{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T04:49:18Z","timestamp":1792039758287,"version":"4.4.0"},"reference-count":33,"publisher":"Wiley","issue":"23-24","license":[{"start":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T00:00:00Z","timestamp":1791936000000},"content-version":"vor","delay-in-days":13,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100009193","name":"Marsden Fund","doi-asserted-by":"publisher","award":["23\u2010UOO\u2010148"],"award-info":[{"award-number":["23\u2010UOO\u2010148"]}],"id":[{"id":"10.13039\/501100009193","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008247","name":"University of Otago","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008247","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Statistics in Medicine"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Quantitative histology often requires assigning each site or cell to one of two classes from continuous stain intensities. In practice, large\u2010scale illumination and contrast fluctuations bias thresholds and obscure true biological differences. Standard correction methods preprocess the image to remove these artifacts, but do not propagate uncertainty from the correction into subsequent classification. We propose a spatial hidden Markov model that performs probabilistic, illumination\u2010adjusted classification directly on raw stain intensities. A deterministic, data\u2010driven \u201cgate\u201d rescales each site's effective decision threshold according to local brightness, while an autologistic prior encourages spatial coherence. Bayesian inference yields posterior class probabilities and parameter summaries of class separation and spatial dependence. Applications to muscle histology demonstrate that the gated SHMM yields physiologically plausible classifications that are robust to uneven illumination while preserving fine\u2010scale biological structure.<\/jats:p>","DOI":"10.1002\/sim.70781","type":"journal-article","created":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T04:36:51Z","timestamp":1792039011000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Gated Spatial Hidden Markov Models for Classification in Histological Samples, With Application to Muscle Fiber\u2010Typing"],"prefix":"10.1002","volume":"45","author":[{"given":"Tilman M.","family":"Davies","sequence":"first","affiliation":[{"name":"Department of Mathematics &amp; Statistics University of Otago  Dunedin New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,14]]},"reference":[{"key":"e_1_2_13_2_1","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.22.02864"},{"key":"e_1_2_13_3_1","doi-asserted-by":"publisher","DOI":"10.3390\/jcm7030054"},{"key":"e_1_2_13_4_1","doi-asserted-by":"publisher","DOI":"10.1111\/imcb.12450"},{"key":"e_1_2_13_5_1","doi-asserted-by":"publisher","DOI":"10.1152\/physrev.00031.2010"},{"key":"e_1_2_13_6_1","doi-asserted-by":"publisher","DOI":"10.1158\/1055\u20109965.EPI\u201010\u20100097"},{"key":"e_1_2_13_7_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13000\u2010014\u20100221\u20109"},{"key":"e_1_2_13_8_1","doi-asserted-by":"publisher","DOI":"10.1109\/TSMC.1979.4310076"},{"key":"e_1_2_13_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0031\u20103203(99)00055\u20102"},{"key":"e_1_2_13_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14836"},{"key":"e_1_2_13_11_1","doi-asserted-by":"crossref","unstructured":"M.Macenko M.Niethammer J. S.Marron et al. \u201cA Method for Normalizing Histology Slides for Quantitative Analysis \u201d(2009) Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging (ISBI). IEEE. Boston MA USA: 1107\u20131110.","DOI":"10.1109\/ISBI.2009.5193250"},{"key":"e_1_2_13_12_1","doi-asserted-by":"publisher","DOI":"10.1109\/TMI.2016.2529665"},{"key":"e_1_2_13_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2019"},{"key":"e_1_2_13_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb\u20102006\u20107\u201010\u2010r100"},{"key":"e_1_2_13_15_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.2005970"},{"key":"e_1_2_13_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010017\u201017204\u20105"},{"key":"e_1_2_13_17_1","doi-asserted-by":"publisher","DOI":"10.1152\/japplphysiol.00762.2017"},{"key":"e_1_2_13_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010025\u201099522\u20107"},{"key":"e_1_2_13_19_1","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1007\/978-3-319-24574-4_28","volume-title":"Medical Image Computing and Computer\u2010Assisted Intervention\u2014MICCAI 2015","author":"Ronneberger O.","year":"2015"},{"key":"e_1_2_13_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.media.2017.07.005"},{"key":"e_1_2_13_21_1","volume-title":"Muscle Biopsy: A Practical Approach","author":"Dubowitz V.","year":"2020"},{"key":"e_1_2_13_22_1","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.15757"},{"key":"e_1_2_13_23_1","unstructured":"A. K.Redmond \u201cStatistical Models for Analysis of Spatial Patterns in Muscle Fibre Type Distributions \u201d(2023) PhD thesis. Dept. of Mathematics and Statistics University of Otago."},{"key":"e_1_2_13_24_1","doi-asserted-by":"publisher","DOI":"10.1214\/18\u2010AOAS1214"},{"key":"e_1_2_13_25_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13395\u2010023\u201000316\u20100"},{"key":"e_1_2_13_26_1","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1111\/j.2517-6161.1974.tb00999.x","article-title":"Spatial Interaction and the Statistical Analysis of Lattice Systems (With Discussion)","volume":"36","author":"Besag J. E.","year":"1974","journal-title":"Journal of the Royal Statistical Society. Series B, Statistical Methodology"},{"key":"e_1_2_13_27_1","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1002\/mus.880150617","article-title":"Modeling Fiber Type Grouping by a Binary Markov Random Field","volume":"15","author":"Venema H. W.","year":"1992","journal-title":"Muscle & Nerve"},{"key":"e_1_2_13_28_1","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1093\/imammb\/10.2.115","article-title":"Estimation of the Parameters of a Binary Markov Random Field on a Graph With Application to Fibre Type Distributions in a Muscle Cross\u2010Section","volume":"10","author":"Venema H. W.","year":"1993","journal-title":"IMA Journal of Mathematics Applied in Medicine and Biology"},{"key":"e_1_2_13_29_1","doi-asserted-by":"publisher","DOI":"10.1002\/sim.5806"},{"key":"e_1_2_13_30_1","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4899-4493-1","volume-title":"Kernel Smoothing","author":"Wand M. P.","year":"1995"},{"key":"e_1_2_13_31_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF02980577"},{"key":"e_1_2_13_32_1","volume-title":"Exactly Solved Models in Statistical Mechanics","author":"Baxter R. J.","year":"1982"},{"issue":"1","key":"e_1_2_13_33_1","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1109\/42.906424","article-title":"Segmentation of Brain MR Images Through a Hidden Markov Random Field Model and the Expectation\u2013Maximization Algorithm","volume":"20","author":"Zhang Y.","year":"2001","journal-title":"IEEE Transactions on Medical Imaging"},{"key":"e_1_2_13_34_1","unstructured":"R Core Team \u201cR: A Language and Environment for Statistical Computing \u201d(2025) R Foundation for Statistical Computing; Vienna Austria."}],"container-title":["Statistics in Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/sim.70781","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/sim.70781","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/sim.70781","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T04:37:07Z","timestamp":1792039027000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/sim.70781"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10]]},"references-count":33,"journal-issue":{"issue":"23-24","published-print":{"date-parts":[[2026,10]]}},"alternative-id":["10.1002\/sim.70781"],"URL":"https:\/\/doi.org\/10.1002\/sim.70781","archive":["Portico"],"relation":{},"ISSN":["0277-6715","1097-0258"],"issn-type":[{"value":"0277-6715","type":"print"},{"value":"1097-0258","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10]]},"assertion":[{"value":"2025-10-19","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-10-06","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-10-14","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70781"}}