Difference between revisions of "Whole Brain Connectivity Atlas"

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<span style="font-family: georgia, serif;">Whole Brain Connectivity Atlas is part of the [http://rbwb.org/ 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.</span>
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== About ==
 +
[[File:S1wiring.png|200px|thumb|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.[[File:2Dviewer.png|200px|thumb|2-D-image "filmstrip" viewer]]
  
 +
== 2-D image repository ==
 +
T'''<nowiki/>'''he 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 atlas system for brain-wide mapping of axonal connectivity in rat. PLoS ONE 2011;6(8):e22669.
  
== <span style="font-family:georgia,serif;">About</span> ==
+
{| class="wikitable"
 
+
!Injection site cartoon
<span style="font-family: georgia, serif;">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.</span>
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!Injected S1 region, tracer (case#)
 
+
!Image repository
<span style="font-family: georgia, serif;">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).&nbsp;</span>
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!Experimental details  
 
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!Download images
<span style="font-family: georgia, serif;">Currently, the atlas contains the results from six experiments in which an anterograde tracer, either&nbsp;''biotinylated dextran amine ''(BDA) or&nbsp;''Phaseolus vulgaris leucoagglutinin&nbsp;''(Pha-L),&nbsp;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.</span>
 
 
 
<span style="font-family:georgia,serif;"><gallery class="center" mode="traditional" widths="300px">
 
File:SIwiring.jpg|Cortical and subcortical projections of SI (modified from Welker et al., Exp Brain Res 73:411-435).
 
File:InjectionSite.jpg|Axonal tracer injection in SI and labelling visible in secondary somatosensory cortex (SII), corpus callosum and thalamus.
 
</gallery></span>
 
 
 
=== <span style="font-family:georgia,serif;">Features</span> ===
 
 
 
*<span style="font-family:georgia,serif;">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</span>
 
*<span style="font-family:georgia,serif;">About 1500 images of coronal sections showing:</span>
 
**<span style="font-family:georgia,serif;">the distribution of labelling (BDA or Pha-L)</span>
 
**<span style="font-family:georgia,serif;">cytoarchitectural features (Neutral red or thionine counterstaining)</span>
 
**<span style="font-family:georgia,serif;">SI chemoarchitecture (every other section stained for cytochrome oxidase)</span>
 
**<span style="font-family: georgia, serif;">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)</span>
 
 
 
 
 
 
 
=== <span style="font-family:georgia,serif;">Methods</span> ===
 
 
 
<span style="font-family:georgia,serif;">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)</span>
 
<div style="clear:both;"></div><div style="clear:both;"><br/></div>
 
<br/><span style="font-family:georgia,serif;"><gallery class="center" mode="traditional" widths="300px">
 
File:NR_vs_no_stain_final.jpg|The location of injection sites and BDA labelling can be localized on the basis of anatomical landmarks and cytoarchitectonic features.
 
File:Injectionsites final.jpg|Weak counterstaining with Neutral Red is used to visualize cytoarchitecture without compromising the pattern of BDA labelling.
 
</gallery></span>
 
 
 
=== <span style="font-family:georgia,serif;">Staining abbreviations</span> ===
 
 
 
{| border="1" cellpadding="0"
 
 
|-
 
|-
| style="width:160px;" |  
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|[[File:R601.png|75px|center]]
<span style="font-family:georgia,serif;">'''Abbreviations'''</span>
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|S1/M1 forelimb, BDA (R601)
 
+
|[http://cmbn-navigator.uio.no/navigator/filmstrip_viewer.html?publicOnly=true&publicOnly=true&entityType=block&entityId=1941&selectIndex=60&metadataKeyName=Bregma%20Level Filmstrip viewer]
| style="width:160px;" |  
+
|[[media:Metadata R601.pdf|Details (pdf)]]
<span style="font-family:georgia,serif;">'''Description'''</span>
+
|[http://cmbn-navigator.uio.no/navigator/feeder/all_originals/?id=1941 R601 (tiff)]
 
