{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T11:01:35Z","timestamp":1789729295098,"version":"4.0.1"},"reference-count":30,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100013589","name":"Research England","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013589","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Microscopy"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Lattice light\u2010sheet microscopy (LLSM) has revolutionised live\u2010cell imaging with its ability to resolve sub\u2010cellular detail with high spatiotemporal resolution and minimal phototoxicity. However, LLSM often generates large terabyte\u2010scale datasets that require complex preprocessing, creating bottlenecks in storage, data handling and analysis. These challenges are not unique to LLSM but also apply to oblique plane microscopy (OPM). To bridge this gap and reduce the time from large raw data acquisition to biological insight we developed napari\u2010lattice, an open\u2010source tool designed for scalable and modular LLSM workflows. napari\u2010lattice provides a graphical user interface (GUI) for visualisation and analysis, and a command\u2010line interface optimised for High\u2010Performance Computing (HPC) environments.<\/jats:p>\n                  <jats:p>In this article, we demonstrate the capabilities of napari\u2010lattice by quantifying cellular dynamics of human blood neutrophils using an LLSM. Data preprocessing and image analysis were combined into an end\u2010to\u2010end pipeline that used ilastik for cell segmentation and scikit\u2010image for measuring cell morphology and intensity over time. This pipeline was then parallelised over regions of interest (ROIs) on an HPC node using napari\u2010lattice. Restricting the analysis to ROIs reduced the deskewed data size \u223c2.6\u2010fold, allowing the full analysis pipeline to complete in \u223c12 h, compared to the full field\u2010of\u2010view processing, which did not finish within 48 h. We also demonstrate how napari\u2010lattice can be used with publicly available oblique plane microscopy (OPM) datasets of different configurations. Together, napari\u2010lattice streamlines LLSM data analysis and visualisation, making analysis of complex, feature\u2010rich datasets more accessible. This empowers researchers to fully leverage the potential of LLSM and OPM data.<\/jats:p>","DOI":"10.1111\/jmi.70167","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T12:00:25Z","timestamp":1788955225000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["napari\u2010lattice: A user\u2010friendly image processing tool for lattice light\u2010sheet microscopy data"],"prefix":"10.1111","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1983-7244","authenticated-orcid":false,"given":"Pradeep","family":"Rajasekhar","sequence":"first","affiliation":[{"name":"Walter and Eliza Hall Institute of Medical Research  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8965-2595","authenticated-orcid":false,"given":"Michael","family":"Milton","sequence":"additional","affiliation":[{"name":"Walter and Eliza Hall Institute of Medical Research  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niall D.","family":"Geoghegan","sequence":"additional","affiliation":[{"name":"Walter and Eliza Hall Institute of Medical Research  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-5983-165X","authenticated-orcid":false,"given":"Ishrat","family":"Zaman","sequence":"additional","affiliation":[{"name":"Walter and Eliza Hall Institute of Medical Research  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7392-3995","authenticated-orcid":false,"given":"George W.","family":"Ashdown","sequence":"additional","affiliation":[{"name":"Walter and Eliza Hall Institute of Medical Research  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Parkville Victoria Australia"},{"name":"Biosciences, Aston Institute for Membrane Excellence Aston University Birmingham UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5949-2327","authenticated-orcid":false,"given":"Robert","family":"Haase","sequence":"additional","affiliation":[{"name":"ScaDS.AI Dresden\/Leipzig Leipzig University Leipzig Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3426-4376","authenticated-orcid":false,"given":"Julie","family":"Iskander","sequence":"additional","affiliation":[{"name":"Walter and Eliza Hall Institute of Medical Research  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7086-2621","authenticated-orcid":false,"given":"Anna K.","family":"Coussens","sequence":"additional","affiliation":[{"name":"Walter and Eliza Hall Institute of Medical Research  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly L.","family":"Rogers","sequence":"additional","affiliation":[{"name":"Walter and Eliza Hall Institute of Medical Research  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4388-9642","authenticated-orcid":false,"given":"Lachlan","family":"Whitehead","sequence":"additional","affiliation":[{"name":"Walter and Eliza Hall Institute of Medical Research  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1257998"},{"key":"e_1_2_6_3_1","unstructured":"Leica Microsystems. (2026). Viventis SCAPE: Single\u2010objective light\u2010sheet system for volumetric imaging.Leica Microsystems."},{"key":"e_1_2_6_4_1","doi-asserted-by":"crossref","unstructured":"Sapoznik E. Chang B. J. Huh J. Ju R. J. Azarova E. V. Pohlkamp T. Welf E. S. Broadbent D. Carisey A. F. Stehbens S. J. &Lee K. M.(2020).A versatile oblique plane microscope for large\u2010scale and high\u2010resolution imaging of subcellular dynamics.eLife 9 e57681.","DOI":"10.7554\/eLife.57681"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02475-4"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1364\/OL.44.001706"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1364\/OPTICA.558420"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23626-7"},{"key":"e_1_2_6_9_1","unstructured":"Lambert T. Shao L. &Hilsenstein V.(2023). tlambert03\/LLSpy. 0.5.0 ed. 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Ultralytics YOLO26: Unified real\u2010time end\u2010to\u2010end vision models. arXiv preprint arXiv:260603748."}],"container-title":["Journal of Microscopy"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/jmi.70167","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/jmi.70167","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/jmi.70167","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T10:02:31Z","timestamp":1789725751000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/jmi.70167"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,9]]},"references-count":30,"alternative-id":["10.1111\/jmi.70167"],"URL":"https:\/\/doi.org\/10.1111\/jmi.70167","archive":["Portico"],"relation":{},"ISSN":["0022-2720","1365-2818"],"issn-type":[{"value":"0022-2720","type":"print"},{"value":"1365-2818","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,9]]},"assertion":[{"value":"2026-02-27","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-08-26","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-09","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"jmi.70167"}}