Projekt

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Neural Circuit Reconstruction

Titel Englisch Neural Circuit Reconstruction
Gesuchsteller/in Hahnloser Richard
Nummer 130470
Förderungsinstrument Sinergia
Forschungseinrichtung Institut für Neuroinformatik Universität Zürich Irchel und ETH Zürich
Hochschule Universität Zürich – ZH
Hauptdisziplin Neurophysiologie und Hirnforschung
Beginn/Ende 01.01.2011 - 31.12.2014
Bewilligter Betrag 1'500'000.00
Alle Daten anzeigen

Alle Disziplinen (2)

Disziplin
Neurophysiologie und Hirnforschung
Informatik

Keywords (14)

Electron microscopy; Light microscopy; Computer vision; Histology; Image processing; Connectome; Brain wiring; Synapse; Circuit; Neural network; Brain; Network; segmentation; algorithm

Lay Summary (Englisch)

Lead
Lay summary
Understanding structure-function relationships is one of the most successful strategies in biology that in the context of neuroscience requires exhaustive measurements of connectivity between neurons to extract the topology of synaptic interactions in neuronal circuits. This goal is considered "one of the holy grails of Neuroscience" since it would pave the way for a systematic analysis of neuronal circuit function based on computational modeling.The recent development of 3-D electron microscopy (3DEM) techniques allows the ultrastructural analysis of biological tissues throughout large volumes (up to a few hundred micrometers in each dimension). Although 3DEM has an enormous potential for advancing our understanding of brain function in health and disease, its biomedical application is currently impeded by the lack of accessory technologies, particularly informatics tools for the automated analysis of large and complex sets of image data. Automated processing and interpretation of light and electron microscopy images represents an extremely challenging problem even when supervision information is provided. New computational tools must be developed for the registration of light and electron microscopy images, for annotating features to identify synapses and other subcellular structures, for classifying image voxels to aid volumetric image segmentation, and for tracing of neuron morphologies based on local and global information. Our project is interdisciplinary and we are composed of neurobiologists and computer vision scientists. We are divided into groups that work on different animal models and pursue different electron microscopy approaches.
Direktlink auf Lay Summary Letzte Aktualisierung: 21.02.2013

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
Pyramidal cells make specific connections onto smooth (GABAergic) cells in mouse visual cortex.
Bopp R Macarico Da Costa N Kampa BM Martin KAC Roth MM (2014), Pyramidal cells make specific connections onto smooth (GABAergic) cells in mouse visual cortex., in PLoS Biology, 12(8), 1.
Anisotropic ssTEM Image Segmentation Using Dense Correspondence across Sections
Dmitry Laptev Alexander Vezhnevets Sarvesh Dwivedi Joachim M. Buhmann (2012), Anisotropic ssTEM Image Segmentation Using Dense Correspondence across Sections, in Medical Image Computing and Computer-Assisted Intervention – MICCAI 2012, Nice, FranceSpringer Publishing, New York, US.
Efficient Automatic 3D-Reconstruction of Branching Neurons from EM Data
Funke J. Andres B. Hamprecht F. Cardona A. and Cook M. (2012), Efficient Automatic 3D-Reconstruction of Branching Neurons from EM Data, in Computer Vision and Pattern Recognition, Piscataway, New Jersey, USInstitute of Electrical and Electronics Engineers, New Jersey, US.
Elastic volume reconstruction from series of ultra-thin microscopy sections
Saalfeld S. Fetter R. Cardona A. and Tomancak P. (2012), Elastic volume reconstruction from series of ultra-thin microscopy sections, in Nature Methods, 9, 717-720.
Robust Non-Rigid Registration of 2D and 3D Graphs
E. Serradell F. Moreno J. Kybic and P. Fua (2012), Robust Non-Rigid Registration of 2D and 3D Graphs, in Computer Vision and Pattern Recognition, Providence, RI, USAInstitute of Electrical and Electronics Engineers, New Jersey, US.
Altered synaptic dynamics during normal brain aging
Mostany R Anstey JE Crump KL Maco B Knott G and Portera-Cailliau C, Altered synaptic dynamics during normal brain aging, in Journal of Neuroscience.
Correlative in vivo 2 Photon and Focused Ion Beam Scanning Electron Microscopy of Cortical Neurons
Maco B Holtmaat A Cantoni M Kreshuk A Straehle CN Hamprecht F Knott GW, Correlative in vivo 2 Photon and Focused Ion Beam Scanning Electron Microscopy of Cortical Neurons, in PLoSONE.
Diversity of thalamorecipient spine morphology in cat visual cortex and its implication for synaptic plasticity
N. M. Costa, Diversity of thalamorecipient spine morphology in cat visual cortex and its implication for synaptic plasticity, in Journal of Comparative Neurology, 2058-2066.
Functional development of the olfactory system in zebrafish
Miyasaka N Wanner AA Li J Mack-Bucher J Genoud C Yoshihara Y Friedrich RW, Functional development of the olfactory system in zebrafish, in Mech Dev.
SuperSlicing frame restoration for anisotropic ssTEM
Laptev Dmitry, Vezhnevets Alexander, Buhmann Joachim, SuperSlicing frame restoration for anisotropic ssTEM, in IEEE 11th International Symposium on Biomedical Imaging ISBI 2014, BeijingMicrotome Publishing, -.

