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In optical nerve transection model of the retina, the retrograde degeneration of retinal ganglion cells induces microglial activations to a unique morphology termed rod microglia. A few studies described the rod microglia in the cortex and retina; however, the spatial characteristic of rod microglia is not fully understood. In this study, we built a mathematical model to characterize the spatial trait of rod microglia. In addition, we developed a Matlab-based image processing pipeline that consists of log enhancement, image segmentation, mathematical morphology based cell detection, area calculation and angle analysis. This computer program provides researchers a powerful tool to quickly analyze the spatial trait of rod microglia.<\/jats:p>","DOI":"10.1038\/srep21816","type":"journal-article","created":{"date-parts":[[2016,2,18]],"date-time":"2016-02-18T11:27:37Z","timestamp":1455794857000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["Image processing methods to elucidate spatial characteristics of retinal microglia after optic nerve transection"],"prefix":"10.1038","volume":"6","author":[{"given":"Yudong","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo","family":"Peng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuihua","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu-Xiang","family":"Liang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiquan","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kwok-Fai","family":"So","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ti-Fei","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,2,18]]},"reference":[{"key":"BFsrep21816_CR1","doi-asserted-by":"publisher","first-page":"e30763","DOI":"10.1371\/journal.pone.0030763","volume":"7","author":"RA Jonas","year":"2012","unstructured":"Jonas, R. 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