 
 
|-
 
|-
|  
+
||[[File:R602.png|75px|center]]
<span style="font-family:georgia,serif;">CO</span>
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|S1 whisker D2, BDA (R602)
 
+
|[http://cmbn-navigator.uio.no/navigator/filmstrip_viewer.html?publicOnly=true&entityType=block&entityId=1961&selectIndex=130&metadataKeyName=Bregma%20Level Filmstrip viewer]
|  
+
|[[media:Metadata R602.pdf|Details (pdf)]]
<span style="font-family:georgia,serif;">Stained for cytochrome oxidase&nbsp;</span>
+
|[http://cmbn-navigator.uio.no/navigator/feeder/all_originals/?id=1961 R602 (tiff)]
 
 
|-
 
|  
 
<span style="font-family:georgia,serif;">BDA_ABC</span>
 
 
 
|
 
<span style="font-family:georgia,serif;">Stained for biotinylated dextran amine, ABC method</span>
 
 
 
 
|-
 
|-
|  
+
||[[File:R603.png|75px|center]]
<span style="font-family:georgia,serif;">BDA_ABC_NR</span>
+
|S1 forelimb, BDA (R603)
 
+
|[http://cmbn-navigator.uio.no/navigator/filmstrip_viewer.html?publicOnly=true&entityType=block&entityId=1981&selectIndex=100&metadataKeyName=Bregma%20Level Filmstrip viewer]
|  
+
|[[media:Metadata R603.pdf|Details (pdf)]]
<span style="font-family:georgia,serif;">Stained for biotinylated dextran amine, ABC method, counterstained with Neutral Red</span>
+
|[http://cmbn-navigator.uio.no/navigator/feeder/all_originals/?id=1981 R603 (tiff)]
 
 
 
|-
 
|-
|  
+
|[[File:R604.png|75px|center]]
<span style="font-family:georgia,serif;">Pha-L_PAP</span>
+
|S1 whisker D3, BDA (R604)
 
+
|[http://cmbn-navigator.uio.no/navigator/filmstrip_viewer.html?publicOnly=true&entityType=block&entityId=2001&selectIndex=92&metadataKeyName=Bregma%20Level Filmstrip viewer]
|  
+
|[[media:Metadata R604.pdf|Details (pdf)]]
<span style="font-family:georgia,serif;">Stained for Phaseolus vulgaris leucoagglutinin, PAP method</span>
+
|[http://cmbn-navigator.uio.no/navigator/feeder/all_originals/?id=2001 R604 (tiff)]
 
 
 
|-
 
|-
|  
+
|[[File:R605.png|75px|center]]
<span style="font-family:georgia,serif;">Pha-L_PAP_thio</span>
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|S1 forelimb, Pha-L (R605)
 
+
|[http://cmbn-navigator.uio.no/navigator/filmstrip_viewer.html?publicOnly=true&entityType=block&entityId=2002&selectIndex=89&metadataKeyName=Bregma%20Level Filmstrip viewer]
|  
+
|[[media:Metadata R605.pdf|Details (pdf)]]
<span style="font-family:georgia,serif;">Stained for Phaseolus vulgaris leucoagglutinin, PAP method, counterstained with thionine</span>
+
|[http://cmbn-navigator.uio.no/navigator/feeder/all_originals/?id=2002 R605 (tiff)]
 
 
 
|-
 
|-
|  
+
|[[File:R606.png|75px|center]]
<span style="font-family:georgia,serif;">Pha-L_ABC</span>
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|S1 whisker D5, Pha-L (R606)
 
+
|[http://cmbn-navigator.uio.no/navigator/filmstrip_viewer.html?publicOnly=true&entityType=block&entityId=2003&selectIndex=61&metadataKeyName=Bregma%20Level Filmstrip viewer]
|  
+
|[[media:Metadata R606.pdf|Details (pdf)]]
<span style="font-family:georgia,serif;">Stained for Phaseolus vulgaris leucoagglutinin, ABC method</span>
+
|[http://cmbn-navigator.uio.no/navigator/feeder/all_originals/?id=2003 R606 (tiff)]
 