Zusammenarbeit

Gruppe / Person Land
Formen der Zusammenarbeit
Massachusetts Institute of Technology (MIT) Vereinigte Staaten von Amerika (Nordamerika)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
Society for Neuroscience 2016 Poster Automated dense collection of ultrathin sections directly onto silicon wafers 12.11.2016 San Diego, Vereinigte Staaten von Amerika Hahnloser Richard; Templier Thomas;
Pattern Theory Lunch Seminar Series Einzelvortrag Big data in neuroscience: Where is the information? 04.12.2013 Brown University, Providence, Vereinigte Staaten von Amerika Buhmann Joachim;
Society for Neuroscience 2013 Poster A correlative light and electron microscopy approach for reconstructing syringeal motor neuron circuits in a songbird 07.11.2013 San Diego, Vereinigte Staaten von Amerika Hahnloser Richard; Templier Thomas;
Fall 2013 GRASP Seminar Einzelvortrag Big Data: Where is the information? 27.09.2013 GRASP Lab, University of Pennsylvania, Vereinigte Staaten von Amerika Buhmann Joachim;
ZNZ Symposium 2013 Poster Quantifying the local circuit of macaque cortex. 13.09.2013 Zurich, Schweiz Martin Kevan;
Informatik-Kolloquium Einzelvortrag Big Data: where is the information 13.08.2013 TU Braunschweig, Deutschland Buhmann Joachim;
HHMI Janelia workshop Vortrag im Rahmen einer Tagung Pattern classification in the olfactory system 09.06.2013 Ashburn, VA, Vereinigte Staaten von Amerika Friedrich Rainer;
IbPRIA 2013 Vortrag im Rahmen einer Tagung Big Data: Where is the information? 05.06.2013 Madeira, Portugal Buhmann Joachim;
Sinergia 2013 Vortrag im Rahmen einer Tagung EM reconstructions of synaptic targets of Layer2/3 pyramidal neurons in cat visual cortex 25.05.2013 Zurich, Schweiz Martin Kevan;
Giessbach Meeting Vortrag im Rahmen einer Tagung Reconstruction of neuronal activity and connectivity patterns in the zebrafish olfactory bulb 23.05.2013 Giessbach, Schweiz Wanner Adrian;
25th Aniversary of the IWR, Heidelberg Vortrag im Rahmen einer Tagung Big data: where is the information? 21.02.2013 Universiät Heidelberg, Deutschland Buhmann Joachim;
Songbird European meeting 2013 Poster A correlative light and electron microscopy sample preparation for large scale mapping of neuronal connectivity 04.02.2013 Odensee, Dänemark Hahnloser Richard; Templier Thomas;
Swiss Society for Neuroscience (SSN) Annual Meeting 2013 Poster Auditory versus motor cortex, a structurual comparison in the mouse 02.02.2013 Geneva, Schweiz Martin Kevan;
Swiss Society of Neuroscience 2013 Poster A correlative light and electron microscopy sample preparation for large scale mapping of neuronal connectivity 02.02.2013 Geneva, Schweiz Hahnloser Richard; Templier Thomas;
Neuroscience 2012 Poster Reconstruction of neuronal activity and connectivity patterns in the zebrafish olfactory 13.10.2012 New Orleans, Vereinigte Staaten von Amerika Wanner Adrian; Friedrich Rainer;
