Literature DB >> 34168373

Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set.

Julia Buhmann1,2, Arlo Sheridan1, Caroline Malin-Mayor1, Philipp Schlegel3, Stephan Gerhard4,5, Tom Kazimiers1, Renate Krause1,2, Tri M Nguyen4, Larissa Heinrich1, Wei-Chung Allen Lee6, Rachel Wilson4, Stephan Saalfeld1, Gregory S X E Jefferis3, Davi D Bock7, Srinivas C Turaga1, Matthew Cook2, Jan Funke8.   

Abstract

We develop an automatic method for synaptic partner identification in insect brains and use it to predict synaptic partners in a whole-brain electron microscopy dataset of the fruit fly. The predictions can be used to infer a connectivity graph with high accuracy, thus allowing fast identification of neural pathways. To facilitate circuit reconstruction using our results, we develop CIRCUITMAP, a user interface add-on for the circuit annotation tool CATMAID.

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Year:  2021        PMID: 34168373      PMCID: PMC7611460          DOI: 10.1038/s41592-021-01183-7

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  9 in total

Review 1.  Structural neurobiology: missing link to a mechanistic understanding of neural computation.

Authors:  Winfried Denk; Kevin L Briggman; Moritz Helmstaedter
Journal:  Nat Rev Neurosci       Date:  2012-02-22       Impact factor: 34.870

2.  Automated synaptic connectivity inference for volume electron microscopy.

Authors:  Sven Dorkenwald; Philipp J Schubert; Marius F Killinger; Gregor Urban; Shawn Mikula; Fabian Svara; Joergen Kornfeld
Journal:  Nat Methods       Date:  2017-02-27       Impact factor: 28.547

3.  Large Scale Image Segmentation with Structured Loss Based Deep Learning for Connectome Reconstruction.

Authors:  Jan Funke; Fabian Tschopp; William Grisaitis; Arlo Sheridan; Chandan Singh; Stephan Saalfeld; Srinivas C Turaga
Journal:  IEEE Trans Pattern Anal Mach Intell       Date:  2018-05-24       Impact factor: 6.226

4.  Dense connectomic reconstruction in layer 4 of the somatosensory cortex.

Authors:  Alessandro Motta; Manuel Berning; Kevin M Boergens; Benedikt Staffler; Marcel Beining; Sahil Loomba; Philipp Hennig; Heiko Wissler; Moritz Helmstaedter
Journal:  Science       Date:  2019-10-24       Impact factor: 47.728

5.  Y-Net: a one-to-two deep learning framework for digital holographic reconstruction.

Authors:  Kaiqiang Wang; Jiazhen Dou; Qian Kemao; Jianglei Di; Jianlin Zhao
Journal:  Opt Lett       Date:  2019-10-01       Impact factor: 3.776

6.  Quantitative neuroanatomy for connectomics in Drosophila.

Authors:  Casey M Schneider-Mizell; Stephan Gerhard; Mark Longair; Tom Kazimiers; Feng Li; Maarten F Zwart; Andrew Champion; Frank M Midgley; Richard D Fetter; Stephan Saalfeld; Albert Cardona
Journal:  Elife       Date:  2016-03-18       Impact factor: 8.140

7.  U-Net: deep learning for cell counting, detection, and morphometry.

Authors:  Thorsten Falk; Dominic Mai; Robert Bensch; Özgün Çiçek; Ahmed Abdulkadir; Yassine Marrakchi; Anton Böhm; Jan Deubner; Zoe Jäckel; Katharina Seiwald; Alexander Dovzhenko; Olaf Tietz; Cristina Dal Bosco; Sean Walsh; Deniz Saltukoglu; Tuan Leng Tay; Marco Prinz; Klaus Palme; Matias Simons; Ilka Diester; Thomas Brox; Olaf Ronneberger
Journal:  Nat Methods       Date:  2018-12-17       Impact factor: 28.547

8.  Fully-Automatic Synapse Prediction and Validation on a Large Data Set.

Authors:  Gary B Huang; Louis K Scheffer; Stephen M Plaza
Journal:  Front Neural Circuits       Date:  2018-10-29       Impact factor: 3.492

