{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T02:50:49Z","timestamp":1791427849129,"version":"4.3.3"},"reference-count":49,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T00:00:00Z","timestamp":1776384000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T00:00:00Z","timestamp":1776384000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[2026,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Cryo\u2010electron tomography (cryoET) enables visualization of macromolecular complexes within intact cellular environments. Continued improvements in instrumentation, sample preparation, and data\u2010processing pipelines have increased both the scale and the complexity of cryoET datasets, making manual analysis challenging. To support scalable, collaborative annotation, we developed copick, an open\u2010source dataset application programming interface (API) and accompanying tool suite for cryoET analysis. Copick provides standardized access to tomograms, segmentations, point annotations, meshes, and feature maps across local storage, high\u2010performance computing systems, cloud platforms, and public repositories. Plugins for napari and ChimeraX enable human\u2010in\u2010the\u2010loop workflows for particle picking, segmentation, inspection of machine\u2010learning outputs, and project\u2010level collaboration. A multi\u2010resolution Open Microscopy Environment (OME)\u2010Zarr architecture supports responsive visualization and cross\u2010platform access. Copick additionally provides a Model Context Protocol interface enabling automated generation of annotation\u2010curation pipelines using natural\u2010language instructions. Together, these tools support reproducible, scalable, and collaborative cryoET analysis.<\/jats:p>","DOI":"10.1002\/pro.70578","type":"journal-article","created":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T06:26:31Z","timestamp":1776493591000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["copick: An open\n                    <scp>dataset interface<\/scp>\n                    and toolkit for collaborative annotation and analysis of\n                    <scp>cryo\u2010electron tomography<\/scp>\n                    data"],"prefix":"10.1002","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4685-037X","authenticated-orcid":false,"given":"Utz Heinrich","family":"Ermel","sequence":"first","affiliation":[{"name":"Dynamic Structural Biology Biohub  Redwood City California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Schwartz","sequence":"additional","affiliation":[{"name":"Dynamic Structural Biology Biohub  Redwood City California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuowen","family":"Zhao","sequence":"additional","affiliation":[{"name":"Dynamic Structural Biology Biohub  Redwood City California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Ji","sequence":"additional","affiliation":[{"name":"Dynamic Structural Biology Biohub  Redwood City California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ariana","family":"Peck","sequence":"additional","affiliation":[{"name":"Dynamic Structural Biology Biohub  Redwood City California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Yu","sequence":"additional","affiliation":[{"name":"Dynamic Structural Biology Biohub  Redwood City California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammadreza","family":"Paraan","sequence":"additional","affiliation":[{"name":"Dynamic Structural Biology Biohub  Redwood City California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0624-5020","authenticated-orcid":false,"given":"Bridget","family":"Carragher","sequence":"additional","affiliation":[{"name":"Dynamic Structural Biology Biohub  Redwood City California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8067-6611","authenticated-orcid":false,"given":"Achilleas S.","family":"Frangakis","sequence":"additional","affiliation":[{"name":"Buchmann Institute for Molecular Life Sciences and Institute for Biophysics Goethe University Frankfurt  Frankfurt am Main Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyle I. S.","family":"Harrington","sequence":"additional","affiliation":[{"name":"AI Research Biohub  Redwood City California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,4,17]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/B978-012387582-2\/50040-X"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/iyad031"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-023-01401-2"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2021.167187"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1107\/S2059798317007859"},{"key":"e_1_2_8_7_1","unstructured":"BurtA GaifasL HookerJ ElferichJ LiuH LoweAR et al.teamtomo\/starfile: v0.5.13.2025.https:\/\/zenodo.org\/records\/4064754[accessed 27 Feb 2026]"},{"key":"e_1_2_8_8_1","unstructured":"BurtA ToaderB WarshamanageR vonK\u00fcgelgenA PyleE ZivanovJ et al.An image processing pipeline for electron cryo\u2010tomography in RELION\u20105. bioRxiv [Internet].2024.https:\/\/www.biorxiv.org\/content\/early\/2024\/04\/27\/2024.04.26.591129"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms241713375"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2015.04.002"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-47839-8"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01746-2"},{"key":"e_1_2_8_13_1","doi-asserted-by":"crossref","unstructured":"DobbsJM JensenRK MahamidJ.Single\u2010cell visual proteomics of a minimal bacterium reveals structural coordination in gene expression.2025https:\/\/doi.org\/10.1101\/2025.10.13.682074v1","DOI":"10.1101\/2025.10.13.682074"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02373-9"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01690-1"},{"key":"e_1_2_8_16_1","unstructured":"ErmelU.uermel\/chimerax\u2010ome\u2010zarr: chimerax\u2010OME\u2010Zarr