MICCAI Poster TBD 01.10.2012 Nice, France, Frankreich Hahnloser Richard;
Computer Vision and Pattern Recognition (CVPR) 2012 Poster TBA 16.06.2012 Providence, RI, USA, Vereinigte Staaten von Amerika Funke Jan;
NCCR Neuro Concluding Symposium 2012 Poster Who's who in the cortical neuropil? An immuno ultrastructural studyof macaque area V1. 14.06.2012 Zurich, Schweiz Martin Kevan;
Neuronal Circuits 2012 Poster A quantitative comparision between the visual cortex of the cat and the auditory cortex of the mouse 28.03.2012 Cold Spring Harbor, Vereinigte Staaten von Amerika Martin Kevan;
Primate Neurobiology Meeting 2012 Poster Who's who in the cortical neuropil? An immuno ultrastructural studyof macaque area V1. 12.03.2012 Tuebingen, Deutschland Martin Kevan;
Microscopy conference Vortrag im Rahmen einer Tagung Reconstruction of neuronal activity and connectivity patterns in the zebrafish olfactory bulb. Invited talk at “International symposium on 3D microscopy 09.03.2012 Les Diablerets, Schweiz Wanner Adrian;
Swiss Society of Optics and Microscopy 3D-Symposium 2012 Vortrag im Rahmen einer Tagung The thalamocortical pathway artistically considered 05.03.2012 Les Diablerets, Switzerland, Schweiz Martin Kevan;
Meeting of Swiss Society for Neuroscience 2012 Poster How many synapses does a mouse auditory cortical neuron form? 03.02.2012 Zürich, Switzerland, Schweiz Martin Kevan;
ZNZ Symposium 2011 Poster The diversity of thalamorecipient spine morphology in cat visual cortex and its implication for synaptic plasticity 16.09.2011 Zurich, Switzerland, Schweiz Martin Kevan;
Janelia Farm/HHMI Meeting on “High resolution circuit reconstruction” Vortrag im Rahmen einer Tagung TrakEM2 and CATMAID software for neural circuit reconstruction from serial section EM 11.09.2011 Ashburn, VA, USA, Vereinigte Staaten von Amerika Cardona Albert; Funke Jan;
Janelia Meeting Circuit Reconstruction Vortrag im Rahmen einer Tagung Analysis of activity and connectivity patterns in the zebrafish olfactory system 09.09.2011 Ashburn, VA, Vereinigte Staaten von Amerika Friedrich Rainer;
Janelia Meeting Circuit Reconstruction Poster High-resolution analysis of synaptic connectivity in the olfactory bulb of zebrafish larvae 09.09.2011 Ashburn, VA, Vereinigte Staaten von Amerika Friedrich Rainer; Wanner Adrian;
Janelia Meeting Circuit Reconstruction Poster Reconstruction of neuronal activity and connectivity patterns in the zebrafish olfactory bulb 09.09.2011 Ashburn, VA, Vereinigte Staaten von Amerika Friedrich Rainer; Wanner Adrian;
Portuguese Society for Neuroscience 2011 Poster The diversity of thalamorecipient spine morphology in cat visual cortex and its implication for synaptic plasticity 25.05.2011 Lisbon, Portugal Martin Kevan;
Swiss Society for Neuroscience meeting 2011 Poster The diversity of thalamorecipient spine morphology in cat visual cortex and its implication for synaptic plasticity 26.03.2011 Basel, Switzerland, Schweiz Martin Kevan;