 
 
|-
 
|-
|
 
<span style="font-family:georgia,serif;">Pha-L_ABC_thio</span>
 
 
|
 
<span style="font-family:georgia,serif;">Stained for Phaseolus vulgaris leucoagglutinin, ABC method, counterstained with thionine</span>
 
 
 
|}
 
|}
 
+
{| class="wikitable"
== <span style="font-family:georgia,serif;">News</span> ==
+
!Filename abbreviations
 
+
!Description
<span style="font-family:georgia,serif;">2015-04 Atlas moved to NeSys wiki. New image viewer was made available and additional image material has been added</span>
 
 
 
<span style="font-family: georgia, serif;">2014-02 Second article with examples of analysis of the rat SI connectivity based on the histological data from the existing database was published:&nbsp;</span><span style="font-family:georgia,serif;">[http://journal.frontiersin.org/article/10.3389/fninf.2014.00005/abstract [1]]</span>
 
 
 
<span style="font-family:georgia,serif;">2011-08 Open access following publication in PLoS ONE</span>
 
 
 
<span style="font-family: georgia, serif;">2011-07 First article published, including an open source platform with histological data from six axonal tract-tracing experi</span>ments:&nbsp;[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022669 [2]]
 
 
 
<span style="font-family:georgia,serif;">2009-09 Poster / demonstration, 2nd INCF Congress of Neuroinformatics, Plzen, Czech Republic</span>
 
 
 
 
 
 
 
== <span style="font-family:georgia,serif;">Access images</span> ==
 
 
 
<span style="font-family:georgia,serif;">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</span>
 
 
 
<span style="font-family:georgia,serif;">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&nbsp;[[#Tutorial|Tutorial]]&nbsp;</span>
 
 
 
{| class="wikitable" style="margin: 1em auto 1em auto;"
 
 
|-
 
|-
! Injection site<br/>
+
|CO
! Location area
+
|Cytochrome oxidase
! Images
 
! About the case
 
 
|-
 
|-
| style="text-align: center;" | [[File:Case R602.png|center]]<br/>
+
|BDA_ABC
| SI forelimb, BDA (R601)
+
|Biotinylated dextran amine, ABC method
| [http://cmbn-navigator.uio.no/navigator/filmstrip_viewer.html?entityType=animal&entityId=1501&metadataKeyName=Bregma%20Level Open viewer]
 
| [https://wiki.uio.no/projects/navigator3/images/2/2e/Metadata_R601.pdf More details (pdf)]
 
 
|-
 
|-
| style="text-align: center;" | [[File:Case R602.png|center]]<br/>
+
|BDA_ABC_NR
| SI whisker D2, BDA (R602)
+
|Biotinylated dextran amine, ABC method, counterstained with Neutral Red
| [http://cmbn-navigator.uio.no/navigator/filmstrip_viewer.html?entityType=animal&entityId=1502&&metadataKeyName=Bregma%20Level Open viewer]
 
| [https://wiki.uio.no/projects/navigator3/images/3/3a/Metadata_R602.pdf More details (pdf)]
 
 
|-
 
|-
| [[File:Case R603.png|center]]<br/>
+
|Pha-L_PAP
| SI forelimb, BDA (R603)
+
|Phaseolus vulgaris leucoagglutinin, PAP method
| [http://cmbn-navigator.uio.no/navigator/filmstrip_viewer.html?entityType=animal&entityId=1503&metadataKeyName=Bregma%20Level Open viewer]
 
| [https://wiki.uio.no/projects/navigator3/images/e/eb/Metadata_R603.pdf More details (pdf)]
 
 
|-
 
|-
| [[File:Case R604.png|center]]<br/>
+
|Pha-L_PAP_thio
| SI whisker D3, BDA (R604)
+
|Phaseolus vulgaris leucoagglutinin, PAP method, counterstained with thionine
| [http://cmbn-navigator.uio.no/navigator/filmstrip_viewer.html?entityType=animal&entityId=1504&metadataKeyName=Bregma%20Level Open viewer]
 