v0.5.6.2025a. [accessed 2026 February 27].https:\/\/zenodo.org\/records\/17799943"},{"key":"e_1_2_8_17_1","unstructured":"ErmelU.copick\/chimerax\u2010copick: chimerax\u2010copick: v1.6.0.2025b.https:\/\/zenodo.org\/records\/17799783[accessed 2026 February 27]"},{"key":"e_1_2_8_18_1","unstructured":"ErmelU.copick\/copick\u2010shared\u2010ui: copick\u2010shared\u2010ui: v0.3.0.2025c. [accessed 2026 February 27].https:\/\/zenodo.org\/records\/17799860"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4472"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02477-2"},{"key":"e_1_2_8_21_1","unstructured":"ErmelU HarringtonKIS.copick\/copick\u2010mcp: copick\u2010mcp: v0.5.0.2025. [accessed 2026 February 27].https:\/\/zenodo.org\/records\/17800059"},{"key":"e_1_2_8_22_1","unstructured":"ErmelU HarringtonKIS JiD SchwartzJ SweetA ZhaoZ(K).copick\/copick: copick: v1.17.1.2025. [accessed 2026 February 27].https:\/\/zenodo.org\/records\/17799612"},{"key":"e_1_2_8_23_1","unstructured":"HarringtonKIS ErmelU.copick\/napari\u2010copick: napari\u2010copick: v1.3.0.2025. [accessed 2026 February 27].https:\/\/zenodo.org\/records\/17799844"},{"key":"e_1_2_8_24_1","unstructured":"HarringtonKIS ErmelU SchwartzJ.copick\/copick\u2010torch: copick\u2010torch: v1.4.0.2025. [accessed 2026 February 27].https:\/\/zenodo.org\/records\/17807122"},{"key":"e_1_2_8_25_1","unstructured":"HarringtonKIS SchwartzJ ErmelU ZhaoZ(K).copick\/copick\u2010utils: copick\u2010utils: v1.4.0.2025.https:\/\/zenodo.org\/records\/17799968"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02403-6"},{"key":"e_1_2_8_27_1","unstructured":"IsenseeF RokussM Kr\u00e4merL DinkelackerS RavindranA StritzkeF et al.nnInteractive: redefining 3D promptable segmentation.2025.http:\/\/arxiv.org\/abs\/2503.08373"},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1062"},{"key":"e_1_2_8_29_1","unstructured":"KelleyR KhavnekarS RighettoRD HeebnerJ ObrM ZhangX et al.Towards community\u2010driven visual proteomics with large\u2010scale cryo\u2010electron tomography ofChlamydomonas reinhardtii.2024;86:P213\u2013230.E7.https:\/\/doi.org\/10.1101\/2024.12.28.630444v1"},{"key":"e_1_2_8_30_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.70506"},{"key":"e_1_2_8_31_1","doi-asserted-by":"crossref","unstructured":"LammL ZuffereyS RighettoRD WietrzynskiW YamauchiKA BurtA et al.MemBrain v2: an end\u2010to\u2010end tool for the analysis of membranes in cryo\u2010electron tomography.2024https:\/\/doi.org\/10.1101\/2024.01.05.574336v1","DOI":"10.1101\/2024.01.05.574336"},{"key":"e_1_2_8_32_1","doi-asserted-by":"crossref","unstructured":"LastMGF VoortmanLM SharpTH.Scaling data analyses in cellular cryoET using comprehensive segmentation. bioRxiv.2025https:\/\/doi.org\/10.1101\/2025.01.16.633326v1","DOI":"10.1101\/2025.01.16.633326"},{"key":"e_1_2_8_33_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2015.07.012"},{"key":"e_1_2_8_34_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth1014"},{"key":"e_1_2_8_35_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2014.02.015"},{"key":"e_1_2_8_36_1","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4792"},{"key":"e_1_2_8_37_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00418-023-02209-1"},{"key":"e_1_2_8_38_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2004.10.006"},{"key":"e_1_2_8_39_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-025-02800-5"},{"key":"e_1_2_8_40_1","doi-asserted-by":"publisher","DOI":"10.1017\/S1431927617001349"},{"key":"e_1_2_8_41_1","unstructured":"PidhorskyiS MoreheadM JonesQ SpirouG DorettoG.syGlass: interactive exploration of multidimensional images using virtual reality head\u2010mounted displays [Internet].2018.https:\/\/arxiv.org\/abs\/1804.08197v4[accessed 2026 February 27]"},{"key":"e_1_2_8_42_1","doi-asserted-by":"publisher","DOI":"10.1039\/D2FD00022A"},{"key":"e_1_2_8_43_1","unstructured":"SchwartzJ ErmelUH JiD ZhaoZ.Octopi: v1.4.2026. [accessed 2026 February 27].https:\/\/zenodo.org\/records\/18511915"},{"key":"e_1_2_8_44_1","unstructured":"SofroniewN LambertT BokotaG Nunez\u2010IglesiasJ SobolewskiP SweetA et al.napari: a multi\u2010dimensional image viewer for Python.2025. [accessed 2026 February 27].https:\/\/zenodo.org\/records\/17367124"},{"key":"e_1_2_8_45_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-01054-7"},{"key":"e_1_2_8_46_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad1019"},{"key":"e_1_2_8_47_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2012.07.003"},{"key":"e_1_2_8_48_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky949"},{"key":"e_1_2_8_49_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biophys-111622-091327"},{"key":"e_1_2_8_50_1","unstructured":"ZhaoZ HenkelC KhvedchenyaE.TopCUP: top Cryoet U\u2010net picker.2026. [accessed 2026 February 27].https:\/\/zenodo.org\/records\/18501364"}],"container-title":["Protein Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pro.70578","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/pro.70578","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pro.70578","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T07:04:30Z","timestamp":1777446270000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/pro.70578"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,17]]},"references-count":49,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,5]]}},"alternative-id":["10.1002\/pro.70578"],"URL":"https:\/\/doi.org\/10.1002\/pro.70578","archive":["Portico"],"relation":{},"ISSN":["0961-8368","1469-896X"],"issn-type":[{"value":"0961-8368","type":"print"},{"value":"1469-896X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,17]]},"assertion":[{"value":"2025-12-04","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-04-06","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-04-17","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70578"}}