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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.
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. Among authors: schindelin j. Methods. 2017 Feb 15;115:80-90. doi: 10.1016/j.ymeth.2016.09.016. Epub 2016 Oct 3. Methods. 2017. PMID: 27713081 Free 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.
A high-level 3D visualization API for Java and ImageJ.
Schmid B, Schindelin J, Cardona A, Longair M, Heisenberg M. Schmid B, et al. BMC Bioinformatics. 2010 May 21;11:274. doi: 10.1186/1471-2105-11-274. BMC Bioinformatics. 2010. PMID: 20492697 Free PMC article.
Software for bead-based registration of selective plane illumination microscopy data.
Preibisch S, Saalfeld S, Schindelin J, Tomancak P. Preibisch S, et al. Nat Methods. 2010 Jun;7(6):418-9. doi: 10.1038/nmeth0610-418. Nat Methods. 2010. PMID: 20508634 No abstract available.
OpenSPIM: an open-access light-sheet microscopy platform.
Pitrone PG, Schindelin J, Stuyvenberg L, Preibisch S, Weber M, Eliceiri KW, Huisken J, Tomancak P. Pitrone PG, et al. Among authors: schindelin j. Nat Methods. 2013 Jul;10(7):598-9. doi: 10.1038/nmeth.2507. Epub 2013 Jun 9. Nat Methods. 2013. PMID: 23749304 Free PMC article. No abstract available.
ImageJ2: ImageJ for the next generation of scientific image data.
Rueden CT, Schindelin J, Hiner MC, DeZonia BE, Walter AE, Arena ET, Eliceiri KW. Rueden CT, et al. Among authors: schindelin j. BMC Bioinformatics. 2017 Nov 29;18(1):529. doi: 10.1186/s12859-017-1934-z. BMC Bioinformatics. 2017. PMID: 29187165 Free PMC article.
Cooperativity among Rev-associated nuclear export signals regulates HIV-1 gene expression and is a determinant of virus species tropism.
Aligeti M, Behrens RT, Pocock GM, Schindelin J, Dietz C, Eliceiri KW, Swanson CM, Malim MH, Ahlquist P, Sherer NM. Aligeti M, et al. Among authors: schindelin j. J Virol. 2014 Dec;88(24):14207-21. doi: 10.1128/JVI.01897-14. Epub 2014 Oct 1. J Virol. 2014. PMID: 25275125 Free PMC article.
Genetic oscillations. A Doppler effect in embryonic pattern formation.
Soroldoni D, Jörg DJ, Morelli LG, Richmond DL, Schindelin J, Jülicher F, Oates AC. Soroldoni D, et al. Among authors: schindelin j. Science. 2014 Jul 11;345(6193):222-5. doi: 10.1126/science.1253089. Science. 2014. PMID: 25013078 Free article.
Generation of dispersed presomitic mesoderm cell cultures for imaging of the zebrafish segmentation clock in single cells.
Webb AB, Soroldoni D, Oswald A, Schindelin J, Oates AC. Webb AB, et al. Among authors: schindelin j. J Vis Exp. 2014 Jul 24;(89):50307. doi: 10.3791/50307. J Vis Exp. 2014. PMID: 25078855 Free PMC article.
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