| [https://wiki.uio.no/projects/navigator3/images/d/d3/Metadata_R604.pdf More details (pdf)]
 
 
|-
 
|-
| [[File:Case R605.png|center]]<br/>
+
|Pha-L_ABC
| forelimb, Pha-L (R605)
+
|Phaseolus vulgaris leucoagglutinin, ABC method
| [http://cmbn-navigator.uio.no/navigator/filmstrip_viewer.html?entityType=animal&entityId=1505&metadataKeyName=Bregma%20Level Open viewer]
 
| [https://wiki.uio.no/projects/navigator3/images/d/d8/Metadata_R605.pdf More details (pdf)]
 
 
|-
 
|-
| [[File:Case R606.png|center]]<br/>
+
|Pha-L_ABC_thio
| SI whisker D5, Pha-L (R606)
+
|Phaseolus vulgaris leucoagglutinin, ABC method, counterstained with thionine
| [http://cmbn-navigator.uio.no/navigator/filmstrip_viewer.html?entityType=animal&entityId=1506&metadataKeyName=Bregma%20Level Open viewer]
 
| [https://wiki.uio.no/projects/navigator3/images/c/cf/Metadata_R606.pdf More details (pdf)]
 
 
|}
 
|}
 +
[[File:3Dviewer.png|200px|thumb|3-D image viewer]]
  
== <span style="font-family:georgia,serif;">Tutorial</span> ==
+
== 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.
  
<span style="font-family:georgia,serif;">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 sagittal drawing (right column) indicates the anterioposterior position of the selected image.''<br/><br/>The viewer has the following options for navigating the images:</span>
+
'''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.
 
+
{| class="wikitable"
*<span style="font-family:georgia,serif;">'Zoom'&nbsp;(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)</span>
+
!Injection site cartoon
*<span style="font-family:georgia,serif;">'Pan'&nbsp;(click the arrows in the tool bar, or left-click and drag the images freely in the viewer)</span>
+
!Injected S1 region, tracer (case#)
*<span style="font-family:georgia,serif;">'Reset'&nbsp;(to reset viewer to default, click the reset button in the toolbar)</span>
+
!3-D image repository
*<span style="font-family:georgia,serif;">'Annotation'(currently, no annotations are provided)</span>
+
!Experimental details
*<span style="font-family:georgia,serif;">'Scale bar'&nbsp;(the scale bar shows a scale bare for the image panels. The bar is transparent and can be moved to make crude measurements in the images)</span>
+
!Download image volume
 
+
|-
<span style="font-family:georgia,serif;">The right column provides information about the sections, and link to further details about the experiment.&nbsp;<br/><br/>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).&nbsp;<br/><br/>To download images (at viewer resolution) use the download button 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</span>
+
|[[File:R601.png|75px|center]]
 
+
|S1/M1 forelimb, BDA (R601)
 
+
|[http://cmbn-navigator.uio.no/navigator/simple_viinii_viewer.html?id=36037 3-D viewer]
 
+
|[[media:Metadata R601.pdf|Details (pdf)]]
== <span style="font-family:georgia,serif;">Work in progress</span> ==
+
|[http://cmbn-navigator.uio.no/navigator/feeder/original/?id=36037 R601 (nii) 566mb]
 
+
|-
*<span style="font-family:georgia,serif;">Preparation of interactive tabular listing of label distributions, reciprocally linked with image viewer</span>
+
||[[File:R602.png|75px|center]]
 
+
|S1 whisker, BDA (R602)
 
+
|[http://cmbn-navigator.uio.no/navigator/simple_viinii_viewer.html?id=36038 3-D viewer]
 
+
|[[media:Metadata R602.pdf|Details (pdf)]]
== <span style="font-family:georgia,serif;">Documentation</span> ==
+
|[http://cmbn-navigator.uio.no/navigator/feeder/original/?id=36038 R602 (nii) 566mb]
 
