Garrido-Trigo, Alba
Corraliza, Ana M. http://orcid.org/0000-0002-3067-7763
Veny, Marisol
Dotti, Isabella
Melón-Ardanaz, Elisa
Rill, Aina http://orcid.org/0000-0001-9885-0705
Crowell, Helena L. http://orcid.org/0000-0002-4801-1767
Corbí, Ángel http://orcid.org/0000-0003-1980-5733
Gudiño, Victoria
Esteller, Miriam
Álvarez-Teubel, Iris
Aguilar, Daniel
Masamunt, M. Carme
Killingbeck, Emily http://orcid.org/0000-0002-5108-5089
Kim, Youngmi
Leon, Michael http://orcid.org/0000-0003-3982-2063
Visvanathan, Sudha
Marchese, Domenica
Caratù, Ginevra http://orcid.org/0000-0003-1085-8062
Martin-Cardona, Albert http://orcid.org/0000-0002-7090-0106
Esteve, Maria
Ordás, Ingrid
Panés, Julian
Ricart, Elena
Mereu, Elisabetta http://orcid.org/0000-0001-6101-8472
Heyn, Holger http://orcid.org/0000-0002-3276-1889
Salas, Azucena
Article History
Received: 5 January 2023
Accepted: 14 July 2023
First Online: 26 July 2023
Change Date: 29 January 2024
Change Type: Update
Change Details: The original version of this Article contained an error in the code availability statement, pages 15-16, sub section code deposition, which incorrectly omitted the hyperlinks to the author’s code deposition: ‘Full code for scRNAseq analysis is available at
Change Details: https://github.com/ibd-bcn/ibd-bcn_single_cell
Change Details: and our webpage
Change Details: https://servidor2-ciberehd.upc.es/external/garrido/methods2/
Change Details: . Full code for analysis of CosMx SMI data can be found at
Change Details: https://github.com/HelenaLC/CosMx-SMI-IBD’
Change Details: . This has been corrected in both the PDF and HTML versions of the Article.
Change Date: 29 January 2024
Change Type: Correction
Change Details: A Correction to this paper has been published:
Change Details: https://doi.org/10.1038/s41467-024-45212-3
Competing interests
: H.H. is co-founder of Omniscope, a scientific advisory board member of MiRXES and consultant to Moderna. A.S. is the recipient of research grants from Roche-Genentech, Abbvie, GSK, Scipher Medicine, Pfizer, Alimentiv, Inc, Boehringer Ingelheim and Agomab; receives consulting fees from Genentech, GSK, Pfizer, HotSpot Therapeutics, Alimentiv, Origo Biopharma, Deep Track Capital, Great Point Partners and Boxer Capital; and is on the advisory boards of BioMAdvanced Diagnostics, Goodgut and Orikine. MaE. has received support for conference attendance and research support from Abbvie, Biogen, Faes Farma, Ferring, Jannsen, MSD, Pfizer, Takeda, and Tillotts. J.P. received financial support for research from AbbVie and Pfizer; consultancy fees/honorarium from AbbVie, Arena, Athos, Atomwise, Boehringer Ingelheim, Celgene, Celltrion, Ferring, Galapagos, Genentech/Roche, GlaxoSmithKline, Janssen, Mirum, Morphic, Nestlé, Origo, Pandion, Pfizer, Progenity, Protagonist, Revolo, Robarts, Takeda, Theravance and Wasserman; reports payment for lectures including service on speaker bureau from Abbott, Ferring, Janssen, Pfizer and Takeda; and reports payment for development of educational presentations from Abbott, Janssen, Pfizer Roche and Takeda. A.M-C has received financial support for conference attendance, educational activities, and research support from Abbvie, Biogen, Ferring, Jannsen, MSD, Takeda, Dr. Falk Pharma and Tillotts. E.K., Y.K., and M.L. are current/former employees and shareholders of NanoString Technologies. S.V. is a current employee of Boehringer-Ingelheim Pharmaceuticals. The remaining authors declare no competing interests.