Computer Assisted Assembly of Connectomes from Electron Micrographs: Application to Caenorhabditis elegans
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{"title"=>"Computer Assisted Assembly of Connectomes from Electron Micrographs: Application to Caenorhabditis elegans", "type"=>"journal", "authors"=>[{"first_name"=>"Meng", "last_name"=>"Xu", "scopus_author_id"=>"56390235100"}, {"first_name"=>"Travis A.", "last_name"=>"Jarrell", "scopus_author_id"=>"55322743900"}, {"first_name"=>"Yi", "last_name"=>"Wang", "scopus_author_id"=>"56638782100"}, {"first_name"=>"Steven J.", "last_name"=>"Cook", "scopus_author_id"=>"55890052700"}, {"first_name"=>"David H.", "last_name"=>"Hall", "scopus_author_id"=>"7404434893"}, {"first_name"=>"Scott W.", "last_name"=>"Emmons", "scopus_author_id"=>"7005094342"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23342070", "issn"=>"19326203", "sgr"=>"84872457021", "doi"=>"10.1371/journal.pone.0054050", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84872457021", "pui"=>"368133821"}, "id"=>"292c1293-a1cc-35f7-a980-934f91d40ba3", "abstract"=>"A rate-limiting step in determining a connectome, the set of all synaptic connections in a nervous system, is extraction of the relevant information from serial electron micrographs. Here we introduce a software application, Elegance, that speeds acquisition of the minimal dataset necessary, allowing the discovery of new connectomes. We have used Elegance to obtain new connectivity data in the nematode worm Caenorhabditis elegans. We analyze the accuracy that can be obtained, which is limited by unresolvable ambiguities at some locations in electron microscopic images. Elegance is useful for reconstructing connectivity in any region of neuropil of sufficiently small size.", "link"=>"http://www.mendeley.com/research/computer-assisted-assembly-connectomes-electron-micrographs-application-caenorhabditis-elegans", "reader_count"=>44, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>4, "Student > Master"=>5, "Student > Bachelor"=>8, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>4, "Student > Master"=>5, "Student > Bachelor"=>8, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Agricultural and Biological Sciences"=>23, "Medicine and Dentistry"=>3, "Neuroscience"=>7, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>5, "Psychology"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Neuroscience"=>{"Neuroscience"=>7}, "Physics and Astronomy"=>{"Physics and Astronomy"=>5}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>23}, "Computer Science"=>{"Computer Science"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>4, "Japan"=>1, "Germany"=>3}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/506176"], "description"=>"<p>A. 2D map of the <i>C. elegans</i> neuron LUAL in the adult male <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054050#pone.0054050-Jarrell1\" target=\"_blank\">[9]</a>. The scale indicates section number (70–90 nm section thickness). The cell body (solid blue box) is in the left lumbar ganglion and is connected through a commissure to a process in the pre-anal ganglion which is dense with synapses. B. Enlargement of a small region of the LUAL map, showing branching architecture and locations of synapses; line thickness indicates synapse size (red: chemical input, magenta: chemical output, green: gap junctions). C. Portion of the adjacency matrix of chemical connectivity in the <i>C. elegans</i> male posterior nervous system <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054050#pone.0054050-Jarrell1\" target=\"_blank\">[9]</a>, generated by Elegance and formatted in Excel. Pre-synaptic neurons to left, post-synaptic neurons at top, connection strength in number of serial sections.</p>", "links"=>[], "tags"=>["physiology", "Computational biology", "neuroscience", "computer science"], "article_id"=>176686, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Physiology"], "users"=>["Meng Xu", "Travis A. Jarrell", "Yi Wang", "Steven J. Cook", "David H. Hall", "Scott W. Emmons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054050.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Elegance_output_/176686", "title"=>"Elegance output.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 16:56:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/506060"], "description"=>"<p>Cell profiles are marked by open blue squares. Different chains of connected objects are labeled with a colored number for ease of recognition. The pink 215 neuron branches between the central and left-hand images. Synapses are marked by red circles.</p>", "links"=>[], "tags"=>["physiology", "Computational biology", "neuroscience", "computer science"], "article_id"=>176566, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Physiology"], "users"=>["Meng Xu", "Travis A. Jarrell", "Yi Wang", "Steven J. Cook", "David H. Hall", "Scott W. Emmons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054050.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Elegance_screenshot_/176566", "title"=>"Elegance screenshot.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 16:56:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/506288"], "description"=>"<p>Average and distribution of edge weights (total amount of synaptic interaction) determined by three separate individuals for the 55 edges connecting the male-specific interneuron PVX to its 55 synaptic partners in the <i>C. elegans</i> male posterior connectome <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054050#pone.0054050-Jarrell1\" target=\"_blank\">[9]</a>. Edge weights are represented by the number of 70–90 nm serial sections of pre-synaptic densities. The weights are for a single edge except where indicated. Values of edge weights (abscissa) are the weights assigned by one of the three scorers, arbitrarily chosen. Weight values typically differed by 1 to 2 sections.</p>", "links"=>[], "tags"=>["determining"], "article_id"=>176807, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Physiology"], "users"=>["Meng Xu", "Travis A. Jarrell", "Yi Wang", "Steven J. Cook", "David H. Hall", "Scott W. Emmons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054050.g003", "stats"=>{"downloads"=>3, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Error_in_determining_connection_strength_/176807", "title"=>"Error in determining connection strength.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 16:57:26"}

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Relative Metric

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