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Items: 1 to 20 of 22


Assessing microscope image focus quality with deep learning.

Yang SJ, Berndl M, Michael Ando D, Barch M, Narayanaswamy A, Christiansen E, Hoyer S, Roat C, Hung J, Rueden CT, Shankar A, Finkbeiner S, Nelson P.

BMC Bioinformatics. 2018 Mar 15;19(1):77. doi: 10.1186/s12859-018-2087-4.


ImageJ2: ImageJ for the next generation of scientific image data.

Rueden CT, Schindelin J, Hiner MC, DeZonia BE, Walter AE, Arena ET, Eliceiri KW.

BMC Bioinformatics. 2017 Nov 29;18(1):529. doi: 10.1186/s12859-017-1934-z.


FunImageJ: a Lisp framework for scientific image processing.

Harrington KIS, Rueden CT, Eliceiri KW.

Bioinformatics. 2018 Mar 1;34(5):899-900. doi: 10.1093/bioinformatics/btx710.


Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification.

Arganda-Carreras I, Kaynig V, Rueden C, Eliceiri KW, Schindelin J, Cardona A, Sebastian Seung H.

Bioinformatics. 2017 Aug 1;33(15):2424-2426. doi: 10.1093/bioinformatics/btx180.


SCIFIO: an extensible framework to support scientific image formats.

Hiner MC, Rueden CT, Eliceiri KW.

BMC Bioinformatics. 2016 Dec 7;17(1):521.


Quantitating the cell: turning images into numbers with ImageJ.

Arena ET, Rueden CT, Hiner MC, Wang S, Yuan M, Eliceiri KW.

Wiley Interdiscip Rev Dev Biol. 2017 Mar;6(2). doi: 10.1002/wdev.260. Epub 2016 Dec 2. Review.


ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability.

Hiner MC, Rueden CT, Eliceiri KW.

Bioinformatics. 2017 Feb 15;33(4):629-630. doi: 10.1093/bioinformatics/btw681.


The ImageJ ecosystem: An open platform for biomedical image analysis.

Schindelin J, Rueden CT, Hiner MC, Eliceiri KW.

Mol Reprod Dev. 2015 Jul-Aug;82(7-8):518-29. doi: 10.1002/mrd.22489. Epub 2015 Jul 7. Review.


Noninvasive sorting of stem cell aggregates based on intrinsic markers.

Buschke DG, Squirrell JM, Vivekanandan A, Rueden CT, Eliceiri KW, Ogle BM.

Cytometry A. 2014 Apr;85(4):353-8. doi: 10.1002/cyto.a.22436. Epub 2014 Jan 17.


Large particle multiphoton flow cytometry to purify intact embryoid bodies exhibiting enhanced potential for cardiomyocyte differentiation.

Buschke DG, Vivekanandan A, Squirrell JM, Rueden CT, Eliceiri KW, Ogle BM.

Integr Biol (Camb). 2013 Jul 24;5(7):993-1003. doi: 10.1039/c3ib20286k. Epub 2013 Jun 13.


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.

Nat Methods. 2012 Jun 28;9(7):676-82. doi: 10.1038/nmeth.2019.


Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software.

Kamentsky L, Jones TR, Fraser A, Bray MA, Logan DJ, Madden KL, Ljosa V, Rueden C, Eliceiri KW, Carpenter AE.

Bioinformatics. 2011 Apr 15;27(8):1179-80. doi: 10.1093/bioinformatics/btr095. Epub 2011 Feb 23.


Multiphoton flow cytometry to assess intrinsic and extrinsic fluorescence in cellular aggregates: applications to stem cells.

Buschke DG, Squirrell JM, Ansari H, Smith MA, Rueden CT, Williams JC, Lyons GE, Kamp TJ, Eliceiri KW, Ogle BM.

Microsc Microanal. 2011 Aug;17(4):540-54. doi: 10.1017/S1431927610000280. Epub 2010 Aug 5.


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.

J Cell Biol. 2010 May 31;189(5):777-82. doi: 10.1083/jcb.201004104.


Nonlinear optical microscopy and computational analysis of intrinsic signatures in breast cancer.

Rueden CT, Conklin MW, Provenzano PP, Keely PJ, Eliceiri KW.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:4077-80. doi: 10.1109/IEMBS.2009.5334523.


Nonlinear optical imaging and spectral-lifetime computational analysis of endogenous and exogenous fluorophores in breast cancer.

Provenzano PP, Rueden CT, Trier SM, Yan L, Ponik SM, Inman DR, Keely PJ, Eliceiri KW.

J Biomed Opt. 2008 May-Jun;13(3):031220. doi: 10.1117/1.2940365.


Collagen density promotes mammary tumor initiation and progression.

Provenzano PP, Inman DR, Eliceiri KW, Knittel JG, Yan L, Rueden CT, White JG, Keely PJ.

BMC Med. 2008 Apr 28;6:11. doi: 10.1186/1741-7015-6-11.


Visualization approaches for multidimensional biological image data.

Rueden CT, Eliceiri KW.

Biotechniques. 2007 Jul;43(1 Suppl):31, 33-6. Review.


Applications of combined spectral lifetime microscopy for biology.

Yan L, Rueden CT, White JG, Eliceiri KW.

Biotechniques. 2006 Sep;41(3):249, 251, 253 passim. Review.


Tools for visualizing multidimensional images from living specimens.

Eliceiri KW, Rueden C.

Photochem Photobiol. 2005 Sep-Oct;81(5):1116-22. Review.


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