Literature DB >> 20801638

Machines that learn to segment images: a crucial technology for connectomics.

Viren Jain1, H Sebastian Seung, Srinivas C Turaga.   

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.
Copyright © 2010 Elsevier Ltd. All rights reserved.

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Year:  2010        PMID: 20801638      PMCID: PMC2975605          DOI: 10.1016/j.conb.2010.07.004

Source DB:  PubMed          Journal:  Curr Opin Neurobiol        ISSN: 0959-4388            Impact factor:   6.627


  33 in total

1.  Reconstruct: a free editor for serial section microscopy.

Authors:  J C Fiala
Journal:  J Microsc       Date:  2005-04       Impact factor: 1.758

Review 2.  Towards neural circuit reconstruction with volume electron microscopy techniques.

Authors:  Kevin L Briggman; Winfried Denk
Journal:  Curr Opin Neurobiol       Date:  2006-09-08       Impact factor: 6.627

Review 3.  Circuit reconstruction tools today.

Authors:  Stephen J Smith
Journal:  Curr Opin Neurobiol       Date:  2007-12-21       Impact factor: 6.627

4.  AN OPTIMAL-PATH APPROACH FOR NEURAL CIRCUIT RECONSTRUCTION.

Authors:  Elizabeth Jurrus; Ross Whitaker; Bryan W Jones; Robert Marc; Tolga Tasdizen
Journal:  Proc IEEE Int Symp Biomed Imaging       Date:  2008-05

5.  ENHANCEMENT OF CELL BOUNDARIES IN TRANSMISSION ELECTRON MICROSCOPY IMAGES.

Authors:  Tolga Tasdizen; Ross Whitaker; Robert Marc; Bryan Jones
Journal:  Proc Int Conf Image Proc       Date:  2005

6.  Watershed cuts: minimum spanning forests and the drop of water principle.

Authors:  Jean Cousty; Gilles Bertrand; Laurent Najman; Michel Couprie
Journal:  IEEE Trans Pattern Anal Mach Intell       Date:  2009-08       Impact factor: 6.226

7.  Convolutional networks can learn to generate affinity graphs for image segmentation.

Authors:  Srinivas C Turaga; Joseph F Murray; Viren Jain; Fabian Roth; Moritz Helmstaedter; Kevin Briggman; Winfried Denk; H Sebastian Seung
Journal:  Neural Comput       Date:  2010-02       Impact factor: 2.026

8.  Detection of neuron membranes in electron microscopy images using a serial neural network architecture.

Authors:  Elizabeth Jurrus; Antonio R C Paiva; Shigeki Watanabe; James R Anderson; Bryan W Jones; Ross T Whitaker; Erik M Jorgensen; Robert E Marc; Tolga Tasdizen
Journal:  Med Image Anal       Date:  2010-06-18       Impact factor: 8.545

Review 9.  The human connectome: A structural description of the human brain.

Authors:  Olaf Sporns; Giulio Tononi; Rolf Kötter
Journal:  PLoS Comput Biol       Date:  2005-09       Impact factor: 4.475

10.  Dictionary learning algorithms for sparse representation.

Authors:  Kenneth Kreutz-Delgado; Joseph F Murray; Bhaskar D Rao; Kjersti Engan; Te-Won Lee; Terrence J Sejnowski
Journal:  Neural Comput       Date:  2003-02       Impact factor: 2.026

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  54 in total

Review 1.  Large-scale automated histology in the pursuit of connectomes.

Authors:  David Kleinfeld; Arjun Bharioke; Pablo Blinder; Davi D Bock; Kevin L Briggman; Dmitri B Chklovskii; Winfried Denk; Moritz Helmstaedter; John P Kaufhold; Wei-Chung Allen Lee; Hanno S Meyer; Kristina D Micheva; Marcel Oberlaender; Steffen Prohaska; R Clay Reid; Stephen J Smith; Shinya Takemura; Philbert S Tsai; Bert Sakmann
Journal:  J Neurosci       Date:  2011-11-09       Impact factor: 6.167

2.  Direct maximization of protein identifications from tandem mass spectra.

Authors:  Marina Spivak; Jason Weston; Daniela Tomazela; Michael J MacCoss; William Stafford Noble
Journal:  Mol Cell Proteomics       Date:  2011-11-03       Impact factor: 5.911

3.  Comparative performance evaluation of automated segmentation methods of hippocampus from magnetic resonance images of temporal lobe epilepsy patients.

Authors:  Mohammad-Parsa Hosseini; Mohammad-Reza Nazem-Zadeh; Dario Pompili; Kourosh Jafari-Khouzani; Kost Elisevich; Hamid Soltanian-Zadeh
Journal:  Med Phys       Date:  2016-01       Impact factor: 4.071

4.  Understanding complexity in the human brain.

Authors:  Danielle S Bassett; Michael S Gazzaniga
Journal:  Trends Cogn Sci       Date:  2011-04-14       Impact factor: 20.229

Review 5.  Beyond counts and shapes: studying pathology of dendritic spines in the context of the surrounding neuropil through serial section electron microscopy.

Authors:  M Kuwajima; J Spacek; K M Harris
Journal:  Neuroscience       Date:  2012-05-01       Impact factor: 3.590

Review 6.  Molecular neuroanatomy: a generation of progress.

Authors:  Jonathan D Pollock; Da-Yu Wu; John S Satterlee
Journal:  Trends Neurosci       Date:  2013-12-31       Impact factor: 13.837

Review 7.  Cellular-resolution connectomics: challenges of dense neural circuit reconstruction.

Authors:  Moritz Helmstaedter
Journal:  Nat Methods       Date:  2013-06       Impact factor: 28.547

Review 8.  Segmentation of joint and musculoskeletal tissue in the study of arthritis.

Authors:  Valentina Pedoia; Sharmila Majumdar; Thomas M Link
Journal:  MAGMA       Date:  2016-02-25       Impact factor: 2.310

9.  Measurement-oriented deep-learning workflow for improved segmentation of myelin and axons in high-resolution images of human cerebral white matter.

Authors:  Predrag Janjic; Kristijan Petrovski; Blagoja Dolgoski; John Smiley; Panche Zdravkovski; Goran Pavlovski; Zlatko Jakjovski; Natasa Davceva; Verica Poposka; Aleksandar Stankov; Gorazd Rosoklija; Gordana Petrushevska; Ljupco Kocarev; Andrew J Dwork
Journal:  J Neurosci Methods       Date:  2019-08-01       Impact factor: 2.390

Review 10.  From functional architecture to functional connectomics.

Authors:  R Clay Reid
Journal:  Neuron       Date:  2012-07-26       Impact factor: 17.173

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