Difference between revisions of "Whole Brain Connectivity Atlas"

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== <span style="font-family:georgia,serif;">Documentation</span> ==
 
== <span style="font-family:georgia,serif;">Documentation</span> ==
  
<span style="font-family:georgia,serif;">'''''Connectivity atlas system:'''''<br/>Zakiewicz IM, van Dongen YC, Leergaard TB, Bjaalie JG (2010) Workflow and database system for mapping the axonal connectivity of the rat brain. Submitted manuscript&nbsp;<br/><br/>Zakiewicz IM, van Dongen YC, Moene IA, Leergaard TB and Bjaalie JG (2009) Towards an interactive digital atlas system for exploring anatomical connectivity patterns in the entire rat brain. Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics. doi: 10.3389/conf.neuro.11.2009.08.014&nbsp;<br/><br/>'''''Database architecture:'''''<br/>Moene IA, Subramaniam S, Darine D, Leergaard TB, Bjaalie JG (2007). Towards a workbench for rodent brain image data: systems architecture and design. Neuroinformatics; 5: 35-58&nbsp;<br/><br/>Bjaalie JG, Leergaard TB, Lillehaug S, Odeh F, Moene IA, Kjøde JO, Darine D (2005) Database and tools for analysis of topographic organization and map transformations in major projection systems of the brain. Neuroscience 2005; 136:681-696</span>
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<span style="font-size:small;"><span style="font-family:georgia,serif;">'''''Connectivity atlas system:'''''</span></span>
  
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<span style="font-size:small;"><span style="font-family:georgia,serif;">''Zakiewicz IM, van Dongen YC, Leergaard TB, Bjaalie JG (2010) Workflow and database system for mapping the axonal connectivity of the rat brain. Submitted manuscript&nbsp;<br/><br/>Zakiewicz IM, van Dongen YC, Moene IA, Leergaard TB and Bjaalie JG (2009) Towards an interactive digital atlas system for exploring anatomical connectivity patterns in the entire rat brain. Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics. doi: 10.3389/conf.neuro.11.2009.08.014&nbsp;</span></span>
  
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<span style="font-size:small;"><span style="font-family:georgia,serif;"><br/><br/>'''''Database architecture:'''''</span></span>
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<span style="font-size:small;"><span style="font-family:georgia,serif;">''</span></span><span style="font-family: georgia, serif; font-size: small;">Moene IA, Subramaniam S, Darine D, Leergaard TB, Bjaalie JG (2007). Towards a workbench for rodent brain image data: systems architecture and design. Neuroinformatics; 5: 35-58&nbsp;</span>
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<span style="font-size:small;"><span style="font-family:georgia,serif;"><br/>Bjaalie JG, Leergaard TB, Lillehaug S, Odeh F, Moene IA, Kjøde JO, Darine D (2005) Database and tools for analysis of topographic organization and map transformations in major projection systems of the brain. Neuroscience 2005; 136:681-696</span></span>
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<span style="font-size:small;"><span style="font-family:georgia,serif;"></span></span>
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<span style="font-family:georgia,serif;"><span style="font-size:small;">'''''Database usability:'''''</span></span>
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<span style="font-family: georgia, serif;">Zakiewicz IM, Leergaard TB, Bjaalie JG (2014) Brain-wide map of efferent projections from rat barrel cortex, Front. Neuroinform., 05 February 2014 | doi: 10.3389/fninf.2014.00005</span>
  
 
== <span style="font-family:georgia,serif;">Contact</span> ==
 
== <span style="font-family:georgia,serif;">Contact</span> ==

Revision as of 04:49, 13 May 2015

Whole Brain Connectivity Atlas is part of the Rodent Brain WorkBench, a new research and development project funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union.


About

The Whole Brain Connectivity Atlas is an interactive resource providing access to brainwide experimental tract-tracing data showing the distribution of axonal connections arising from the primary somatosensory cortex (SI) in the rat brain.

The atlas is a resource for mapping and sharing of connectivity data derived from histological axonal tract-tracing experiments. It has been developed to provide access to high-resolution images of histological sections showing the distribution of anterogradely labelled axons arising from the rat primary somatosensory and primary motor cortex (SI ans MI). 

Currently, the atlas contains the results from six experiments in which an anterograde tracer, either biotinylated dextran amine (BDA) or Phaseolus vulgaris leucoagglutinin (Pha-L), was injected in the SI forelimb or whisker representations in M1. The results include images of ~1500 coronal sections showing the distribution of tracer labelled axons across the entire rat brain.

Features

  • Tract-tracing results from six experiments in which an anterograde tracer was injected in the forelimb or whisker representations in the rat SI or MI
  • About 1500 images of coronal sections showing:
    • the distribution of labelling (BDA or Pha-L)
    • cytoarchitectural features (Neutral red or thionine counterstaining)
    • SI chemoarchitecture (every other section stained for cytochrome oxidase)
    • assigned bregma values based on the anatomical features revealed by the NR, CO and thionine staining, corresponding to a standard stereotaxic space of the rat brain (Paxinos & Watson, 2007)


Methods

The tract-tracing experiments were conducted in four adult Sprague Dawley rats and two adult Wistar rats. In each animal, an anterograde axonal tracer (biotinylated dextran amine, BDA or Phaseolus vulgaris leucoagglutinin, Pha-L) was iontophoretically injected in the whisker or forelimb representation of SI (five cases) or MI (one case). Coronal brain sections were stained to visualize BDA or Pha-L and counterstained to visualize cytoarchitectural features. Selected sections were stained for cytochrome oxidase to visualize the characteristic SI barrel organization. Images were obtained through an automated Olympus Bx52 microscope, equipped with a high-precision motorized stage running the Neurolucida v6.0 Virtual Slice software (MicroBrightField Inc., Williston, VT, USA). (For further details, see Zakiewicz et al., 2011, PLoS One, 6(8):e22669)



