Whole Brain Connectivity Atlas

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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).

The atlas contains the results of 6 experiments in which an anterograde tracer was injected in SI forelimb or whisker representations. The results include images of ~1200 coronal sections showing the distribution of tracer labelled axons across the entire brain.

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.


Cortical and subcortical projections SI (modified from Welker et al., Exp Brain Res 73:411-435)


Axonal tracer injection in SI and labelling visible in SII, corpus callosum and thalamus.


News

2011-07 Open access following publication in PLoS ONE

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


Work in progress

  • Analysis of complete distribution of labelled axons
  • Preparation of interactive tabular listing of label distributions, reciprocally linked with image viewer


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 

+ list with functionality + links


Tutorial

To use the Image repository (Access atlas), first drag the slider [1] below the row of thumbnail images horizontally to select an anterioposterior level of interest (Bregma coordinates are indicated [2]). Click on a thumbnail image to open it in the viewer [3]. The sagittal drawing (right column [4]) indicates the anterioposterior position of the selected image.

The viewer has the following options for navigating the images [5]:

  • 'Zoom' (click the + button in the toolbar or press the shift key to zoom in; click the – button or press the ctrl key to zoom out)
  • 'Pan' (click the arrows in the tool bar, or left-click and drag the images freely in the viewer)
  • 'Reset' (to reset viewer to default, click the reset button in the toolbar)
  • 'Annotation'(currently, no annotations are provided)
  • 'Scale bar' (the ZoomScale bar shows a scale bare for the image panels. The bar is transparent and can be moved to make crude measurements in the images)

The right column provides information about the sections [6], and link to further details about the experiment. 

[7] The Bregma value shows the estimated position of the section anterior (positive values) or posterior (negative values) relative to Bregma. The Atlas bregma and Atlas interaural values show the anterioposterior coordinates for the closest diagram in The Rat Brain In Stereotaxic Coordinates (Paxinos and Watson, 2007). 

To download images (at viewer resolution) use the download button [8] in the right column. To print images, either use the print screen functionality of your computer, or use the print function available in the Menu toolbar [9]

+ image with numbers

About

The Whole Brain Connectivity Atlas is an interactive resource for mapping and sharing of connectivity data derived from axonal tract-tracing experiments. The atlas has been developed to provide access to raw connectivity data in high-resolution images of histological sections showing the distribution of anterogradely labelled axons arising from the rat SI cortex.

Features
Methods
Documentation
Contact
Credits
Contributing laboratories
Technical requirements

Features

Top ↑

  • Tract-tracing results from 6 experiments in which an anterograde tracer was injected in the forelimb or whisker representations in the rat primary somatosensory cortex
  • About 1200 images of coronal sections showing:
    • the distribution of labelling (BDA or Pha-L)
    • cytoarchitectural features (Neutral red or thionine counterstaining)
    • SI chemoarchitecture (staining for cytochrome oxidase)
  • All images are registred to a standard stereotaxic space by assigning anterioposterior position values (distance from bregma) on the basis of anatomical features


Methods

The atlas is based on data from 6 tract-tracing experiments, 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 the primary somatosensory cortex. 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)

[[File:|http://cmbn-approd01.uio.no/zoomgen/img/NR_vs_no_stain_final.jpg]]

[[File:|http://cmbn-approd01.uio.no/zoomgen/img/Injectionsites_final.jpg]]

The location of injection site and BDA labelling can be localized on basis of anatomical landmarks and cytoarchitectonic features.

Weak counterstaining with Neutral Red is used to visualize cytoarchitecture without compromising the pattern of BDA labelling.

 

Staining abbriviations :

Abbreviations

Description

cytochrome oxidase

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

 

 

Documentation

Top ↑

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

Contact

Top ↑

Connectivity and digital brain atlasing:

j.g.bjaalie@medisin.uio.no

Technical issues and functionality:

i.a.moene@medisin.uio.no

Credits

Top ↑

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