+
|-
<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>
+
||[[File:R603.png|75px|center]]
 
+
|S1 forelimb, BDA (R603)
 
+
|[http://cmbn-navigator.uio.no/navigator/simple_viinii_viewer.html?id=36039 3-D viewer]
 
+
|[[media:Metadata R603.pdf|Details (pdf)]]
== <span style="font-family:georgia,serif;">Contact</span> ==
+
|[http://cmbn-navigator.uio.no/navigator/feeder/original/?id=36039 R603 (nii) 566mb]
 
+
|-
<span style="font-family:georgia,serif;">Connectivity and digital brain atlasing:&nbsp;[mailto:j.g.bjaalie@medisin.uio.no j.g.bjaalie@medisin.uio.no]</span>
+
|[[File:R604.png|75px|center]]
 
+
|S1 whisker, BDA (R604)
<span style="font-family:georgia,serif;">Technical issues and functionality:&nbsp;[mailto:d.a.darine@medisin.uio.no d.a.darine@medisin.uio.no]</span>
+
|[http://cmbn-navigator.uio.no/navigator/simple_viinii_viewer.html?id=36040 3-D viewer]
 
+
|[[media:Metadata R604.pdf|Details (pdf)]]
 
+
|[http://cmbn-navigator.uio.no/navigator/feeder/original/?id=36040 R604 (nii) 566mb]
 
+
|-
== <span style="font-family:georgia,serif;">Credits</span> ==
+
|}
 
 
<span style="font-family:georgia,serif;">'''NeSys and CMBN atlas development team:&nbsp;'''</span>
 
 
 
<span style="font-family:georgia,serif;">Izabela M. Zakiewicz, M.Sc.</span>
 
 
 
<span style="font-family:georgia,serif;">Yvette C. van Dongen, Ph.D</span>
 
 
 
<span style="font-family:georgia,serif;">Anna Torbjørg Bore</span>
 
 
 
<span style="font-family:georgia,serif;">Jan Olav Kjode, M.Sc.</span>
 
 
 
<span style="font-family:georgia,serif;">Ivar Andre Moene, M.Sc.</span>
 
 
 
<span style="font-family:georgia,serif;">Trygve B. Leergaard, M.D., Ph.D.</span>
 
  
<span style="font-family:georgia,serif;">Jan G. Bjaalie, M.D., Ph.D.</span>
+
== 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).
  
<span style="font-family:georgia,serif;">Funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union</span>
+
== 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 atlas system for brain-wide mapping of axonal connectivity in rat. 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
  
== <span style="font-family:georgia,serif;">Contributing laboratories</span> ==
+
== Funded by: ==
 +
* EMBIO/MLS@UIO (PS-V08, http://www.uio.no/forskning/tverrfak/mls/om/)
 +
* The Research Council of Norway (Norwegian Node of the International Neuroinformatics Coordinating Facility, project ID 214842, http://www.forskningsradet.no)
 +
* Human Brain Project through the European Union Seventh Framework Program (FP7/2007-2013) under grant agreement no. 604102 (HBP)
 +
* https://www.humanbrainproject.eu/)
  
<span style="font-family:georgia,serif;">'''Neural Systems and Graphics Computing Laboratory'''<br/>Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences&nbsp;<br/>Deptartment of Anatomy&nbsp;<br/>University of Oslo&nbsp;<br/>P.O. Box 1105 Blindern&nbsp;<br/>N - 0317 Oslo&nbsp;<br/>Norway&nbsp;<br/>[http://www.nesys.uio.no/ http://www.nesys.uio.no]</span>
+
== Contributing laboratories ==
 +
* '''Neural Systems Laboratory '''([http://www.nesys.uio.no) 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''
  
[[Category:Pages with broken file links|Pages_with_broken_file_links]]
+
== Contact ==
 +
* j.g.bjaalie@medisin.uio.no

Revision as of 10:31, 13 March 2018

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 atlas system for brain-wide mapping of axonal connectivity in rat. 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 atlas system for brain-wide mapping of axonal connectivity in rat. 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