel consists of over 18,000 RNA probes attached to sequencing barcodes via a photocleavable linker. ROIs are selected and exposed to light to cleave all barcodes in the region. Sequencing of barcodes quantifies the RNA probes in each ROI to generate data for downstream analysis. b Bladder cancer TMAs from the BCON cohort stained with PanCK and CD45 (left) and haematoxylin & eosin. c TMA cores showing selection of ROIs. In each core a 300 µm diameter circle was selected and segmented using morphology marker staining for tumour, stroma, and immune infiltrated ROIs.