Whole Brain Connectivity Atlas

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About

Diagram of S1 cortical and subcortical projections (from Zakiewicz et al., 2011, PLoS One, 6(8):e22669)
The Whole Brain Connectivity Atlas is an interactive resource providing access to experimental tract-tracing data, showing the brain-wide distribution of efferent axonal connections originating in the rat primary somatosensory cortex. 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. Re-use of data from these repositories is allowed provided that reference is given to original publications as specified below.
2-D-image "filmstrip" viewer

2-D image repository

The 2-D image repository contains ~1200 coronal microscopic images showing data from 6 axonal tracing experiments. Image show distribution of BDA or Pha-L labeling, cytoarchitectural features (Neutral red or thinone counterstain), or chemoarchitecture in S1 (cytochrome oxidase staining). Bregma values are based on comparison with The Rat Brain in Stereotaxic Coordinates (Paxinos and Watson, 2007, Elsevier). The virtual microscopy viewer allows interactive zooming and panning. Original images are available for download via separate link.

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 (2011) Workflow and database system for mapping the axonal connectivity of the rat brain. PLoS ONE 2011;6(8):e22669.

Injection site cartoon Injected S1 region, tracer (case#) Image repository Experimental details Download images
R601.png
S1/M1 forelimb, BDA (R601) Filmstrip viewer Details (pdf) R601 (tiff)
R602.png
S1 whisker D2, BDA (R602) Filmstrip viewer Details (pdf) R602 (tiff)
R603.png
S1 forelimb, BDA (R603) Filmstrip viewer Details (pdf) R603 (tiff)
R604.png
S1 whisker D3, BDA (R604) Filmstrip viewer Details (pdf) R604 (tiff)
R605.png
S1 forelimb, Pha-L (R605) Filmstrip viewer Details (pdf) R605 (tiff)
R606.png
S1 whisker D5, Pha-L (R606) Filmstrip viewer Details (pdf) R606 (tiff)
Filename abbreviations Description
CO Cytochrome oxidase
BDA_ABC Biotinylated dextran amine, ABC method
BDA_ABC_NR Biotinylated dextran amine, ABC method, counterstained with Neutral Red
Pha-L_PAP Phaseolus vulgaris leucoagglutinin, PAP method
Pha-L_PAP_thio Phaseolus vulgaris leucoagglutinin, PAP method, counterstained with thionine
Pha-L_ABC Phaseolus vulgaris leucoagglutinin, ABC method
Pha-L_ABC_thio Phaseolus vulgaris leucoagglutinin, ABC method, counterstained with thionine
3-D image viewer

3-D image repository

The 3-D image repository contains volumetric reconstructions of the histological images from 4 of the tract-tracing experiments available in the 2-D image repository. Technical details are provided in Zakiwicz et al. (2015, PLoS One, 10(9):e0137571), while the experimental material is described in Zakiewicz et al. (2011, PLoS One, 6(8):e22669), see also 2-D image repository. The histology volumes can be inspected in online viewer tools or downloaded as Neuroimaging Informatics Technology Initiative (NIfTI) format images for offline viewing or analysis.

Re-use of data from this repository is allowed provided that reference is given to the following publication: Zakiewicz IM, Majka P, Wójcik DK, Bjaalie JG, Leergaard TB. Three-dimensional histology volume reconstruction of axonal tract tracing data: exploring topographical organization in subcortical projections from rat barrel cortex. PLoS ONE, 10(9):e0137571.

Injection site cartoon Injected S1 region, tracer (case#) 3-D image repository Experimental details Download image volume
R601.png
S1/M1 forelimb, BDA (R601) 3-D viewer Details (pdf) R601 (nii) 566mb
R602.png
S1 whisker, BDA (R602) 3-D viewer Details (pdf) R602 (nii) 566mb
R603.png
S1 forelimb, BDA (R603) 3-D viewer Details (pdf) R603 (nii) 566mb
R604.png
S1 whisker, BDA (R604) 3-D viewer Details (pdf) R604 (nii) 566mb

Experimental procedures in brief

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). Serial image were assigned anterio-posterior Bregma coordinates by identification of anatomical landmarks and comparison with a rat brain atlas  (The Rat Brain In Stereotaxic Coordinates, Paxinos and Watson, 2007). For further details about tract-tracing experiments and the 2-D image repository, see Zakiewicz et al., 2011, PLoS One, 6(8):e22669). For methodological details about 3-D histological reconstructions, see Zakiewicz et al., 2015, PLoS One, 10(9):e0137571).

History

  • 2015-09 - 3-D image repository launched (Zakiewicz et al., PloS One, 2015, 10(9):e0137571)
  • 2015-09 - Wiki pages established, new filmstrip viewer system
  • 2014-02 - Analysis of brain-wide distribution of S1 efferent projections (Zakiewicz et al., Front Neuroinf 2014; doi: 10.3389/fninf.2014.00005)
  • 2011-07 - 2-D image repository launched (Zakiewicz et al., PLoS One 2011;6(8):e22669)
  • 2009-09 - Poster/demo, 2nd INCF Congress of Neuroinformatics, Plzen, Czech Republic

Documentation

  • Zakiewicz IM, Majka P, Wojcik DK, Bjaalie JG, Leergaard TB (2015) Three-dimensional histology volume reconstruction of axonal tract tracing data: exploring topographical organization in subcortical projections from rat barrel cortex. PloS One; 10(9):e0137571.
  • Zakiewicz IM, Bjaalie JG, Leergaard TB (2014) Brain-wide map of efferent projections from rat barrel cortex, Front. Neuroinform 8:5, doi: 10.3389/fninf.2014.00005 
  • Zakiewicz IM, van Dongen YC, Leergaard TB, Bjaalie JG (2011) Workflow and database system for mapping the axonal connectivity of the rat brain. PLoS One; 6(8):e22669. doi: 10.1371/journal.pone.0022669  
  • 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; 136:681-696

Atlas development team

Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo

  • Izabela M. Zakiewicz
  • Yvette C. van Dongen
  • Jan Olav Kjøde
  • Ivar Andre Moene
  • Gergely Csucs
  • Dmitri Darine
  • Trygve B. Leergaard
  • Jan G. Bjaalie

Funded by:

Contributing laboratories

  • Neural Systems Laboratory (http://www.nesys.uio.no), Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, Department of Anatomy, University of Oslo, P.O. Box 1105 Blindern, N - 0317 Oslo, Norway: Experimental work, brain-wide mapping, atlas repository.
  • Laboratory of Neuroinformatics (http://en.nencki.gov.pl/laboratory-of-neuroinformatics), Department of Neurophysiology, Nencki Institute of Experimental Biology, 02-093 Warszawa, Poland: 3-D histology volume reconstructions

Contact

  • j.g.bjaalie@medisin.uio.no