9.  A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster.

Authors:  Zhihao Zheng; J Scott Lauritzen; Eric Perlman; Camenzind G Robinson; Matthew Nichols; Daniel Milkie; Omar Torrens; John Price; Corey B Fisher; Nadiya Sharifi; Steven A Calle-Schuler; Lucia Kmecova; Iqbal J Ali; Bill Karsh; Eric T Trautman; John A Bogovic; Philipp Hanslovsky; Gregory S X E Jefferis; Michael Kazhdan; Khaled Khairy; Stephan Saalfeld; Richard D Fetter; Davi D Bock
Journal:  Cell       Date:  2018-07-19       Impact factor: 41.582

  9 in total
  12 in total

1.  Neural network organization for courtship-song feature detection in Drosophila.

Authors:  Christa A Baker; Claire McKellar; Rich Pang; Aljoscha Nern; Sven Dorkenwald; Diego A Pacheco; Nils Eckstein; Jan Funke; Barry J Dickson; Mala Murthy
Journal:  Curr Biol       Date:  2022-07-05       Impact factor: 10.900

2.  Chemoreceptor co-expression in Drosophila melanogaster olfactory neurons.

Authors:  Darya Task; Chun-Chieh Lin; Alina Vulpe; Ali Afify; Sydney Ballou; Maria Brbic; Philipp Schlegel; Joshua Raji; Gregory Jefferis; Hongjie Li; Karen Menuz; Christopher J Potter
Journal:  Elife       Date:  2022-04-20       Impact factor: 8.713

3.  Drosophila gustatory projections are segregated by taste modality and connectivity.

Authors:  Stefanie Engert; Gabriella R Sterne; Davi D Bock; Kristin Scott
Journal:  Elife       Date:  2022-05-25       Impact factor: 8.713

4.  CleftNet: Augmented Deep Learning for Synaptic Cleft Detection From Brain Electron Microscopy.

Authors:  Yi Liu; Shuiwang Ji
Journal:  IEEE Trans Med Imaging       Date:  2021-11-30       Impact factor: 10.048

5.  Deep learning is widely applicable to phenotyping embryonic development and disease.

Authors:  Thomas Naert; Özgün Çiçek; Paulina Ogar; Max Bürgi; Nikko-Ideen Shaidani; Michael M Kaminski; Yuxiao Xu; Kelli Grand; Marko Vujanovic; Daniel Prata; Friedhelm Hildebrandt; Thomas Brox; Olaf Ronneberger; Fabian F Voigt; Fritjof Helmchen; Johannes Loffing; Marko E Horb; Helen Rankin Willsey; Soeren S Lienkamp
Journal:  Development       Date:  2021-11-05       Impact factor: 6.868

Review 6.  Neural architectures in the light of comparative connectomics.

Authors:  Elizabeth Barsotti; Ana Correia; Albert Cardona
Journal:  Curr Opin Neurobiol       Date:  2021-11-24       Impact factor: 6.627

7.  Integrated Array Tomography for 3D Correlative Light and Electron Microscopy.

Authors:  Ryan Lane; Anouk H G Wolters; Ben N G Giepmans; Jacob P Hoogenboom
Journal:  Front Mol Biosci       Date:  2022-01-19

8.  Synaptic counts approximate synaptic contact area in Drosophila.

Authors:  Christopher L Barnes; Daniel Bonnéry; Albert Cardona
Journal:  PLoS One       Date:  2022-04-04       Impact factor: 3.240

9.  RealNeuralNetworks.jl: An Integrated Julia Package for Skeletonization, Morphological Analysis, and Synaptic Connectivity Analysis of Terabyte-Scale 3D Neural Segmentations.

Authors:  Jingpeng Wu; Nicholas Turner; J Alexander Bae; Ashwin Vishwanathan; H Sebastian Seung
Journal:  Front Neuroinform       Date:  2022-03-02       Impact factor: 4.081

10.  Automated Synapse Detection Method for Cerebellar Connectomics.

Authors:  Changjoo Park; Jawon Gim; Sungjin Lee; Kea Joo Lee; Jinseop S Kim
Journal:  Front Neuroanat       Date:  2022-03-11       Impact factor: 3.856

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