{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T15:00:14Z","timestamp":1791385214816,"version":"4.3.3"},"reference-count":19,"publisher":"American Chemical Society (ACS)","issue":"10","license":[{"start":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:00:00Z","timestamp":1790035200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100024870","name":"Exacte en Natuurwetenschappen","doi-asserted-by":"publisher","award":["NWA.1389.20.182"],"award-info":[{"award-number":["NWA.1389.20.182"]}],"id":[{"id":"10.13039\/501100024870","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023271","name":"Interreg Vlaanderen-Nederland","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023271","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020979","name":"Provincie Limburg","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020979","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003246","name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["19013"],"award-info":[{"award-number":["19013"]}],"id":[{"id":"10.13039\/501100003246","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Mass spectrometry imaging (MSI) is now a routine modality for spatial molecular profiling and is increasingly combined with histology, multiplexed imaging, and spatial transcriptomics to build richer descriptions of tissue than any single technique can provide. The conceptual case for this multimodal paradigm was settled a decade ago, but the data infrastructure needed to operationalize it at scale has not kept up. Vendor binaries and the imzML exchange format keep MSI outside the OME-NGFF, Zarr, and SpatialData stacks on which the rest of spatial omics has converged, leaving each new experiment to rebuild ad hoc converters from scratch. Here, we present Thyra, an open-source Python library that converts raw vendor and imzML MSI data directly into the SpatialData format. A two-pass streaming sparse matrix engine writes the spectral matrix straight into the output Zarr store, keeping peak memory bounded near 200 MB regardless of data set size and supporting 100+ GB acquisitions. On a representative mouse brain MALDI data set, this yields three- to 4-fold storage reductions and an order-of-magnitude improvement in m\/z range query latency, the bottleneck for ion image generation. Once converted, MSI data are directly composable with the scverse analysis ecosystem; we quantify this with an scverse readiness benchmark in which spatial autocorrelation, pixel clustering, and neighborhood enrichment, all standard operations in spatial transcriptomics, run as a one-liner on the converted object. A brief exploratory analysis of a skin biopsy from a psoriasis patient illustrates the analytical surface that the unified container exposes.<\/jats:p>","DOI":"10.1021\/jasms.6c00169","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T17:01:34Z","timestamp":1790096494000},"page":"2379-2387","source":"Crossref","is-referenced-by-count":0,"title":["Native, Memory-Bounded Conversion of Mass Spectrometry\nImaging Data into the SpatialData Ecosystem"],"prefix":"10.1021","volume":"37","author":[{"given":"Theodoros","family":"Visvikis","sequence":"first","affiliation":[{"name":"Maastricht University , , ,","place":["Maastricht, The Netherlands, 6229 ER"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wouter-Michiel","family":"Vierdag","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory , , ,","place":["Heidelberg, Germany, 69117"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Marconato","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory , , ,","place":["Heidelberg, Germany, 69117"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-7505-0557","authenticated-orcid":true,"given":"Angeliki","family":"Birmpili","sequence":"additional","affiliation":[{"name":"Maastricht University , , ,","place":["Maastricht, The Netherlands, 6229 ER"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6533-7179","authenticated-orcid":true,"given":"Ron M.A.","family":"Heeren","sequence":"additional","affiliation":[{"name":"Maastricht University , , ,","place":["Maastricht, The Netherlands, 6229 ER"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6411-2461","authenticated-orcid":true,"given":"Eva","family":"Cuypers","sequence":"additional","affiliation":[{"name":"Maastricht University , , ,","place":["Maastricht, The Netherlands, 6229 ER"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,22]]},"reference":[{"issue":"29","key":"2026100710064982000_cit1","doi-asserted-by":"publisher","first-page":"15517","DOI":"10.1021\/acs.analchem.4c05249","article-title":"Mass Spectrometry Imaging","volume":"97","author":"Korber","year":"2025","journal-title":"Anal. Chem."},{"issue":"1","key":"2026100710064982000_cit2","doi-asserted-by":"publisher","DOI":"10.1002\/jms.4803","article-title":"Time-of-flight secondary\nion mass spectrometry imaging in cultural heritage: a focus on old\npaintings","volume":"57","author":"Bouvier","year":"2022","journal-title":"J. Mass Spectrom."},{"issue":"25","key":"2026100710064982000_cit3","doi-asserted-by":"publisher","first-page":"3946","DOI":"10.1016\/j.chroma.2010.01.033","article-title":"A concise review\nof mass spectrometry imaging","volume":"1217","author":"van Hove","year":"2010","journal-title":"J. Chromatogr.