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The mechanical damage of the primary injury phase is followed and exacerbated by a secondary injury phase, characterized by the release of free radicals and pro\u2010inflammatory cytokines that lead to chronic inflammation. Microglia, as the resident immune cells of the central nervous system, play a critical role in orchestrating this inflammatory response. Studying their dynamics after SCI not only deepens our understanding of injury pathology but also advances the development of microglia\u2010targeted immunotherapies. However, trauma\u2010induced transcriptional and phenotypic changes mean that markers used to identify homeostatic microglia may be unreliable when applied to their reactive counterparts. Another major challenge lies within discriminating resident microglia from infiltrating monocyte\u2010derived macrophages (MDM), which permeate the blood\u2010spinal cord barrier (BSCB) after injury. In this review, we examine three key variables for selecting appropriate strategies for labeling microglia in mice: (i) time (in relation to injury); (ii) efficacy (within the chosen murine SCI model); and (iii) specificity (to microglia). We discuss the transcriptional landscape of murine microglia pre\u2010injury and its alteration post\u2010injury, evaluate the strengths and limitations of commonly used markers, and highlight emerging tools and approaches for studying microglia in preclinical murine SCI research.<\/jats:p>","DOI":"10.1002\/glia.70240","type":"journal-article","created":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T05:13:27Z","timestamp":1792473207000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Microglial Labeling in Mouse Spinal Cord Injury: A Review of Timing, Efficacy, and Specificity"],"prefix":"10.1002","volume":"74","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1766-7154","authenticated-orcid":false,"given":"Ruth","family":"Colbert","sequence":"first","affiliation":[{"name":"School of Medicine, Health Sciences Centre University College Dublin  Dublin 4 Ireland"},{"name":"UCD Conway Institute of Biomolecular &amp; Biomedical Research, University College Dublin  Dublin 4 Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3825-9803","authenticated-orcid":false,"given":"Julia","family":"Di Stefano","sequence":"additional","affiliation":[{"name":"School of Medicine, Health Sciences Centre University College Dublin  Dublin 4 Ireland"},{"name":"UCD Conway Institute of Biomolecular &amp; Biomedical Research, University College Dublin  Dublin 4 Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5337-1831","authenticated-orcid":false,"given":"Dearbhaile","family":"Dooley","sequence":"additional","affiliation":[{"name":"School of Medicine, Health Sciences Centre University College Dublin  Dublin 4 Ireland"},{"name":"UCD Conway Institute of Biomolecular &amp; Biomedical Research, University College Dublin  Dublin 4 Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,19]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010024\u201002476\u20103"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrdp.2017.18"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00011\u2010025\u201002089\u20102"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/nn2014"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/0165\u20105728(90)90055\u2010R"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0165\u20103806(99)00113\u20103"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.7150\/thno.97254"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2024.05.005"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1002\/glia.20477"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010019\u201008446\u20100"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1525528113"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopsych.2025.11.010"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010022\u201031797\u20100"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00417\u2010017\u20103845\u20100"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/nn.3599"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1038\/ni.3585"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/nn1715"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1002\/eji.201948342"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.4172\/1939\u2010067X.1000143"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.exer.2015.07.012"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/nn1472"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jneumeth.2007.11.011"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrn3053"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13073\u2010024\u201001368\u20107"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbi.2024.07.008"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1002\/glia.20993"},{"issue":"3","key":"e_1_2_10_28_1","first-page":"589","article-title":"The Heterogeneity of Mononuclear Phagocytes in Lymphoid Organs: Distinct Macrophage Subpopulations in the Rat Recognized by Monoclonal Antibodies ED1, ED2 and ED3","volume":"54","author":"Dijkstra C. 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