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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.
Serial two-photon tomography for automated ex vivo mouse brain imaging.
Ragan T, Kadiri LR, Venkataraju KU, Bahlmann K, Sutin J, Taranda J, Arganda-Carreras I, Kim Y, Seung HS, Osten P. Ragan T, et al. Nat Methods. 2012 Jan 15;9(3):255-8. doi: 10.1038/nmeth.1854. Nat Methods. 2012. PMID: 22245809 Free PMC article.
Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy.
Abdeladim L, Matho KS, Clavreul S, Mahou P, Sintes JM, Solinas X, Arganda-Carreras I, Turney SG, Lichtman JW, Chessel A, Bemelmans AP, Loulier K, Supatto W, Livet J, Beaurepaire E. Abdeladim L, et al. Among authors: arganda carreras i. Nat Commun. 2019 Apr 10;10(1):1662. doi: 10.1038/s41467-019-09552-9. Nat Commun. 2019. PMID: 30971684 Free PMC article.
Designing Image Analysis Pipelines in Light Microscopy: A Rational Approach.
Arganda-Carreras I, Andrey P. Arganda-Carreras I, et al. Methods Mol Biol. 2017;1563:185-207. doi: 10.1007/978-1-4939-6810-7_13. Methods Mol Biol. 2017. PMID: 28324610
MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ.
Legland D, Arganda-Carreras I, Andrey P. Legland D, et al. Bioinformatics. 2016 Nov 15;32(22):3532-3534. doi: 10.1093/bioinformatics/btw413. Epub 2016 Jul 13. Bioinformatics. 2016. PMID: 27412086
BoneJ: Free and extensible bone image analysis in ImageJ.
Doube M, Kłosowski MM, Arganda-Carreras I, Cordelières FP, Dougherty RP, Jackson JS, Schmid B, Hutchinson JR, Shefelbine SJ. Doube M, et al. Bone. 2010 Dec;47(6):1076-9. doi: 10.1016/j.bone.2010.08.023. Epub 2010 Sep 15. Bone. 2010. PMID: 20817052 Free PMC article.
Publisher Correction: Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy.
Abdeladim L, Matho KS, Clavreul S, Mahou P, Sintes JM, Solinas X, Arganda-Carreras I, Turney SG, Lichtman JW, Chessel A, Bemelmans AP, Loulier K, Supatto W, Livet J, Beaurepaire E. Abdeladim L, et al. Among authors: arganda carreras i. Nat Commun. 2019 May 9;10(1):2160. doi: 10.1038/s41467-019-10225-w. Nat Commun. 2019. PMID: 31073140 Free PMC article.
Mapping social behavior-induced brain activation at cellular resolution in the mouse.
Kim Y, Venkataraju KU, Pradhan K, Mende C, Taranda J, Turaga SC, Arganda-Carreras I, Ng L, Hawrylycz MJ, Rockland KS, Seung HS, Osten P. Kim Y, et al. Cell Rep. 2015 Jan 13;10(2):292-305. doi: 10.1016/j.celrep.2014.12.014. Epub 2014 Dec 31. Cell Rep. 2015. PMID: 25558063 Free PMC article.
A Statistically Representative Atlas for Mapping Neuronal Circuits in the Drosophila Adult Brain.
Arganda-Carreras I, Manoliu T, Mazuras N, Schulze F, Iglesias JE, Bühler K, Jenett A, Rouyer F, Andrey P. Arganda-Carreras I, et al. Front Neuroinform. 2018 Mar 23;12:13. doi: 10.3389/fninf.2018.00013. eCollection 2018. Front Neuroinform. 2018. PMID: 29628885 Free PMC article.
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