\nA"},{"issue":"4","key":"2026100710064982000_cit4","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/nmeth.3296","article-title":"Image fusion of mass spectrometry and microscopy: a\nmultimodality paradigm for molecular tissue mapping","volume":"12","author":"Van de Plas","year":"2015","journal-title":"Nat. Methods"},{"issue":"8","key":"2026100710064982000_cit5","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1038\/s41576-023-00580-2","article-title":"Methods and applications\nfor single-cell and spatial multi-omics","volume":"24","author":"Vandereyken","year":"2023","journal-title":"Nat.\nRev. Genet."},{"issue":"11","key":"2026100710064982000_cit6","doi-asserted-by":"publisher","first-page":"MSB202110571","DOI":"10.15252\/msb.202110571","article-title":"Enablers and challenges\nof spatial\nomics, a melting pot of technologies","volume":"19","author":"Alexandrov","year":"2023","journal-title":"Mol. Syst.\nBiol."},{"issue":"12","key":"2026100710064982000_cit7","doi-asserted-by":"publisher","first-page":"1496","DOI":"10.1038\/s41592-021-01326-w","article-title":"OME-NGFF:\na next-generation file format for expanding\nbioimaging data-access strategies","volume":"18","author":"Moore","year":"2021","journal-title":"Nat. Methods"},{"key":"2026100710064982000_cit8","article-title":"Anndata: Annotated\ndata","author":"Virshup","year":"2021","journal-title":"bioRxiv"},{"issue":"1","key":"2026100710064982000_cit9","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1038\/s41592-024-02212-x","article-title":"SpatialData: an open\nand universal data framework\nfor spatial omics","volume":"22","author":"Marconato","year":"2025","journal-title":"Nat. Methods"},{"issue":"5","key":"2026100710064982000_cit10","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1038\/s41587-023-01733-8","article-title":"The scverse project\nprovides a computational ecosystem for single-cell omics data analysis","volume":"41","author":"Virshup","year":"2023","journal-title":"Nat. Biotechnol."},{"issue":"16","key":"2026100710064982000_cit11","doi-asserted-by":"publisher","first-page":"5106","DOI":"10.1016\/j.jprot.2012.07.026","article-title":"imzML:\nA common data\nformat for the flexible exchange and processing of mass spectrometry\nimaging data","volume":"75","author":"Schramm","year":"2012","journal-title":"J. Proteomics"},{"key":"2026100710064982000_cit12","unstructured":"metaspace-converter: Download and Convert METASPACE\ndatasets; GitHub; 2024. https:\/\/github.com\/metaspace2020\/metaspace-converter."},{"issue":"2","key":"2026100710064982000_cit13","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1038\/s41592-021-01358-2","article-title":"Squidpy: a scalable framework for spatial omics analysis","volume":"19","author":"Palla","year":"2022","journal-title":"Nat. Methods"},{"issue":"1","key":"2026100710064982000_cit14","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale\nsingle-cell gene\nexpression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol."},{"key":"2026100710064982000_cit15","volume-title":"napari: a\nmulti-dimensional image\nviewer for Python","author":"Ahlers","year":"2023"},{"key":"2026100710064982000_cit16","article-title":"EasyVitessce: auto-magically\nadding interactivity to Scverse single-cell and spatial biology plots","author":"Luo","year":"2025","journal-title":"arXiv"},{"issue":"3","key":"2026100710064982000_cit17","doi-asserted-by":"publisher","first-page":"btag122","DOI":"10.1093\/bioinformatics\/btag122","article-title":"Scalable analysis of\nwhole slide spatial proteomics with Harpy","volume":"42","author":"Rombaut","year":"2026","journal-title":"Bioinformatics"},{"issue":"1","key":"2026100710064982000_cit18","doi-asserted-by":"publisher","first-page":"42660","DOI":"10.1038\/s41598-025-26735-1","article-title":"One section, two worlds:\nsingle-cell integration of\nMALDI-MSI and spatial transcriptomics on the same single tissue section","volume":"15","author":"Hendriks","year":"2025","journal-title":"Sci. Rep."},{"key":"2026100710064982000_cit19","article-title":"Segger: Fast\nand accurate\ncell segmentation of imaging-based spatial transcriptomics data","author":"Heidari","year":"2025","journal-title":"bioRxiv"}],"container-title":["Journal of the American Society for Mass Spectrometry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/jasms.6c00169","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jamsef\/article-pdf\/37\/10\/2379\/68605863\/jasms.6c00169.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jamsef\/article-pdf\/37\/10\/2379\/68605863\/jasms.6c00169.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T14:29:02Z","timestamp":1791383342000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jamsef\/article\/37\/10\/2379\/5435687\/Native-Memory-Bounded-Conversion-of-Mass"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,22]]},"references-count":19,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,9,22]]},"published-print":{"date-parts":[[2026,10,7]]}},"URL":"https:\/\/doi.org\/10.1021\/jasms.6c00169","relation":{},"ISSN":["1044-0305","1879-1123"],"issn-type":[{"value":"1044-0305","type":"print"},{"value":"1879-1123","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,22]]}}}