{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T15:44:29Z","timestamp":1791992669395,"version":"4.4.0"},"reference-count":47,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T00:00:00Z","timestamp":1791936000000},"content-version":"vor","delay-in-days":43,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2572025AW97"],"award-info":[{"award-number":["2572025AW97"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Physiologia Plantarum"],"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Spatial transcriptomics enables the spatial architecture and transcriptional dynamics of plant organ development to be resolved in\u00a0situ. However, integrating plant spatial transcriptomic data across developmental stages is challenging because genuine developmental variation can be confounded with technical variation arising from section source, capture region and sequencing batch, making it difficult to attenuate technical effects without compromising developmental signals. To address this challenge, we developed STADIA, a spatio\u2010temporal deep\u2010learning framework for plant developmental spatial transcriptomics. STADIA combines a graph\u2010attention autoencoder with structural\u2010context\u2010conditioned batch\u2010predictability suppression, stage\u2010order constraints, PCGrad\u2010based gradient coordination and hierarchical unbalanced optimal transport to learn an integrated latent representation that attenuates batch\u2010associated variation while preserving spatial organization and developmental continuity and accommodating non\u2010equivalent tissue transitions. In a semi\u2010synthetic benchmark, STADIA maintained balanced performance across batch mixing, anatomical\u2010domain preservation and developmental\u2010information preservation under strong batch effects and high sparsity. In the same\u2010stage replicate sections from the soybean early\u2010maturation stage (EMS), STADIA increased local between\u2010section mixing while retaining major anatomical compartments. In a poplar stem developmental series spanning the shoot apex to internode 7, the integrated representation showed increased cross\u2010stage continuity while retaining stage\u2010specific organization and spatially coherent tissue compartments, and supported exploratory identification of cambium\u2010associated trajectory candidates. Together, these results support STADIA as a framework for cross\u2010stage integration of plant spatial transcriptomic data and for downstream analysis of spatial domains and developmentally ordered transcriptional patterns.<\/jats:p>","DOI":"10.1111\/ppl.71143","type":"journal-article","created":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T14:45:59Z","timestamp":1791989159000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["<scp>STADIA<\/scp>\n                    : A Spatio\u2010Temporal Deep\u2010Learning Framework for Cross\u2010Stage Integration and Batch Correction of Plant Developmental Spatial Transcriptomics"],"prefix":"10.1111","volume":"178","author":[{"given":"Dezhi","family":"Zhi","sequence":"first","affiliation":[{"name":"College of Control and Information Engineering Northeast Forestry University  Harbin Heilongjiang China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-5497-1546","authenticated-orcid":false,"given":"Xuemei","family":"Guan","sequence":"additional","affiliation":[{"name":"College of Control and Information Engineering Northeast Forestry University  Harbin Heilongjiang China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liuyan","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Control and Information Engineering Northeast Forestry University  Harbin Heilongjiang China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenhui","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Control and Information Engineering Northeast Forestry University  Harbin Heilongjiang China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,14]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/s41592-018-0254-1","article-title":"A Test Metric for Assessing Single\u2010Cell RNA\u2010Seq Batch Correction","volume":"16","author":"B\u00fcttner M.","year":"2019","journal-title":"Nature Methods"},{"key":"e_1_2_10_3_1","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1016\/j.cell.2022.04.003","article-title":"Spatiotemporal Transcriptomic Atlas of Mouse Organogenesis Using DNA Nanoball\u2010Patterned Arrays","volume":"185","author":"Chen A.","year":"2022","journal-title":"Cell"},{"key":"e_1_2_10_4_1","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1105\/tpc.18.00620","article-title":"Hierarchical Transcription Factor and Chromatin Binding Network for Wood Formation in Black Cottonwood (\n                     Populus trichocarpa\n                  )","volume":"31","author":"Chen H.","year":"2019","journal-title":"Plant Cell"},{"key":"e_1_2_10_5_1","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1038\/s41588-022-01256-z","article-title":"SpiceMix Enables Integrative Single\u2010Cell Spatial Modeling of Cell Identity","volume":"55","author":"Chidester B.","year":"2023","journal-title":"Nature Genetics"},{"key":"e_1_2_10_6_1","doi-asserted-by":"crossref","first-page":"2563","DOI":"10.1090\/mcom\/3303","article-title":"Scaling Algorithms for Unbalanced Optimal Transport Problems","volume":"87","author":"Chizat L.","year":"2018","journal-title":"Mathematics of Computation"},{"key":"e_1_2_10_7_1","volume-title":"International Conference on Learning Representations (ICLR)","author":"Clevert D. 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