Staining abbreviations

Abbreviations

Description

CO

Stained for cytochrome oxidase 

BDA_ABC

Stained for biotinylated dextran amine, ABC method

BDA_ABC_NR

Stained for biotinylated dextran amine, ABC method, counterstained with Neutral Red

Pha-L_PAP

Stained for Phaseolus vulgaris leucoagglutinin, PAP method

Pha-L_PAP_thio

Stained for Phaseolus vulgaris leucoagglutinin, PAP method, counterstained with thionine

Pha-L_ABC

Stained for Phaseolus vulgaris leucoagglutinin, ABC method

Pha-L_ABC_thio

Stained for Phaseolus vulgaris leucoagglutinin, ABC method, counterstained with thionine

News

2015-04 Atlas moved to NeSys wiki. New image viewer was made available and additional image material has been added

2014-02 Second article with examples of analysis of the rat SI connectivity based on the histological data from the existing database was published: [1]

2011-08 Open access following publication in PLoS ONE

2011-07 First article published, including an open source platform with histological data from six axonal tract-tracing experiments: [2]

2009-09 Poster / demonstration, 2nd INCF Congress of Neuroinformatics, Plzen, Czech Republic


Access images

Re-use of data from this repository is allowed provided that reference is given to the following publication: Zakiewicz IM, van Dongen YC, Leergaard TB, Bjaalie JG (2010) Workflow and database system for mapping the axonal connectivity of the rat brain. PLoS ONE 2011;6(8):e22669

The image repository contains ~1200 coronal images showing data from 6 axonal tracing experiments. The viewer allows interactive zooming and panning. Select experiment of interest in the list below. For further details, see Tutorial 

Injection site
Location area Images About the case

SI forelimb, BDA (R601) Open viewer More details (pdf)

SI whisker D2, BDA (R602) Open viewer More details (pdf)

SI forelimb, BDA (R603) Open viewer More details (pdf)

SI whisker D3, BDA (R604) Open viewer More details (pdf)

forelimb, Pha-L (R605) Open viewer More details (pdf)

SI whisker D5, Pha-L (R606) Open viewer More details (pdf)

Tutorial

To use the Image repositories and viewer, first drag the slider below the row of thumbnail images horizontally to select an anterioposterior level of interest (bregma coordinates are indicated). Click on a thumbnail image to open it in the viewer. 


The viewer has the following options for navigating the images:

  • 'Zoom' (zoom in and out by using mouse scroll button or two-finger pan on touchpad)
  • 'Pan' (left-click and drag the images freely in the viewer, after enlarging the image you can chose the area of interest by left-clicking on the preview window)
  • 'Reset' (click “view all” button)
  • 'Annotation (under development)

The information about selected section is avaliable in the upper right corner with the possibility for downloading the image. To download images (at viewer resolution) use the download button in the upper right corner. To print images, either use the print screen functionality of your computer.

Each section has assigned bregma value, visible under every thumbnail and in the image information corner. The value was assigned based on section landmarks revealed by counterstain or CO-staining and corresponds to the popular stereotaxic rat brain atlas (The Rat Brain In Stereotaxic Coordinates, Paxinos and Watson, 2007). 

Work in progress

  • Preparation of interactive tabular listing of label distributions, reciprocally linked with image viewer
  • 3D reconstruction of projection patterns (article submitted for reviewing)
  • 3D data / connectivity project (co-registration within Waxholm space)

Documentation

Connectivity atlas system:

Zakiewicz IM, van Dongen YC, Leergaard TB, Bjaalie JG (2010) Workflow and database system for mapping the axonal connectivity of the rat brain. Submitted manuscript 

Zakiewicz IM, van Dongen YC, Moene IA, Leergaard TB and Bjaalie JG (2009) Towards an interactive digital atlas system for exploring anatomical connectivity patterns in the entire rat brain. Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics. doi: 10.3389/conf.neuro.11.2009.08.014 



Database architecture:

Moene IA, Subramaniam S, Darine D, Leergaard TB, Bjaalie JG (2007). Towards a workbench for rodent brain image data: systems architecture and design. Neuroinformatics; 5: 35-58 


Bjaalie JG, Leergaard TB, Lillehaug S, Odeh F, Moene IA, Kjøde JO, Darine D (2005) Database and tools for analysis of topographic organization and map transformations in major projection systems of the brain. Neuroscience 2005; 136:681-696

Database usability:

Zakiewicz IM, Leergaard TB, Bjaalie JG (2014) Brain-wide map of efferent projections from rat barrel cortex, Front. Neuroinform., 05 February 2014 | doi: 10.3389/fninf.2014.00005

Contact

Connectivity and digital brain atlasing: j.g.bjaalie@medisin.uio.no

Technical issues and functionality: d.a.darine@medisin.uio.no


Credits

NeSys and CMBN atlas development team: 

Izabela M. Zakiewicz, M.Sc.

Yvette C. van Dongen, Ph.D

Anna Torbjørg Bore

Jan Olav Kjode, M.Sc.

Ivar Andre Moene, M.Sc.

Trygve B. Leergaard, M.D., Ph.D.

Jan G. Bjaalie, M.D., Ph.D.

Funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union


Contributing laboratories

Neural Systems and Graphics Computing Laboratory
Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences 
Deptartment of Anatomy 
University of Oslo 
P.O. Box 1105 Blindern 
N - 0317 Oslo 
Norway 
http://www.nesys.uio.no