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Fiji: an open-source platform for biological-image analysis.
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Schindelin J, et al. Nat Methods. 2012 Jun 28;9(7):676-82. doi: 10.1038/nmeth.2019. Nat Methods. 2012. PMID: 22743772 Free PMC article.
Analysis of multidimensional biological image data.
Eliceiri KW, Rueden C, Mohler WA, Hibbard WL, White JG. Eliceiri KW, et al. Biotechniques. 2002 Dec;33(6):1268-73. doi: 10.2144/02336bt01. Biotechniques. 2002. PMID: 12503311 Review. No abstract available.
Imaging Vacuolar Anthocyanins with Fluorescence Lifetime Microscopy (FLIM).
Chanoca A, Burkel B, Grotewold E, Eliceiri KW, Otegui MS. Chanoca A, et al. Methods Mol Biol. 2018;1789:131-141. doi: 10.1007/978-1-4939-7856-4_10. Methods Mol Biol. 2018. PMID: 29916076
Biological imaging software tools.
Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurman N, Swedlow JR, Tomancak P, Carpenter AE. Eliceiri KW, et al. Nat Methods. 2012 Jun 28;9(7):697-710. doi: 10.1038/nmeth.2084. Nat Methods. 2012. PMID: 22743775 Free PMC article.
The ImageJ ecosystem: An open platform for biomedical image analysis.
Schindelin J, Rueden CT, Hiner MC, Eliceiri KW. Schindelin J, et al. Mol Reprod Dev. 2015 Jul-Aug;82(7-8):518-29. doi: 10.1002/mrd.22489. Epub 2015 Jul 7. Mol Reprod Dev. 2015. PMID: 26153368 Free PMC article. Review.
Computational segmentation of collagen fibers from second-harmonic generation images of breast cancer.
Bredfeldt JS, Liu Y, Pehlke CA, Conklin MW, Szulczewski JM, Inman DR, Keely PJ, Nowak RD, Mackie TR, Eliceiri KW. Bredfeldt JS, et al. J Biomed Opt. 2014 Jan;19(1):16007. doi: 10.1117/1.JBO.19.1.016007. J Biomed Opt. 2014. PMID: 24407500 Free PMC article.
TrackMate: An open and extensible platform for single-particle tracking.
Tinevez JY, Perry N, Schindelin J, Hoopes GM, Reynolds GD, Laplantine E, Bednarek SY, Shorte SL, Eliceiri KW. Tinevez JY, et al. Methods. 2017 Feb 15;115:80-90. doi: 10.1016/j.ymeth.2016.09.016. Epub 2016 Oct 3. Methods. 2017. PMID: 27713081
NIH Image to ImageJ: 25 years of image analysis.
Schneider CA, Rasband WS, Eliceiri KW. Schneider CA, et al. Nat Methods. 2012 Jul;9(7):671-5. doi: 10.1038/nmeth.2089. Nat Methods. 2012. PMID: 22930834 Free PMC article.
Metadata matters: access to image data in the real world.
Linkert M, Rueden CT, Allan C, Burel JM, Moore W, Patterson A, Loranger B, Moore J, Neves C, Macdonald D, Tarkowska A, Sticco C, Hill E, Rossner M, Eliceiri KW, Swedlow JR. Linkert M, et al. J Cell Biol. 2010 May 31;189(5):777-82. doi: 10.1083/jcb.201004104. J Cell Biol. 2010. PMID: 20513764 Free PMC article.
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