title: Machines that learn to segment images: a crucial technology for connectomics.
abstract: Connections between neurons can be found by checking whether synapses exist at points of contact, which in turn are determined by neural shapes. Finding these shapes is a special case of image segmentation, which is laborious for humans and would ideally be performed by computers. New metrics properly quantify the performance of a computer algorithm using its disagreement with 'true' segmentations of example images. New machine learning methods search for segmentation algorithms that minimize such metrics. These advances have reduced computer errors dramatically. It should now be faster for a human to correct the remaining errors than to segment an image manually. Further reductions in human effort are expected, and crucial for finding connectomes more complex than that of Caenorhabditis elegans.
authors.affiliation: Howard Hughes Medical Institute and Brain & Cog. Sci. Dept., Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Viren
authors.initials: V
authors.lastname: Jain
authors.forename: H Sebastian
authors.initials: HS
authors.lastname: Seung
authors.forename: Srinivas C
authors.initials: SC
authors.lastname: Turaga
mesh_terms: D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000295:instrumentation / Q000379:methods / Q000639:trends*; D008854:Microscopy, Electron / Q000295:instrumentation / Q000379:methods / Q000639:trends; D036103:Nanotechnology / Q000295:instrumentation / Q000379:methods / Q000639:trends*; D009446:Neurobiology / Q000295:instrumentation / Q000379:methods / Q000639:trends*
references.citation: Proc IEEE Int Symp Biomed Imaging. 2008 May;2008(4541320):1609-1612
references.pmid: 19172170
references.citation: Proc Int Conf Image Proc. 2005;2:129-132
references.pmid: 19169423
references.citation: J Microsc. 2005 Apr;218(Pt 1):52-61
references.pmid: 15817063
references.citation: PLoS Comput Biol. 2005 Sep;1(4):e42
references.pmid: 16201007
references.citation: IEEE Trans Pattern Anal Mach Intell. 2009 Aug;31(8):1362-74
references.pmid: 19542572
references.citation: Med Image Anal. 2010 Dec;14(6):770-83
references.pmid: 20598935
references.citation: Curr Opin Neurobiol. 2006 Oct;16(5):562-70
references.pmid: 16962767
references.citation: Neural Comput. 2010 Feb;22(2):511-38
references.pmid: 19922289
references.citation: Curr Opin Neurobiol. 2007 Oct;17(5):601-8
references.pmid: 18082394
references.citation: Neural Comput. 2003 Feb;15(2):349-96
references.pmid: 12590811
references.citation: Neuron. 2009 Apr 16;62(1):17-29
references.pmid: 19376064
references.citation: IEEE Trans Pattern Anal Mach Intell. 1986 Jun;8(6):679-98
references.pmid: 21869365
references.citation: Annu Rev Biophys Bioeng. 1980;9:347-62
references.pmid: 7396437
references.citation: Neuron. 2010 Sep 23;67(6):1009-20
references.pmid: 20869597
references.citation: J Neurosci Methods. 2008 Jan 30;167(2):349-57
references.pmid: 17870180
references.citation: Science. 2006 Jul 28;313(5786):504-7
references.pmid: 16873662
references.citation: IEEE Trans Pattern Anal Mach Intell. 1984 Jun;6(6):721-41
references.pmid: 22499653
references.citation: Philos Trans R Soc Lond B Biol Sci. 1986 Nov 12;314(1165):1-340
references.pmid: 22462104
references.citation: Science. 2008 Sep 12;321(5895):1465-8
references.pmid: 18703711
references.citation: IEEE Trans Vis Comput Graph. 2009 Nov-Dec;15(6):1505-14
references.pmid: 19834227
references.citation: PLoS Biol. 2004 Nov;2(11):e329
references.pmid: 15514700
references.citation: Neuroimage. 2006 Jul 1;31(3):1116-28
references.pmid: 16545965
references.citation: IEEE Trans Pattern Anal Mach Intell. 2004 May;26(5):530-49
references.pmid: 15460277
references.citation: Curr Opin Neurobiol. 2008 Dec;18(6):633-41
references.pmid: 19361979
references.citation: Curr Opin Neurobiol. 2008 Jun;18(3):346-53
references.pmid: 18801435
references.citation: J Neurosci. 2008 Mar 19;28(12):2959-64
references.pmid: 18353998
references.citation: IEEE Trans Med Imaging. 1994;13(2):351-62
references.pmid: 18218511
references.citation: IEEE Trans Pattern Anal Mach Intell. 2007 Jun;29(6):929-44
references.pmid: 17431294
references.citation: Proc R Soc Lond B Biol Sci. 1980 Feb 29;207(1167):187-217
references.pmid: 6102765
references.citation: J Neurosci. 2006 Nov 22;26(47):12101-3
references.pmid: 17122034
references.citation: Med Image Anal. 2009 Feb;13(1):180-8
references.pmid: 18617436
references.citation: IEEE Comput Graph Appl. 2010 May-Jun;30(3):58-70
references.pmid: 20650718
references.citation: J Neurosci Methods. 2009 Jan 30;176(2):276-89
references.pmid: 18834903