Selber organisiert

Titel Datum Ort
Neural Skircuit Reconstruction Meeting 01.03.2014 Andermatt, Schweiz
Sinergia Meeting 2011 12.04.2011 Zurich, Schweiz

Kommunikation mit der Öffentlichkeit

Kommunikation Titel Medien Ort Jahr
Referate/Veranstaltungen/Ausstellungen Big Data in Medicine: where is the valuable information for patients? Deutschschweiz 2013

Patente

Titel Datum Nummer Erfinder Eigentümer

Verbundene Projekte

Nummer Titel Start Förderungsinstrument
160663 Songbirds as model for speech acquisition in humans 01.03.2015 Resource not found: '228f486d-c393-4df7-b610-84193c83958f'
133846 Focused Ion Beam Scanning Electron Microscope (FIBSEM) 01.11.2011 R'EQUIP
149866 Delineating Trees in Noisy 2D Images and 3D Image-Stacks 01.10.2013 Projektförderung (Abt. I-III)

Abstract

The history of natural sciences has taught us that a new discipline emerges whenever the length scale of investigation is reduced by about three orders of magnitude. The recent development of 3-D electron microscopy (3DEM) techniques induces such a transition by allowing the ultrastructural analysis of biological tissues throughout large volumes (up to a few hundred micrometers in each dimension). Although 3DEM has an enormous potential for advancing our understanding of brain function in health and disease, its biomedical application is currently impeded by the lack of accessory technologies, particularly informatics tools for the automated analysis of large and complex sets of image data. The scope of our Sinergia Proposal is to develop technologies for using 3DEM and reconstruct neuronal circuits in the vertebrate brain.High-throughput 3DEM hardware for large-scale brain imaging is currently developed at a rapid pace. However, there are many experimental hurdles in the way of achieving a synaptic resolution level of analysis of dense neuropil. Most importantly, the tools to extract relevant information from the large and extremely complex image stacks are virtually non-existent. Today, the only available method for 3DEM image processing is manual image segmentation. However, methods with strong reliance on human input are not feasible for the analysis of large tissue volumes. Our goal is therefore to develop automated analysis procedures for 3DEM data based on computer vision approaches. We propose to develop state-of-the-art 3DEM technologies, in which we integrate lower-resolution light microscopy (LM) and multicolor staining techniques. Our technological goal is to design a workflow for the acquisition of high-quality 3D image stacks of brain tissue and to develop computational methods for the automated extraction of all connectivity information contained in 3DEM image stacks. In particular, we will design computational tools for the registration of EM and LM imagery, for annotating features in EM data to identify synapses and other subcellular structures, for classifying image voxels to aid volumetric image segmentation, and for tracing of neuron morphologies based on local and global information. We will apply 3DEM techniques to determine connectivity patterns in three vertebrate model circuits: the olfactory system of zebrafish, the song control system of zebra finches, and the neocortex. Since each of these systems is also intensively studied at the physiological level, the connectivity information we provide through our efforts can be used directly to construct quantitative circuit models and derive structural principles governing circuit function. Our project is interdisciplinary and we are composed of neurobiologists and computer vision scientists. We are divided into groups that work on different animal models and pursue different 3DEM approaches. The groups will benefit from each other’s work on virtually all levels because we develop methods that are compatible among the groups and applicable to essentially all animal species. We anticipate that our methods and developments for ultrastructural imaging and analysis will contribute significantly to a new field of research (sometimes referred to as ‘connectomics’ or ‘projectomics’) and make critical progress towards one of the major goals in systems neurobiology, which is the explanation of how brain circuits function.
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